Bioinformatics
2005
- Increasing the Impact of Bioinformaticsby: Alfonso Valencia, Alex Bateman v. 21 i. 1 p. 1 - 1
- Origins of introns based on the definition of exon modules and their conserved interfacesby: Albert D. G. de Roos v. 21 i. 1 p. 2 - 9
- Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classesby: Kuo-Chen Chou v. 21 i. 1 p. 10 - 19
- A memory-efficient algorithm for multiple sequence alignment with constraintsby: Chin Lung Lu, Yen Pin Huang v. 21 i. 1 p. 20 - 30
- DWE: Discriminating Word Enumeratorby: Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang, Michael Q. Zhang v. 21 i. 1 p. 31 - 38
- Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteinsby: Åsa K. Björklund, Daniel Soeria-Atmadja, Anna Zorzet, Ulf Hammerling, Mats Gustafsson v. 21 i. 1 p. 39 - 50
- Protein structure alignment by deterministic annealingby: Luonan Chen, Tianshou Zhou, Yun Tang v. 21 i. 1 p. 51 - 62
- How many samples are needed to build a classifier: a general sequential approachby: Wenjiang J. Fu, Edward R. Dougherty, Bani K. Mallick, Raymond J. Carroll v. 21 i. 1 p. 63 - 70
- A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray databy: Min Zou, Suzanne D. Conzen v. 21 i. 1 p. 71 - 79
- A rapid method for computationally inferring transcriptome coverage and microarray sensitivityby: Toni Reverter-Gomez, S. M. McWilliam, Wes Barris, Brian P. Dalrymple v. 21 i. 1 p. 80 - 89
- HAPLORE: a program for haplotype reconstruction in general pedigrees without recombinationby: Kui Zhang, Fengzhu Sun, Hongyu Zhao v. 21 i. 1 p. 90 - 103
- Gene clustering by Latent Semantic Indexing of MEDLINE abstractsby: Ramin Homayouni, Kevin Heinrich, Lai Wei, Michael W. Berry v. 21 i. 1 p. 104 - 115
- PIML: the Pathogen Information Markup Languageby: Yongqun He, Richard R. Vines, Alice R. Wattam, Georgiy V. Abramochkin, Allan Dickerman, J. Dana Eckart, Bruno W. S. Sobral v. 21 i. 1 p. 116 - 121
- BlastAlign: a program that uses blast to align problematic nucleotide sequencesby: Robert Belshaw, Aris Katzourakis v. 21 i. 1 p. 122 - 123
- SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping databy: Scott J. Tebbutt, Igor V. Opushnyev, Ben W. Tripp, Ayaz M. Kassamali, Wendy L. Alexander, Marilyn I. Andersen v. 21 i. 1 p. 124 - 127
- MCQTL: multi-allelic QTL mapping in multi-cross designby: Marie-Françoise Jourjon, Sylvain Jasson, Jacques Marcel, Baba Ngom, Brigitte Mangin v. 21 i. 1 p. 128 - 130
- HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithmsby: Kui Zhang, Zhaohui S. Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, Fengzhu Sun v. 21 i. 1 p. 131 - 134
- Network structures and algorithms in Bioconductorby: Vincent Carey, Jeff Gentry, Elizabeth Whalen, Robert Gentleman v. 21 i. 1 p. 135 - 136
- DisProt: a database of protein disorderby: Slobodan Vucetic, Zoran Obradovic, Vladimir Vacic, Predrag Radivojac, Kang Peng, Lilia M. Iakoucheva, Marc S. Cortese, J. David Lawson, Celeste J. Brown, Jason G. Sikes, Crystal D. Newton, A. Keith Dunker v. 21 i. 1 p. 137 - 140
- Filtering of Ineffective siRNAs and Improved siRNA Design Toolby: Siu-Ming Yiu, Prudence W. H. Wong, Tak-Wah Lam, Y. C. Mui, H. F. Kung, Marie Lin, Y. T. Cheung v. 21 i. 2 p. 144 - 151
- A simple and fast secondary structure prediction method using hidden neural networksby: Kuang Lin, Victor A. Simossis, William R. Taylor, Jaap Heringa v. 21 i. 2 p. 152 - 159
- A new algorithm for detecting low-complexity regions in protein sequencesby: Sung W. Shin, Sam Kim v. 21 i. 2 p. 160 - 170
- Outcome signature genes in breast cancer: is there a unique set?by: Liat Ein-Dor, Itai Kela, Gad Getz, David Givol, Eytan Domany v. 21 i. 2 p. 171 - 178
- Construction of robust prognostic predictors by using projective adaptive resonance theory as a gene filtering methodby: Hiro Takahashi, Takeshi Kobayashi, Hiroyuki Honda v. 21 i. 2 p. 179 - 186
- Missing value estimation for DNA microarray gene expression data: local least squares imputationby: Hyunsoo Kim, Gene H. Golub, Haesun Park v. 21 i. 2 p. 187 - 198
- BioLingua: a programmable knowledge environment for biologistsby: J. P. Massar, Michael Travers, Jeff Elhai, Jeff Shrager v. 21 i. 2 p. 199 - 207
- A method for estimating stochastic noise in large genetic regulatory networksby: David Orrell, Stephen Ramsey, Pedro de Atauri, Hamid Bolouri v. 21 i. 2 p. 208 - 217
- Predicting protein-protein interactions using signature productsby: Shawn Martin, Diana C. Roe, Jean-Loup Faulon v. 21 i. 2 p. 218 - 226
- Superiority of network motifs over optimal networks and an application to the revelation of gene network evolutionby: Sascha Ott, A. Hansen, SunYong Kim, Satoru Miyano v. 21 i. 2 p. 227 - 238
- Predicting protein functions with message passing algorithmsby: Michele Leone, Andrea Pagnani v. 21 i. 2 p. 239 - 247
- Gene name ambiguity of eukaryotic nomenclaturesby: Lifeng Chen, Hongfang Liu, Carol Friedman v. 21 i. 2 p. 248 - 256
- RALEE--RNA ALignment Editor in Emacsby: Sam Griffiths-Jones v. 21 i. 2 p. 257 - 259
- RDP2: recombination detection and analysis from sequence alignmentsby: Darren Martin, C. Williamson, David Posada v. 21 i. 2 p. 260 - 262
- Haploview: analysis and visualization of LD and haplotype mapsby: Jeffrey C. Barrett, B. Fry, Julian Maller, Mark Daly v. 21 i. 2 p. 263 - 265
- SNPP: automating large-scale SNP genotype data managementby: Lan-Juan Zhao, Miao-Xin Li, Yan-Fang Guo, Fu-Hua Xu, Jin-Long Li, Hong-Wen Deng v. 21 i. 2 p. 266 - 268
- Simulating genetic networks made easy: network construction with simple building blocksby: Steven Vercruysse, Martin Kuiper v. 21 i. 2 p. 269 - 271
- ProViz: protein interaction visualization and explorationby: Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David Sherman v. 21 i. 2 p. 272 - 274
- OntologyTraverser: an R package for GO analysisby: Andrew Young, Nathan Whitehouse, J. Cho, Chad A. Shaw v. 21 i. 2 p. 275 - 276
- Protein Refinement: A New Challenge For Casp In Its 10th Anniversaryv. 21 i. 3 p. 277 - 277
- Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombinationby: Graham J. Etherington, Jo L. Dicks, Ian N. Roberts v. 21 i. 3 p. 278 - 281
- Detecting overlapping coding sequences with pairwise alignmentsby: Andrew E. Firth, Chris M. Brown v. 21 i. 3 p. 282 - 292
- Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomicsby: Daniel H. Haft, Jeremy D. Selengut, Lauren M. Brinkac, Nikhat Zafar, Owen White v. 21 i. 3 p. 293 - 306
- Similarity of position frequency matrices for transcription factor binding sitesby: Dustin E. Schones, Pavel Sumazin, Michael Q. Zhang v. 21 i. 3 p. 307 - 313
- Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasetsby: Haiquan Li, Jinyan Li v. 21 i. 3 p. 314 - 324
- Dual-genome primer design for construction of DNA microarraysby: Anders Anderssonn, Rolf Bernander, Peter Nilsson v. 21 i. 3 p. 325 - 332
- Evaluating putative chimeric sequences from PCR-amplified productsby: Juan M. Gonzalez, Johannes Zimmermann, Cesareo Saiz-Jimenez v. 21 i. 3 p. 333 - 337
- A more efficient search strategy for aging genes based on connectivityby: Luca Ferrarini, Luca Bertelli, Jacob Feala, Andrew D. McCulloch, Giovanni Paternostro v. 21 i. 3 p. 338 - 348
- A Bayesian approach to reconstructing genetic regulatory networks with hidden factorsby: Matthew J. Beal, Francesco Falciani, Zoubin Ghahramani, Claudia Rangel, David L. Wild v. 21 i. 3 p. 349 - 356
- Simulation tools for biochemical networks: evaluation of performance and usabilityby: Antti Pettinen, Tommi Aho, Olli-Pekka Smolander, Tiina Manninen, Antti Saarinen, Kaisa-Leena Taattola, Olli Yli-Harja, Marja-Leena Linne v. 21 i. 3 p. 357 - 363
- Iterative Cluster Analysis of Protein Interaction Databy: Vicente Arnau, Sergio Mars, Ignacio Marín v. 21 i. 3 p. 364 - 378
- The Los Alamos hepatitis C sequence databaseby: Carla Kuiken, Karina Yusim, Laura Boykin, Russell Richardson v. 21 i. 3 p. 379 - 384
- SNPbox: a modular software package for large-scale primer designby: Stefan Weckx, Peter De Rijk, Christine Van Broeckhoven, Jurgen Del-Favero v. 21 i. 3 p. 385 - 387
- Tracker: continuous HMMER and BLAST searchingby: Madelaine Marchin, Paul T. Kelly, Jianwen Fang v. 21 i. 3 p. 388 - 389
- Clann: investigating phylogenetic information through supertree analysesby: C. J. Creevey, James O. McInerney v. 21 i. 3 p. 390 - 392
- The SSEA server for protein secondary structure alignmentby: Paolo Fontana, Eckart Bindewald, Stefano Toppo, Riccardo Velasco, Giorgio Valle, Silvio C. E. Tosatto v. 21 i. 3 p. 393 - 395
- Microarray data mining with visual programmingby: Tomaz Curk, Janez Demsar, Qikai Xu, Gregor Leban, Uros Petrovic, Ivan Bratko, Gad Shaulsky, Blaz Zupan v. 21 i. 3 p. 396 - 398
- BarleyExpress: a web-based submission tool for enriched microarray database annotationsby: Xiaoyun Tang, Lishuang Shen, Julie A. Dickerson v. 21 i. 3 p. 399 - 401
- SNAP: workbench management tool for evolutionary population genetic analysisby: Eric W. Price, Ignazio Carbone v. 21 i. 3 p. 402 - 404
- easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analysesby: Tom H. Lindner, K. Hoffmann v. 21 i. 3 p. 405 - 407
- Human-CMouse Gene Searcher: a tool to assist discovery of malformation-associated genes by using phenotype databasesby: Ian Bradford, Robin Winter, Carl Evans, Jonathan Bard v. 21 i. 3 p. 408 - 409
- iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutionsby: Robert D. Finn, Mhairi Marshall, Alex Bateman v. 21 i. 3 p. 410 - 412
- VizRank: finding informative data projections in functional genomics by machine learningby: Gregor Leban, Ivan Bratko, Uros Petrovic, Tomaz Curk, Blaz Zupan v. 21 i. 3 p. 413 - 414
- Capturing biological information with class?Cresponsibility?Ccollaboration cardsby: Daniel Shegogue, W. Jim Zheng v. 21 i. 3 p. 415 - 417
- PhenomicDB: a multi-species genotype/phenotype database for comparative phenomicsby: Abdullah Kahraman, Andrey Avramov, Lyubomir G. Nashev, Dimitar Popov, Rainer Ternes, Hans-Dieter Pohlenz, Bertram Weiss v. 21 i. 3 p. 418 - 420
- Clustering of diverse genomic data using information fusionby: Jyotsna Kasturi, Raj Acharya v. 21 i. 4 p. 423 - 429
- An architecture for biological information extraction and representationby: Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael L. Creech, Annette Adler v. 21 i. 4 p. 430 - 438
- Multidimensional support vector machines for visualization of gene expression databy: Daisuke Komura, Hiroshi Nakamura, Shuichi Tsutsumi, Hiroyuki Aburatani, Sigeo Ihara v. 21 i. 4 p. 439 - 444
- Finding differentially expressed genes for pattern generationby: Osman Abul, Reda Alhajj, Faruk Polat, Ken Barker v. 21 i. 4 p. 445 - 450
- An integrated tool for microarray data clustering and cluster validity assessment by: Nadia Bolshakova, Francisco Azuaje, Padraig Cunningham v. 21 i. 4 p. 451 - 455
- RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic treesby: Alexandros Stamatakis, Thomas Ludwig 0002, Harald Meier v. 21 i. 4 p. 456 - 463
- Improving genome annotations using phylogenetic profile anomaly detectionby: Tarjei S. Mikkelsen, James E. Galagan, Jill P. Mesirov v. 21 i. 4 p. 464 - 470
- Prediction of splice sites with dependency graphs and their expanded bayesian networksby: Te-Ming Chen, Chung-Chin Lu, Wen-Hsiung Li v. 21 i. 4 p. 471 - 482
- SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networksby: Gaurav Sachdeva, Kaushal Kumar, Preti Jain, Srinivasan Ramachandran v. 21 i. 4 p. 483 - 491
- An experimental evaluation of a loop versus a reference design for two-channel microarraysby: Veronica Vinciotti, Raya Khanin, D. D'Alimonte, Xiaohui Liu, N. Cattini, G. Hotchkiss, G. Bucca, O. de Jesus, J. Rasaiyaah, C. P. Smith, Paul Kellam, Ernst Wit v. 21 i. 4 p. 492 - 501
- VarMixt: efficient variance modelling for the differential analysis of replicated gene expression databy: Paul Delmar, Stéphane Robin, Jean-Jacques Daudin v. 21 i. 4 p. 502 - 508
- Identifying time-lagged gene clusters using gene expression databy: Liping Ji, Kian-Lee Tan v. 21 i. 4 p. 509 - 516
- Statistical methods of translating microarray data into clinically relevant diagnostic information in colorectal cancerby: Byung Soo Kim, Inyoung Kim, Sunho Lee, Sangcheol Kim, Sun Young Rha, Hyun Cheol Chung v. 21 i. 4 p. 517 - 528
- A semiparametric approach for marker gene selection based on gene expression databy: Zhong Guan, Hongyu Zhao v. 21 i. 4 p. 529 - 536
- Circular genome visualization and exploration using CGViewby: Paul Stothard, David S. Wishart v. 21 i. 4 p. 537 - 539
- wEMBOSS: a web interface for EMBOSSby: Martín Sarachu, Marc Colet v. 21 i. 4 p. 540 - 541
- tPatternHunter: gapped, fast and sensitive translated homology search by: Derek Kisman, Ming Li, Bin Ma, Li Wang v. 21 i. 4 p. 542 - 544
- Online synonymous codon usage analyses with the ade4 and seqinR packagesby: D. Charif, Jean Thioulouse, J. R. Lobry, Guy Perrière v. 21 i. 4 p. 545 - 547
- TFExplorer: integrated analysis database for predicted transcription regulatory elementsby: Jinsoo Kim, Jungmin Seo, Young Seek Lee, Sangsoo Kim v. 21 i. 4 p. 548 - 550
- Seq2Struct: a resource for establishing sequence-structure linksby: Allegra Via, Andreas Zanzoni, Manuela Helmer-Citterich v. 21 i. 4 p. 551 - 553
- arrayMagic: two-colour cDNA microarray quality control, preprocessingby: Andreas Buness, Wolfgang Huber, Klaus Steiner, Holger Sültmann, Annemarie Poustka v. 21 i. 4 p. 554 - 556
- MAP-O-MAT: internet-based linkage mappingby: X. Kong, Tara Cox Matise v. 21 i. 4 p. 557 - 559
- Modelling cellular systems with PySCeSby: Brett G. Olivier, Johann M. Rohwer, Jan-Hendrik S. Hofmeyr v. 21 i. 4 p. 560 - 561
- A graph-theoretic approach for the separation of b and y ions in tandem mass spectraby: Bo Yan, Chongle Pan, Victor Olman, Robert L. Hettich, Ying Xu v. 21 i. 5 p. 563 - 574
- Understanding protein dispensability through machine-learning analysis of high-throughput databy: Yu Chen, Dong Xu v. 21 i. 5 p. 575 - 581
- RAP: a new computer program for de novo identification of repeated sequences in whole genomesby: Davide Campagna, Chiara Romualdi, Nicola Vitulo, Micky Del Favero, Matej Lexa, Nicola Cannata, Giorgio Valle v. 21 i. 5 p. 582 - 588
- Stepwise detection of recombination breakpoints in sequence alignmentsby: Jinko Graham, Brad McNeney, Françoise Seillier-Moiseiwitsch v. 21 i. 5 p. 589 - 595
- Y. Barash, G. Elidan, T. Kaplan, , N. Friedmanby: Yoseph Barash, Gal Elidan, Tommy Kaplan, Nir Friedman v. 21 i. 5 p. 596 - 600
- Improving promoter prediction Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequencesby: S. Burden, Y.-X. Lin, R. Zhang v. 21 i. 5 p. 601 - 607
- Biological sequence analysis through the one-dimensional percolation transform and its enhanced versionby: Luciano da Fontoura Costa v. 21 i. 5 p. 608 - 616
- PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysisby: Jennifer L. Gardy, M. R. Laird, Fei Chen, S. Rey, C. J. Walsh, Martin Ester, Fiona S. L. Brinkman v. 21 i. 5 p. 617 - 623
- Improving conformational searches by geometric screeningby: Ming Zhang, R. Allen White, Liqun Wang, Ronald N. Goldman, Lydia E. Kavraki, Brendan Hassett v. 21 i. 5 p. 624 - 630
- A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosisby: Alexander R. Statnikov, Constantin F. Aliferis, Ioannis Tsamardinos, Douglas Hardin, Shawn Levy v. 21 i. 5 p. 631 - 643
- Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methodsby: Musa H. Asyali, Musa Alci v. 21 i. 5 p. 644 - 649
- Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specificationby: Itai Yanai, Hila Benjamin-Rodrig, Michael Shmoish, Vered Chalifa-Caspi, Maxim Shklar, Ron Ophir, Arren Bar-Even, Shirley Horn-Saban, Marilyn Safran, Eytan Domany, Doron Lancet, Orit Shmueli v. 21 i. 5 p. 650 - 659
- A simple procedure for estimating the false discovery rateby: Cyril Dalmasso, Philippe Broët, Thierry Moreau v. 21 i. 5 p. 660 - 668
- ESTminer: a Web interface for mining EST contig and cluster databasesby: Yecheng Huang, Janie Pumphrey, Alan R. Gingle v. 21 i. 5 p. 669 - 670
- DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequencesby: Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong v. 21 i. 5 p. 671 - 673
- A simple tool for drawing proteolytic peptide mapsby: Robert J. Beynon v. 21 i. 5 p. 674 - 675
- HyPhy: hypothesis testing using phylogeniesby: Sergei L. Kosakovsky Pond, Simon D. W. Frost, Spencer V. Muse v. 21 i. 5 p. 676 - 679
- APART: Automated Preprocessing for NMR Assignments with Reduced Tediumby: Norma H. Pawley, Jason D. Gans, Ryszard Michalczyk v. 21 i. 5 p. 680 - 682
- Database driven test case generation for protein?Cprotein dockingby: Frank Zöllner, Steffen Neumann, Franz Kummert, Gerhard Sagerer v. 21 i. 5 p. 683 - 684
- COPS - Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure informationby: Doreen Pahlke, Dietmar Leitner, Urs Wiedemann, Dirk Labudde v. 21 i. 5 p. 685 - 686
- Implementation of a gene expression index calculation method based on the PDNN modelby: Henrik Bjørn Nielsen, Laurent Gautier, Steen Knudsen v. 21 i. 5 p. 687 - 688
- LabArray: real-time imaging and analytical tool for microarraysby: Johnson Kian-Kok Ng, Wen-Tso Liu v. 21 i. 5 p. 689 - 690
- ESTminer: a suite of programs for gene and allele identificationby: Rex T. Nelson, David Grant, Randy C. Shoemaker v. 21 i. 5 p. 691 - 693
- MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citationsby: Jing Ding, Daniel Berleant v. 21 i. 5 p. 694 - 695
- DictyMOLD - a Dictyostelium discoideum genome browser databaseby: Marius Felder, Karol Szafranski, Rüdiger Lehmann, Ludwig Eichinger, Angelika A. Noegel, Matthias Platzer, Gernot Glöckner v. 21 i. 5 p. 696 - 697
- OCRE: a novel domain made of imperfect, aromatic-rich octamer repeatsby: Isabelle Callebaut, Jean Paul Mornon v. 21 i. 6 p. 699 - 702
- Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairsby: Xiangqun H. Zheng, Fu Lu, Zhen-Yuan Wang, Fei Zhong, Jeffrey Hoover, Richard J. Mural v. 21 i. 6 p. 703 - 710
- Comparison of different melting temperature calculation methods for short DNA sequences by: Alejandro Panjkovich, Francisco Melo v. 21 i. 6 p. 711 - 722
- Weighted analysis of microarray gene expression using maximum-likelihoodby: David J. Bakewell, Ernst Wit v. 21 i. 6 p. 723 - 729
- Relational patterns of gene expression via non-metric multidimensional scaling analysisby: Y.-h. Taguchi, Y. Oono v. 21 i. 6 p. 730 - 740
- Bayesian analysis of signaling networks governing embryonic stem cell fate decisionsby: Peter J. Woolf, Wendy Prudhomme, Laurence Daheron, George Q. Daley, Douglas A. Lauffenburger v. 21 i. 6 p. 741 - 753
- An empirical Bayes approach to inferring large-scale gene association networksby: Juliane Schäfer, Korbinian Strimmer v. 21 i. 6 p. 754 - 764
- Reconstructing biological networks using conditional correlation analysisby: John Jeremy Rice, Yuhai Tu, Gustavo Stolovitzky v. 21 i. 6 p. 765 - 773
- An enzyme mechanism language for the mathematical modeling of metabolic pathwaysby: Chin-Rang Yang, Bruce E. Shapiro, Eric Mjolsness, G. Wesley Hatfield v. 21 i. 6 p. 774 - 780
- An efficient Monte Carlo approach to assessing statistical significance in genomic studiesby: D. Y. Lin v. 21 i. 6 p. 781 - 787
- Inferring pathways from gene lists using a literature-derived network of biological relationshipsby: Dilip Rajagopalan, Pankaj Agarwal v. 21 i. 6 p. 788 - 793
- GLAD: a system for developing and deploying large-scale bioinformatics gridby: Yong Meng Teo, Xianbing Wang, Yew Kwong Ng v. 21 i. 6 p. 794 - 802
- Expression-based monitoring of transcription factor activity: the TELiS databaseby: Steve W. Cole, Weihong Yan, Zoran Galic, Jesusa Arevalo, Jerome A. Zack v. 21 i. 6 p. 803 - 810
- TRbase: a database relating tandem repeats to disease genes for the human genomeby: T. Boby, A.-M. Patch, S. J. Aves v. 21 i. 6 p. 811 - 816
- ParIS Genome Rearrangement serverby: István Miklós, P. Ittzés, Jotun Hein v. 21 i. 6 p. 817 - 820
- CGH-Explorer: a program for analysis of array-CGH databy: Ole Christian Lingjærde, Lars O. Baumbusch, Knut Liestøl, Ingrid K. Glad, Anne-Lise Børresen-Dale v. 21 i. 6 p. 821 - 822
- The SBW-CMATLAB interfaceby: Cameron Wellock, Vijay Chickarmane, Herbert M. Sauro v. 21 i. 6 p. 823 - 824
- COBrA: a bio-ontology editorby: J. Stuart Aitken, Roman Korf, Bonnie L. Webber, Jonathan Bard v. 21 i. 6 p. 825 - 826
- PDZBase: a protein?Cprotein interaction database for PDZ-domainsby: Thijs Beuming, Lucy Skrabanek, Masha Y. Niv, Piali Mukherjee, Harel Weinstein v. 21 i. 6 p. 827 - 828
- GOChase: correcting errors from Gene Ontology-based annotations for gene productsby: Yu Rang Park, Chan Hee Park, Ju Han Kim v. 21 i. 6 p. 829 - 831
- The MIPS mammalian protein?Cprotein interaction databaseby: Philipp Pagel, Stefan Kovac, Matthias Oesterheld, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Pekka Mark, Volker Stümpflen, Hans-Werner Mewes, Andreas Ruepp, Dmitrij Frishman v. 21 i. 6 p. 832 - 834
- OMGProm: a database of orthologous mammalian gene promotersby: Saranyan K. Palaniswamy, Victor X. Jin, Hao Sun, Ramana V. Davuluri v. 21 i. 6 p. 835 - 836
- AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon contextby: Alex V. Kochetov v. 21 i. 7 p. 837 - 840
- Profile-based detection of microRNA precursors in animal genomesby: Matthieu Legendre, André Lambert, Daniel Gautheret v. 21 i. 7 p. 841 - 845
- ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genomeby: Vladimir Paar, Nenad Pavin, Marija Rosandic, Matko Gluncic, Ivan Basar, Robert Pezer, Sonja Durajlija Zinic v. 21 i. 7 p. 846 - 852
- BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparisonby: Daniela Bartels, Sebastian Kespohl, Stefan Albaum, Tanja Drüke, Alexander Goesmann, Julia Herold, Olaf Kaiser, Alfred Pühler, Friedhelm Pfeiffer, Günter Raddatz, Jens Stoye, Folker Meyer, Stephan C. Schuster v. 21 i. 7 p. 853 - 859
- Genetic algorithm optimization for pre-processing and variable selection of spectroscopic databy: Roger M. Jarvis, Royston Goodacre v. 21 i. 7 p. 860 - 868
- Theoretical and practical advances in genome halvingby: Peng Yin, Alexander J. Hartemink v. 21 i. 7 p. 869 - 879
- Operon prediction without a training setby: B. P. Westover, J. D. Buhler, J. L. Sonnenburg, J. I. Gordon v. 21 i. 7 p. 880 - 888
- A parallel graph decomposition algorithm for DNA sequencing with nanoporesby: Shahid H. Bokhari, Jon R. Sauer v. 21 i. 7 p. 889 - 896
- Accurate identification of alternatively spliced exons using support vector machineby: Gideon Dror, Rotem Sorek, Ron Shamir v. 21 i. 7 p. 897 - 901
- The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositionsby: Yi-Kuo Yu, Stephen F. Altschul v. 21 i. 7 p. 902 - 911
- Fast and accurate database homology search using upper bounds of local alignment scoresby: Masumi Itoh, Susumu Goto, Tatsuya Akutsu, Minoru Kanehisa v. 21 i. 7 p. 912 - 921
- Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sitesby: Chiara Sabatti, Lars Rohlin, Kenneth Lange, James C. Liao v. 21 i. 7 p. 922 - 931
- Rapid motif-based prediction of circular permutations in multi-domain proteinsby: January Weiner, Geraint Thomas, Erich Bornberg-Bauer v. 21 i. 7 p. 932 - 937
- Relation between weight matrix and substitution matrix: motif search by similarityby: Wei-Mou Zheng v. 21 i. 7 p. 938 - 943
- Predicting protein localization in budding Yeastby: Kuo-Chen Chou, Yu-Dong Cai v. 21 i. 7 p. 944 - 950
- Protein homology detection by HMM?CHMM comparisonby: Johannes Söding v. 21 i. 7 p. 951 - 960
- A simple statistical method for discriminating outer membrane proteins with better accuracyby: M. Michael Gromiha, Makiko Suwa v. 21 i. 7 p. 961 - 968
- DPRml: distributed phylogeny reconstruction by maximum likelihoodby: Thomas M. Keane, Thomas J. Naughton, S. A. A. Travers, James O. McInerney, G. P. McCormack v. 21 i. 7 p. 969 - 974
- An alternative model of amino acid replacementby: Gavin E. Crooks, Steven E. Brenner v. 21 i. 7 p. 975 - 980
- A new approach to prediction of short-range conformational propensities in proteinsby: Dominik Gront, Andrzej Kolinski v. 21 i. 7 p. 981 - 987
- PDBML: the representation of archival macromolecular structure data in XMLby: John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman v. 21 i. 7 p. 988 - 992
- Statistical analysis of domains in interacting protein pairsby: Tom M. W. Nye, Carlo Berzuini, Walter R. Gilks, M. Madan Babu, Sarah A. Teichmann v. 21 i. 7 p. 993 - 1001
- Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approachby: Erik Sandelin v. 21 i. 7 p. 1002 - 1009
- Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteinsby: Xin Yuan, Christopher Bystroff v. 21 i. 7 p. 1010 - 1019
- Predicting fold novelty based on ProtoNet hierarchical classificationby: Ilona Kifer, Ori Sasson, Michal Linial v. 21 i. 7 p. 1020 - 1027
- Solving and analyzing side-chain positioning problems using linear and integer programmingby: Carleton L. Kingsford, Bernard Chazelle, Mona Singh v. 21 i. 7 p. 1028 - 1039
- Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory methodby: F. R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, B. Rohrer, Jonas S. Almeida v. 21 i. 7 p. 1037 - 1045
- Superior feature-set ranking for small samples using bolstered error estimationby: Chao Sima, Ulisses Braga-Neto, Edward R. Dougherty v. 21 i. 7 p. 1046 - 1054
- A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samplesby: Yuan Ji, Kam-Wah Tsui, KyungMann Kim v. 21 i. 7 p. 1055 - 1061
- Extracting relations between promoter sequences and their strengths from microarray databy: Hisanori Kiryu, Taku Oshima, Kiyoshi Asai v. 21 i. 7 p. 1062 - 1068
- Clustering of gene expression data using a local shape-based similarity measureby: Rajarajeswari Balasubramaniyan, Eyke Hüllermeier, Nils Weskamp, Jörg Kämper v. 21 i. 7 p. 1069 - 1077
- Normalization of two-channel microarray experiments: a semiparametric approachby: J. E. Eckel, C. Gennings, Terry M. Therneau, L. D. Burgoon, D. R. Boverhof, T. R. Zacharewski v. 21 i. 7 p. 1078 - 1083
- Identifying differentially expressed genes from microarray experiments via statistic synthesisby: Yee Hwa Yang, Yuanyuan Xiao, Mark R. Segal v. 21 i. 7 p. 1084 - 1093
- GoArrays: highly dynamic and efficient microarray probe designby: Sébastien Rimour, David Hill, Cécile Militon, Pierre Peyret v. 21 i. 7 p. 1094 - 1103
- Classification using partial least squares with penalized logistic regressionby: Gersende Fort, Sophie Lambert-Lacroix v. 21 i. 7 p. 1104 - 1111
- Validation of alternative methods of data normalization in gene co-expression studiesby: Antonio Reverter, Wes Barris, Sean McWilliam, Keren A. Byrne, Yong H. Wang, Siok H. Tan, Nick Hudson, Brian P. Dalrymple v. 21 i. 7 p. 1112 - 1120
- Probabilities of spurious connections in gene networks: application to expression time seriesby: David R. Bickel v. 21 i. 7 p. 1121 - 1128
- Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expressionby: Yoram Ben-Shaul, Hagai Bergman, Hermona Soreq v. 21 i. 7 p. 1129 - 1137
- Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arraysby: Sven Bilke, Qing-Rong Chen, Craig C. Whiteford, Javed I. Khan v. 21 i. 7 p. 1138 - 1145
- Quantile smoothing of array CGH databy: Paul H. C. Eilers, Renée X. de Menezes v. 21 i. 7 p. 1146 - 1153
- Inference of S-system models of genetic networks using a cooperative coevolutionary algorithmby: Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya v. 21 i. 7 p. 1154 - 1163
- Comparison of computational methods for the identification of cell cycle-regulated genesby: Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas S. Jensen, Peer Bork, Søren Brunak v. 21 i. 7 p. 1164 - 1171
- Finding regulatory modules through large-scale gene-expression data analysisby: M. Kloster, C. Tang, N. S. Wingreen v. 21 i. 7 p. 1172 - 1179
- Evolutionary optimization with data collocation for reverse engineering of biological networksby: Kuan-Yao Tsai, Feng-Sheng Wang v. 21 i. 7 p. 1180 - 1188
- Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)by: S. A. Rahman, P. Advani, R. Schunk, Rainer Schrader, Dietmar Schomburg v. 21 i. 7 p. 1189 - 1193
- Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signalingby: Gang Liu, Mark T. Swihart, Sriram Neelamegham v. 21 i. 7 p. 1194 - 1202
- An improved algorithm for stoichiometric network analysis: theory and applicationsby: R. Urbanczik, C. Wagner v. 21 i. 7 p. 1203 - 1210
- Intervention in context-sensitive probabilistic Boolean networksby: Ranadip Pal, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty v. 21 i. 7 p. 1211 - 1218
- Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuberby: Ina Koch, Bjørn H. Junker, Monika Heiner v. 21 i. 7 p. 1219 - 1226
- Automatic extraction of gene/protein biological functions from biomedical textby: Asako Koike, Yoshiki Niwa, Toshihisa Takagi v. 21 i. 7 p. 1227 - 1236
- In silico gene function prediction using ontology-based pattern identificationby: Yingyao Zhou, Jason A. Young, Andrey Santrosyan, Kaisheng Chen, S. Frank Yan, Elizabeth A. Winzeler v. 21 i. 7 p. 1237 - 1245
- ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systemsby: Julie Chabalier, Cécile Capponi, Yves Quentin, Gwennaele Fichant v. 21 i. 7 p. 1246 - 1256
- CRAVE: a database, middleware and visualization system for phenotype ontologiesby: Georgios V. Gkoutos, Eain C. J. Green, Simon Greenaway, Andrew Blake, Ann-Marie Mallon, John M. Hancock v. 21 i. 7 p. 1257 - 1262
- Primaclade - a flexible tool to find conserved PCR primers across multiple speciesby: Michael D. Gadberry, Simon T. Malcomber, Andrew N. Doust, Elizabeth A. Kellogg v. 21 i. 7 p. 1263 - 1264
- MapLinker: a software tool that aids physical map-linked whole genome shotgun assemblyby: Jian Xu, Jeffrey I. Gordon v. 21 i. 7 p. 1265 - 1266
- SABmark- a benchmark for sequence alignment that covers the entire known fold spaceby: Ivo Van Walle, Ignace Lasters, Lode Wyns v. 21 i. 7 p. 1267 - 1268
- NetAcet: prediction of N-terminal acetylation sitesby: Lars Kiemer, Jannick Dyrløv Bendtsen, Nikolaj Blom v. 21 i. 7 p. 1269 - 1270
- Multiple sequence alignment with user-defined constraints at GOBICSby: Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff v. 21 i. 7 p. 1271 - 1273
- SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inferenceby: D. Paraskevis, K. Deforche, P. Lemey, G. Magiorkinis, A. Hatzakis, A.-M. Vandamme v. 21 i. 7 p. 1274 - 1275
- TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinatesby: Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon v. 21 i. 7 p. 1276 - 1277
- A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patternsby: Victor E. Gerth, Peter D. Vize v. 21 i. 7 p. 1278 - 1279
- PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear orderby: Gilles Caraux, Sylvie Pinloche v. 21 i. 7 p. 1280 - 1281
- CyDAS: a cytogenetic data analysis systemby: Bernhard Hiller, Jutta Bradtke, Harald Balz, Harald Rieder v. 21 i. 7 p. 1282 - 1283
- Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processesby: Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Kishore R. Sakharkar, Arun Krishnan, Azmi B. M. Ridwan, Sebastian Ho Kok Wah, Mandar Chitre, Hao Zhu v. 21 i. 7 p. 1284 - 1287
- hp-DPI: Helicobacter pylori Database of Protein Interactomes-embracing experimental and inferred interactionsby: Chung-Yen Lin, Chia-Ling Chen, Chi-Shiang Cho, Li-Ming Wang, Chia-Ming Chang, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung v. 21 i. 7 p. 1288 - 1290
- BRAGI: linking and visualization of database information in a 3D viewer and modeling toolby: Joachim Reichelt, Guido Dieterich, Marsel Kvesic, Dietmar Schomburg, Dirk W. Heinz v. 21 i. 7 p. 1291 - 1293
- Synergy of human Pol II core promoter elements revealed by statistical sequence analysisby: Naum I. Gershenzon, Ilya P. Ioshikhes v. 21 i. 8 p. 1295 - 1300
- The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formationby: Alex Bateman, Matthew T. G. Holden, Corin Yeats v. 21 i. 8 p. 1301 - 1303
- The WHy domain mediates the response to desiccation in plants and bacteriaby: Francesca Ciccarelli, Peer Bork v. 21 i. 8 p. 1304 - 1307
- Structural drift: a possible path to protein fold changeby: S. Sri Krishna, Nick V. Grishin v. 21 i. 8 p. 1308 - 1310
- Topology of small-world networks of protein?Cprotein complex structuresby: Antonio del Sol, Hirotomo Fujihashi, Paul O'Meara v. 21 i. 8 p. 1311 - 1315
- Accelerated off-target search algorithm for siRNAby: Tomoyuki Yamada, Shinichi Morishita v. 21 i. 8 p. 1316 - 1324
- Autoregressive modeling of analytical sensor data can yield classifiers in the predictor coefficient parameter spaceby: Melissa D. Krebs, Robert D. Tingley, Julie E. Zeskind, Joung-Mo Kang, Maria E. Holmboe, Cristina E. Davis v. 21 i. 8 p. 1325 - 1331
- SpliceMachine: predicting splice sites from high-dimensional local context representationsby: Sven Degroeve, Yvan Saeys, Bernard De Baets, Pierre Rouzé, Yves Van de Peer v. 21 i. 8 p. 1332 - 1338
- Statistical detection of chromosomal homology using shared-gene density aloneby: S. E. Hampson, B. S. Gaut, Pierre Baldi v. 21 i. 8 p. 1339 - 1348
- Correlation of amino acid preference and mammalian viral genome typeby: John R. Rose, William H. Turkett, Iulia C. Oroian, William W. Laegreid, John W. Keele v. 21 i. 8 p. 1349 - 1357
- Evidence for the regulation of alternative splicing via complementary DNA sequence repeatsby: Yun Lian, Harold R. Garner v. 21 i. 8 p. 1358 - 1364
- YODA: selecting signature oligonucleotidesby: Eric K. Nordberg v. 21 i. 8 p. 1365 - 1370
- A graph based algorithm for generating EST consensus sequencesby: Ketil Malde, Eivind Coward, Inge Jonassen v. 21 i. 8 p. 1371 - 1375
- Highly specific and accurate selection of siRNAs for high-throughput functional assaysby: Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo v. 21 i. 8 p. 1376 - 1382
- Support vector machines for separation of mixed plant?Cpathogen EST collections based on codon usageby: Caroline C. Friedel, Katharina H. V. Jahn, Selina Sommer, Stephen Rudd, Hans-Werner Mewes, Igor V. Tetko v. 21 i. 8 p. 1383 - 1388
- LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genomeby: Matthias B. Wahl, Ulrich Heinzmann, Kenji Imai v. 21 i. 8 p. 1389 - 1392
- LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouseby: Matthias B. Wahl, Ulrich Heinzmann, Kenji Imai v. 21 i. 8 p. 1393 - 1400
- TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNAby: Xiaochen Bo, Shengqi Wang v. 21 i. 8 p. 1401 - 1402
- A fuzzy guided genetic algorithm for operon predictionby: E. Jacob, R. Sasikumar, K. N. R. Nair v. 21 i. 8 p. 1403 - 1407
- Evaluation of iterative alignment algorithms for multiple alignmentby: Iain M. Wallace, Orla O'Sullivan, Desmond G. Higgins v. 21 i. 8 p. 1408 - 1414
- Cysteine separations profiles on protein sequences infer disulfide connectivityby: East Zhao, Hsuan-Liang Liu, Chi-Hung Tsai, Huai-Kuang Tsai, Chen-hsiung Chan, Cheng-Yan Kao v. 21 i. 8 p. 1415 - 1420
- Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penaltiesby: Yasuyuki Nozaki, Matthew I. Bellgard v. 21 i. 8 p. 1421 - 1428
- Implicit motif distribution based hybrid computational kernel for sequence classificationby: Volkan Atalay, Rengül Çetin-Atalay v. 21 i. 8 p. 1429 - 1436
- DbW: automatic update of a functional family-specific multiple alignmentby: Veronique Prigent, Jean-Claude Thierry, Olivier Poch, Frédéric Plewniak v. 21 i. 8 p. 1437 - 1442
- Mapping SNPs to protein sequence and structure databy: A. Cavallo, Andrew C. R. Martin v. 21 i. 8 p. 1443 - 1450
- A structure-based method for protein sequence alignmentby: Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, Stephen H. Bryant v. 21 i. 8 p. 1451 - 1456
- A score matrix to reveal the hidden links in glycansby: Kiyoko F. Aoki, Hiroshi Mamitsuka, Tatsuya Akutsu, Minoru Kanehisa v. 21 i. 8 p. 1457 - 1463
- Convergent evolution of domain architectures (is rare)by: Julian Gough v. 21 i. 8 p. 1464 - 1471
- M-ZDOCK: a grid-based approach for Cn symmetric multimer dockingby: Brian Pierce, Weiwei Tong, Zhiping Weng v. 21 i. 8 p. 1472 - 1478
- Architecture of basic building blocks in protein and domain structural interaction networksby: Hyun S. Moon, Jonghwa Bhak, Kwang Hyung Lee, Doheon Lee v. 21 i. 8 p. 1479 - 1486
- Improved prediction of protein-Cprotein binding sites using a support vector machines approachby: James R. Bradford, David R. Westhead v. 21 i. 8 p. 1487 - 1494
- The ArrayExpress gene expression database: a software engineering and implementation perspectiveby: Ugis Sarkans, Helen E. Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna-Assunta Sansone, Anna Farne, Tim Rayner, Alvis Brazma v. 21 i. 8 p. 1495 - 1501
- Sample size for gene expression microarray experimentsby: Chen-An Tsai, Sue-Jane Wang, Dung-Tsa Chen, James J. Chen v. 21 i. 8 p. 1502 - 1508
- Optimal number of features as a function of sample size for various classification rulesby: Jianping Hua, Zixiang Xiong, James Lowey, Edward Suh, Edward R. Dougherty v. 21 i. 8 p. 1509 - 1515
- Bayesian models for the analysis of genetic structure when populations are correlatedby: Rongwei Fu, Dipak K. Dey, Kent E. Holsinger v. 21 i. 8 p. 1516 - 1529
- HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression databy: Yuhang Wang, Fillia Makedon, James C. Ford, Justin D. Pearlman v. 21 i. 8 p. 1530 - 1537
- Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression databy: Qinghua Cui, Bing Liu, Tianzi Jiang, Songde Ma v. 21 i. 8 p. 1538 - 1541
- Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDSby: Ranadip Pal, Aniruddha Datta, Albert J. Fornace, Michael L. Bittner, Edward R. Dougherty v. 21 i. 8 p. 1542 - 1549
- Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebratesby: Céline Lefebvre, Jean-Christophe Aude, Eric Glémet, Christian Néri v. 21 i. 8 p. 1550 - 1558
- LS Bound based gene selection for DNA microarray databy: Xin Zhou, K. Z. Mao v. 21 i. 8 p. 1559 - 1564
- Differential gene expression detection using penalized linear regression models: the improved SAM statisticsby: Baolin Wu v. 21 i. 8 p. 1565 - 1571
- Quick and simple: quality control of microarray databy: Ursula Sauer, Claudia Preininger, Robert Hany-Schmatzberger v. 21 i. 8 p. 1572 - 1578
- A nearest-neighboring-end algorithm for genetic mappingby: Charles F. Crane, Yan M. Crane v. 21 i. 8 p. 1579 - 1591
- Generalized Venn diagrams: a new method of visualizing complex genetic set relationsby: Hans A. Kestler, André Müller, Thomas M. Gress, Malte Buchholz v. 21 i. 8 p. 1592 - 1595
- VitaPad: visualization tools for the analysis of pathway databy: Matthew Holford, Naixin Li, Prakash M. Nadkarni, Hongyu Zhao v. 21 i. 8 p. 1596 - 1602
- Exploring the diversity of complex metabolic networksby: Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt v. 21 i. 8 p. 1603 - 1609
- Dynamic simulation of protein complex formation on a genomic scaleby: A. Beyer, T. Wilhelm v. 21 i. 8 p. 1610 - 1616
- Investigating the dynamic behavior of biochemical networks using model familiesby: Marc Daniel Haunschild, Bernd Freisleben, Ralf Takors, Wolfgang Wiechert v. 21 i. 8 p. 1617 - 1625
- Dynamic network reconstruction from gene expression data applied to immune response during bacterial infectionby: Reinhard Guthke, Ulrich Möller, Martin Hoffmann, Frank Thies, Susanne Töpfer v. 21 i. 8 p. 1626 - 1634
- GMD@CSB.DB: the Golm Metabolome Databaseby: Joachim Kopka, Nicolas Schauer, Stephan Krueger, Claudia Birkemeyer, Björn Usadel, Eveline Bergmüller, Peter Dörmann, Wolfram Weckwerth, Yves Gibon, Mark Stitt, Lothar Willmitzer, Alisdair R. Fernie, Dirk Steinhauser v. 21 i. 8 p. 1635 - 1638
- Quantifying the relevance of different mediators in the human immune cell networkby: P. Tieri, S. Valensin, V. Latora, G. C. Castellani, M. Marchiori, D. Remondini, C. Franceschi v. 21 i. 8 p. 1639 - 1643
- Predicting gene function through systematic analysis and quality assessment of high-throughput databy: Patrick Kemmeren, Thessa T. J. P. Kockelkorn, Theo Bijma, Rogier Donders, Frank Holstege v. 21 i. 8 p. 1644 - 1652
- Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extractionby: Carlos Santos, Daniela Eggle, David. J. States v. 21 i. 8 p. 1653 - 1658
- Visualizing information across multidimensional post-genomic structured and textual databasesby: Ying Tao, Carol Friedman, Yves A. Lussier v. 21 i. 8 p. 1659 - 1667
- Evaluation of HIV-1 kinetic models using quantitative discrimination analysisby: Andrea L. Knorr, Ranjan Srivastava v. 21 i. 8 p. 1668 - 1677
- A framework for scientific data modeling and automated software developmentby: Rasmus H. Fogh, Wayne Boucher, Wim F. Vranken, Anne Pajon, Tim J. Stevens, T. N. Bhat, John D. Westbrook, John M. C. Ionides, Ernest D. Laue v. 21 i. 8 p. 1678 - 1684
- Constructing ontology-driven protein family databasesby: K. Wolstencroft, Robin McEntire, Robert Stevens, L. Tabernero, Andy Brass v. 21 i. 8 p. 1685 - 1692
- Procom: a web-based tool to compare multiple eukaryotic proteomesby: Jin Billy Li, Miao Zhang, Susan K. Dutcher, Gary D. Stormo v. 21 i. 8 p. 1693 - 1694
- TERMINUS - Telomeric End-Read Mining IN Unassembled Sequencesby: Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, Mark L. Farman v. 21 i. 8 p. 1695 - 1698
- HESAS: HERVs Expression and Structure Analysis Systemby: Tae-Hyung Kim, Yeo-Jin Jeon, Woo-Yeon Kim, Heui-Soo Kim v. 21 i. 8 p. 1699 - 1700
- MultiPLX: automatic grouping and evaluation of PCR primersby: Lauris Kaplinski, Reidar Andreson, Tarmo Puurand, Maido Remm v. 21 i. 8 p. 1701 - 1702
- CARHTA GENE: multipopulation integrated genetic and radiation hybrid mappingby: Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, Thomas Schiex v. 21 i. 8 p. 1703 - 1704
- DSEARCH: sensitive database searching using distributed computingby: Thomas M. Keane, Thomas J. Naughton v. 21 i. 8 p. 1705 - 170
- PatGen - a consolidated resource for searching genetic patent sequencesby: Richard J. D. Rouse, Jesus Castagnetto, Roland H. Niedner v. 21 i. 8 p. 1707 - 1708
- SYMMETREE: whole-tree analysis of differential diversification ratesby: Kai M. A. Chan, Brian R. Moore v. 21 i. 8 p. 1709 - 1710
- RBT - a tool for building refined Buneman treesby: Søren Besenbacher, Thomas Mailund, Lasse Westh-Nielsen, Christian N. S. Pedersen v. 21 i. 8 p. 1711 - 1712
- GeneContent: software for whole-genome phylogenetic analysisby: Xun Gu, Wei Huang, Dongping Xu, Hongmei Zhang v. 21 i. 8 p. 1713 - 1714
- Voro3D: 3D Voronoi tessellations applied to protein structuresby: Franck Dupuis, Jean-François Sadoc, Rémi Jullien, Borislav Angelov, Jean Paul Mornon v. 21 i. 8 p. 1715 - 1716
- The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structuresby: Norihiro Kikuchi, Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Takashi Sato, Toshihide Shikanai, Yoriko Takahashi, Hisashi Narimatsu v. 21 i. 8 p. 1717 - 1718
- Porter: a new, accurate server for protein secondary structure predictionby: Gianluca Pollastri, Aoife McLysaght v. 21 i. 8 p. 1719 - 1720
- PreDs: a server for predicting dsDNA-binding site on protein molecular surfacesby: Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura v. 21 i. 8 p. 1721 - 1723
- OLIN: optimized normalization, visualization and quality testing of two-channel microarray databy: Matthias E. Futschik, Toni Crompton v. 21 i. 8 p. 1724 - 1726
- Bloader - a batch loader application for MIAMExpressby: Christian Schwager, Jonathon Blake v. 21 i. 8 p. 1727 - 1729
- HaploPainter: a tool for drawing pedigrees with complex haplotypesby: Holger Thiele, Peter J. Nürnberg v. 21 i. 8 p. 1730 - 1732
- Serial SimCoal: A population genetics model for data from multiple populations and points in timeby: Christian N. K. Anderson, Uma Ramakrishnan, Yvonne L. Chan, Elizabeth A. Hadly v. 21 i. 8 p. 1733 - 1734
- CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPsby: S. I. Ao, Kevin Yip, Michael Ng, David Cheung, Pui-Yee Fong, Ian Melhado, Pak Chung Sham v. 21 i. 8 p. 1735 - 1736
- In silico fine-mapping: narrowing disease-associated loci by intergenomicsby: Pablo Serrano-Fernández, Saleh M. Ibrahim, Dirk Koczan, Uwe K. Zettl, Steffen Möller v. 21 i. 8 p. 1737 - 1738
- expa: a program for calculating extreme pathways in biochemical reaction networksby: Steven L. Bell, Bernhard O. Palsson v. 21 i. 8 p. 1739 - 1740
- An enhanced Java graph applet interface for visualizing interactomesby: Aaron N. Chang, Jason McDermott, Ram Samudrala v. 21 i. 8 p. 1741 - 1742
- GPSDB: a new database for synonyms expansion of gene and protein namesby: Violaine Pillet, Marc Zehnder, Alexander K. Seewald, Anne-Lise Veuthey, Johann Petrak v. 21 i. 8 p. 1743 - 1744
- BIAS: Bioinformatics Integrated Application Softwareby: G. Finak, N. Godin, M. Hallett, F. Pepin, Z. Rajabi, V. Srivastava, Z. Tang v. 21 i. 8 p. 1745 - 1746
- Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogasterby: Casey M. Bergman, Joseph W. Carlson, Susan E. Celniker v. 21 i. 8 p. 1747 - 1749
- SuperDrug: a conformational drug databaseby: Andrean Goede, Mathias Dunkel, Nina Mester, Cornelius Frömmel, Robert Preissner v. 21 i. 9 p. 1751 - 1753
- AGML Central: web based gel proteomic infrastructureby: Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John Arthur, Jonas S. Almeida v. 21 i. 9 p. 1754 - 1757
- Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)by: Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita v. 21 i. 9 p. 1758 - 1763
- Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrumby: Jeffrey S. Morris, Kevin R. Coombes, John Koomen, Keith A. Baggerly, Ryuji Kobayashi v. 21 i. 9 p. 1764 - 1775
- Gene finding for the helical cytokinesby: Darrell Conklin, Betty Haldeman, Zeren Gao v. 21 i. 9 p. 1776 - 1781
- Efficient implementation of a generalized pair hidden Markov model for comparative gene findingby: William H. Majoros, Mihaela Pertea, Sihaela Salzberg v. 21 i. 9 p. 1782 - 178
- A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areasby: Maria Stepanova, Tatiana Tiazhelova, Mikle Skoblov, Ancha Baranova v. 21 i. 9 p. 1789 - 1796
- Detecting interspecific recombination with a pruned probabilistic divergence measureby: Dirk Husmeier, Frank Wright, Iain Milne v. 21 i. 9 p. 1797 - 1806
- Transcription factor binding site identification using the self-organizing mapby: Shaun Mahony, David Hendrix, Aaron Golden, Terry J. Smith, Daniel S. Rokhsar v. 21 i. 9 p. 1807 - 1814
- Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%by: Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin v. 21 i. 9 p. 1815 - 1824
- Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteinsby: J. M. Cameron, T. Hurd, B. H. Robinson v. 21 i. 9 p. 1825 - 1830
- Prediction of caspase cleavage sites using Bayesian bio-basis function neural networksby: Zheng Rong Yang v. 21 i. 9 p. 1831 - 1837
- A linear programming approach for identifying a consensus sequence on DNA sequencesby: Han-Lin Li, Chang-Jui Fu v. 21 i. 9 p. 1838 - 1845
- Identification of GPI anchor attachment signals by a Kohonen self-organizing mapby: Niklaus Fankhauser, Pascal Mäser v. 21 i. 9 p. 1846 - 1852
- An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomesby: Robel Y. Kahsay, Guang Gao, Li Liao v. 21 i. 9 p. 1853 - 1858
- GMAP: a genomic mapping and alignment program for mRNA and EST sequenceby: Thomas D. Wu, Colin K. Watanabe v. 21 i. 9 p. 1859 - 1875
- On the quality of tree-based protein classificationby: Betty Lazareva-Ulitsky, Karen Diemer, Paul D. Thomas v. 21 i. 9 p. 1876 - 1890
- Prediction of unfolded segments in a protein sequence based on amino acid compositionby: Karen Coeytaux, Anne Poupon v. 21 i. 9 p. 1891 - 1900
- PIBASE: a comprehensive database of structurally defined protein interfacesby: Fred P. Davis, Andrej Sali v. 21 i. 9 p. 1901 - 1907
- Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sitesby: Alasdair T. R. Laurie, Richard M. Jackson v. 21 i. 9 p. 1908 - 1916
- Design of a DNA chip for detection of unknown genetically modified organisms (GMOs)by: Håvard Nesvold, Anja Bråthen Kristoffersen, Arne Holst-Jensen, Knut G. Berdal v. 21 i. 9 p. 1917 - 1926
- Detecting clusters of different geometrical shapes in microarray gene expression databy: Dae-Won Kim, Kwang Hyung Lee, Doheon Lee v. 21 i. 9 p. 1927 - 1934
- Robust estimation of protein expression ratios with lysate microarray technologyby: Cristian Mircean, Ilya Shmulevich, David Cogdell, Woonyoung Choi, Yu Jia, Ioan Tabus, Stanley R. Hamilton, Wei Zhang v. 21 i. 9 p. 1935 - 1942
- Significance analysis of functional categories in gene expression studies: a structured permutation approachby: William T. Barry, Andrew B. Nobel, Fred A. Wright v. 21 i. 9 p. 1943 - 1949
- Testing association of a pathway with survival using gene expression databy: Jelle J. Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob K. Anninga, Hans C. van Houwelingen v. 21 i. 9 p. 1950 - 1957
- Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarraysby: Xiaojun Di, Hajime Matsuzaki, Teresa A. Webster, Earl Hubbell, Guoying Liu, Shoulian Dong, Dan Bartell, Jing Huang, Richard Chiles, Geoffrey Yang, Mei-mei Shen, David Kulp, Giulia C. Kennedy, Rui Mei, Keith W. Jones, Simon Cawley v. 21 i. 9 p. 1958 - 1963
- Small, fuzzy and interpretable gene expression based classifiersby: Staal A. Vinterbo, Eun-Young Kim, Lucila Ohno-Machado v. 21 i. 9 p. 1964 - 1970
- Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray databy: Claudio Lottaz, Rainer Spang v. 21 i. 9 p. 1971 - 1978
- Estimating misclassification error with small samples via bootstrap cross-validationby: Wenjiang J. Fu, Raymond J. Carroll, Suojin Wang v. 21 i. 9 p. 1979 - 1986
- Empirical Bayes screening of many p-values with applications to microarray studiesby: Susmita Datta, Somnath Datta v. 21 i. 9 p. 1987 - 1994
- Evaluation of the gene-specific dye bias in cDNA microarray experimentsby: Marie-Laure Martin-Magniette, Julie Aubert, Eric Cabannes, Jean-Jacques Daudin v. 21 i. 9 p. 1995 - 2000
- Inference of missing SNPs and information quantity measurements for haplotype blocksby: Shih-Chieh Su, C. C. Jay Kuo, Ting Chen v. 21 i. 9 p. 2001 - 2007
- Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilitiesby: Marcin Imielinski, Calin Belta, Ádám M. Halász, Harvey Rubin v. 21 i. 9 p. 2008 - 2016
- On the use of qualitative reasoning to simulate and identify metabolic pathwayby: Ross D. King, Simon M. Garrett, George Macleod Coghill v. 21 i. 9 p. 2017 - 2026
- Modeling of signal-response cascades using decision tree analysisby: Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger v. 21 i. 9 p. 2027 - 2035
- A grid layout algorithm for automatic drawing of biochemical networksby: Weijiang Li, Hiroyuki Kurata v. 21 i. 9 p. 2036 - 2042
- Accurate extraction of functional associations between proteins based on common interaction partners and common domainsby: Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai v. 21 i. 9 p. 2043 - 2048
- Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genesby: Rob Jelier, Guido Jenster, Lambert C. J. Dorssers, C. Christiaan van der Eijk, Erik M. van Mulligen, Barend Mons, Jan A. Kors v. 21 i. 9 p. 2049 - 2058
- Concept-based annotation of enzyme classesby: Oliver Hofmann, Dietmar Schomburg v. 21 i. 9 p. 2059 - 2066
- Use of within-array replicate spots for assessing differential expression in microarray experimentsby: Gordon K. Smyth, Joëlle Michaud, Hamish S. Scott v. 21 i. 9 p. 2067 - 2075
- Online Predicted Human Interaction Databaseby: Kevin R. Brown, Igor Jurisica v. 21 i. 9 p. 2076 - 2082
- SNPsFinder - a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomesby: Jian Song, Yan Xu, Scott White, Kevin W. P. Miller, Murray Wolinsky v. 21 i. 9 p. 2083 - 2084
- PROTEIOS: an open source proteomics initiativeby: Per Gärdén, Rikard Alm, Jari Häkkinen v. 21 i. 9 p. 2085 - 2087
- SpecAlign - processing and alignment of mass spectra datasetsby: Jason W. H. Wong, Gerard Cagney, Hugh M. Cartwright v. 21 i. 9 p. 2088 - 2090
- ExPrimer: to design primers from exon-exon junctionsby: Kuljeet S. Sandhu, Kshitish K. Acharya v. 21 i. 9 p. 2091 - 2092
- SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchorsby: Morris Michael, Christoph Dieterich, Martin Vingron v. 21 i. 9 p. 2093 - 2094
- GOAnno: GO annotation based on multiple alignmentby: Frédéric Chalmel, A. Lardenois, Julie D. Thompson, Jean Muller, J.-A. Sahel, T. Léveillard, Olivier Poch v. 21 i. 9 p. 2095 - 2096
- TruMatch - a BLAST post-processor that identifies bona fide sequence matches to genome assembliesby: Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, Mark L. Farman v. 21 i. 9 p. 2097 - 2098
- Integrative data analysis for functional prediction: a multi-objective optimization approachby: Francisco Azuaje v. 21 i. 9 p. 2099 - 2100
- Selecton: a server for detecting evolutionary forces at a single amino-acid siteby: Adi Doron-Faigenboim, Adi Stern, Itay Mayrose, Eran Bacharach, Tal Pupko v. 21 i. 9 p. 2101 - 2103
- ProtTest: selection of best-fit models of protein evolutionby: Federico Abascal, Rafael Zardoya, David Posada v. 21 i. 9 p. 2104 - 2105
- Mtreemix: a software package for learning and using mixture models of mutagenetic treesby: Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, Thomas Lengauer v. 21 i. 9 p. 2106 - 2107
- ProfDist: a tool for the construction of large phylogenetic trees based on profile distancesby: Joachim Friedrich, Thomas Dandekar, Matthias Wolf, Tobias Müller v. 21 i. 9 p. 2108 - 2109
- PERMOL: restraint-based protein homology modeling using DYANA or CNSby: Andreas Möglich, Daniel Weinfurtner, Wolfram Gronwald, Till Maurer, Hans Robert Kalbitzer v. 21 i. 9 p. 2110 - 2111
- MACAT - microarray chromosome analysis toolby: Joern Toedling, Sebastian Schmeier, Matthias Heinig, Benjamin Georgi, Stefan Roepcke v. 21 i. 9 p. 2112 - 2113
- MAGIC Tool: integrated microarray data analysisby: Laurie J. Heyer, D. Z. Moskowitz, J. A. Abele, P. Karnik, D. Choi, A. Malcolm Campbell, E. E. Oldham, B. K. Akin v. 21 i. 9 p. 2114 - 2115
- CrossChip: a system supporting comparative analysis of different generations of Affymetrix arraysby: Sek Won Kong, Kyu Baek Hwang, Richard D. Kim, Byoung-Tak Zhang, Steven A. Greenberg, Isaac S. Kohane, Peter J. Park v. 21 i. 9 p. 2116 - 2117
- Applications of beta-mixture models in bioinformaticsby: Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, Kevin R. Coombes v. 21 i. 9 p. 2118 - 2122
- ALOHOMORA: a tool for linkage analysis using 10K SNP array databy: Franz Rüschendorf, Peter J. Nürnberg v. 21 i. 9 p. 2123 - 2125
- IntegratedMap: a Web interface for integrating genetic map databy: Hongyu Yang, Hongyu Wang, Alan R. Gingle v. 21 i. 9 p. 2126 - 2127
- PowerMarker: an integrated analysis environment for genetic marker analysisby: Kejun Liu, Spencer V. Muse v. 21 i. 9 p. 2128 - 2129
- TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype treesby: David Posada, Taylor J. Maxwell, Alan R. Templeton v. 21 i. 9 p. 2130 - 2132
- DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequencesby: Chih-Yu (Carol) Chang, Joshua LaBaer v. 21 i. 9 p. 2133 - 2135
- Time accelerated Monte Carlo simulations of biological networks using the binomial r-leap methodby: Abhijit Chatterjee, Kapil Mayawala, Jeremy S. Edwards, Dionisios G. Vlachos v. 21 i. 9 p. 2136 - 2137
- BioIE: extracting informative sentences from the biomedical literatureby: Anna Divoli, Teresa K. Attwood v. 21 i. 9 p. 2138 - 2139
- EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinologyby: Pedro A. Reche, Hong Zhang, John-Paul Glutting, Ellis L. Reinherz v. 21 i. 9 p. 2140 - 2141
- MPSS: an integrated database system for surveying a set of proteinsby: Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Bo-Shu Liu, Jin-Miao Wang, Yi-Xue Li, Yang Zhong v. 21 i. 9 p. 2142 - 2143
- Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidatesby: Svava Ósk Jónsdóttir, Flemming Steen Jørgensen, Søren Brunak v. 21 i. 10 p. 2145 - 2160
- Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading framesby: Prachee Prakash, Sailu Yellaboina, Akash Ranjan, Seyed Ehetsham Hasnain v. 21 i. 10 p. 2161 - 2166
- Recoverable one-dimensional encoding of three-dimensional protein structuresby: Akira R. Kinjo, Ken Nishikawa v. 21 i. 10 p. 2167 - 2170
- Divide-and-conquer approach for the exemplar breakpoint distanceby: C. Thach Nguyen, Y. C. Tay, Louxin Zhang v. 21 i. 10 p. 2171 - 2176
- Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examinedby: Jayson Falkner, Philip Andrews v. 21 i. 10 p. 2177 - 2184
- Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary informationby: Lei Bao, Yan Cui v. 21 i. 10 p. 2185 - 2190
- Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysisby: L. Lancashire, O. Schmid, H. Shah, G. Ball v. 21 i. 10 p. 2191 - 2199
- Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry databy: J. S. Yu, S. Ongarello, R. Fiedler, X. W. Chen, G. Toffolo, C. Cobelli, Z. Trajanoski v. 21 i. 10 p. 2200 - 2209
- A novel approach for clustering proteomics data using Bayesian fast Fourier transformby: Halima Bensmail, Jennifer Golek, Michelle M. Moody, John O. Semmes, Abdelali Haoudi v. 21 i. 10 p. 2210 - 2224
- Using sequence compression to speedup probabilistic profile matchingby: Valerio Freschi, Alessandro Bogliolo v. 21 i. 10 p. 2225 - 2229
- A word-oriented approach to alignment validationby: Robert G. Beiko, Cheong Xin Chan, Mark A. Ragan v. 21 i. 10 p. 2230 - 2239
- A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal lengthby: A. V. Favorov, Mikhail S. Gelfand, A. V. Gerasimova, D. A. Ravcheev, Andrey A. Mironov, Vsevolod Makeev v. 21 i. 10 p. 2240 - 2245
- Predicting a set of minimal free energy RNA secondary structures common to two sequencesby: David H. Mathews v. 21 i. 10 p. 2246 - 2253
- Non-additivity in protein-DNA bindingby: Ruadhan A. O'Flanagan, Guillaume Paillard, Richard Lavery, Anirvan M. Sengupta v. 21 i. 10 p. 2254 - 2263
- Prediction of protein interdomain linker regions by a hidden Markov modelby: Kyounghwa Bae, Bani K. Mallick, Christine G. Elsik v. 21 i. 10 p. 2264 - 2270
- The mutated subsequence problem and locating conserved genesby: Ho-Leung Chan, Tak-Wah Lam, Wing-Kin Sung, Prudence W. H. Wong, Siu-Ming Yiu, X. Fan v. 21 i. 10 p. 2271 - 2278
- Prediction of subcellular localization using sequence-biased recurrent networksby: Mikael Bodén, John Hawkins v. 21 i. 10 p. 2279 - 2286
- Quasi-consensus-based comparison of profile hidden Markov models for protein sequencesby: Robel Y. Kahsay, Guoli Wang, Guang Gao, Li Liao, Roland L. Dunbrack Jr. v. 21 i. 10 p. 2287 - 2293
- Using evolutionary Expectation Maximization to estimate indel ratesby: Ian Holmes v. 21 i. 10 p. 2294 - 2300
- Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matricesby: Dan Tsafrir, Ilan Tsafrir, Liat Ein-Dor, Or Zuk, Daniel A. Notterman, Eytan Domany v. 21 i. 10 p. 2301 - 2308
- Self-organizing and self-correcting classifications of biological databy: George M. Garrity, Timothy G. Lilburn v. 21 i. 10 p. 2309 - 2314
- REVCOM: a robust Bayesian method for evolutionary rate estimationby: Andrew J. Bordner, Ruben Abagyan v. 21 i. 10 p. 2315 - 2321
- Identification and measurement of neighbor-dependent nucleotide substitution processesby: Peter F. Arndt, Terence Hwa v. 21 i. 10 p. 2322 - 2328
- Whole-genome prokaryotic phylogenyby: Stefan R. Henz, Daniel H. Huson, Alexander F. Auch, Kay Nieselt-Struwe, Stephan C. Schuster v. 21 i. 10 p. 2329 - 2335
- Disulfide connectivity prediction using secondary structure information and diresidue frequenciesby: Fabrizio Ferrè, Peter Clote v. 21 i. 10 p. 2336 - 2346
- Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisonsby: Richard J. Morris, Rafael Najmanovich, Abdullah Kahraman, Janet M. Thornton v. 21 i. 10 p. 2347 - 2355
- RNA tertiary structure determination: NOE pathways construction by tabu searchby: Jacek Blazewicz, Marta Szachniuk, Adam Wojtowicz v. 21 i. 10 p. 2356 - 2361
- Multiple flexible structure alignment using partial order graphsby: Yuzhen Ye, Adam Godzik v. 21 i. 10 p. 2362 - 2369
- Improved method for predicting ?-turn using support vector machineby: Qidong Zhang, Sukjoon Yoon, William J. Welsh v. 21 i. 10 p. 2370 - 2374
- A fractional programming approach to efficient DNA melting temperature calculationby: Markus Leber, Lars Kaderali, Alexander Schönhuth, Rainer Schrader v. 21 i. 10 p. 2375 - 2382
- Methodological aspects of the genetic dissection of gene expressionby: Örjan Carlborg, D. J. De Koning, Kenneth F. Manly, E. Chesler, Robert W. Williams, C. S. Haley v. 21 i. 10 p. 2383 - 2393
- Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray databy: Ka Yee Yeung, Roger Eugene Bumgarner, Adrian E. Raftery v. 21 i. 10 p. 2394 - 2402
- Boosting proportional hazards models using smoothing splines, with applications to high-dimensional microarray databy: Hongzhe Li, Yihui Luan v. 21 i. 10 p. 2403 - 2409
- Background correction for cDNA microarray images using the TV+L1 modelby: Wotao Yin, Terrence Chen, Xiang Sean Zhou, Amit Chakraborty v. 21 i. 10 p. 2410 - 2416
- Collateral missing value imputation: a new robust missing value estimation algorithm for microarray databy: Muhammad Shoaib B. Sehgal, Iqbal Gondal, Laurence Dooley v. 21 i. 10 p. 2417 - 2423
- Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray databy: Christian H. Busold, Stefan Winter, Nicole C. Hauser, Andrea Bauer, Jürgen Dippon, Jörg D. Hoheisel, Kurt Fellenberg v. 21 i. 10 p. 2424 - 2429
- Characterizing dye bias in microarray experimentsby: K. K. Dobbin, E. S. Kawasaki, D. W. Petersen, R. M. Simon v. 21 i. 10 p. 2430 - 2437
- Estimating cancer survival and clinical outcome based on genetic tumor progression scoresby: Jörg Rahnenführer, Niko Beerenwinkel, Wolfgang A. Schulz, Christian Hartmann, Andreas von Deimling, Bernd Wullich, Thomas Lengauer v. 21 i. 10 p. 2438 - 2446
- Mapping genome-genome epistasis: a high-dimensional modelby: Yuehua Cui, Rongling Wu v. 21 i. 10 p. 2447 - 2455
- Haplotype reconstruction from SNP fragments by minimum error correctionby: Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, Xiang-Sun Zhang v. 21 i. 10 p. 2456 - 2462
- Partition-distance via the assignment problemby: Dmitry A. Konovalov, Bruce E. Litow, Nigel Bajema v. 21 i. 10 p. 2463 - 2468
- A non-stationary model for functional mapping of complex traitsby: Wei Zhao, Ying Q. Chen, George Casella, James M. Cheverud, Rongling Wu v. 21 i. 10 p. 2469 - 2477
- Bio-Object, a stochastic simulator for post-transcriptional regulationby: Nobukazu Ohki, Masatoshi Hagiwara v. 21 i. 10 p. 2478 - 2487
- Selective integration of multiple biological data for supervised network inferenceby: Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai v. 21 i. 10 p. 2488 - 2495
- An evolution based classifier for prediction of protein interfaces without using protein structuresby: I. Res, I. Mihalek, Olivier Lichtarge v. 21 i. 10 p. 2496 - 2501
- Object-oriented biological system integration: a SARS coronavirus exampleby: Daniel Shegogue, W. Jim Zheng v. 21 i. 10 p. 2502 - 2509
- ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variantsby: Feng-Chi Chen, Trees-Juen Chuang v. 21 i. 10 p. 2510 - 2513
- PLATCOM: a Platform for Computational Comparative Genomicsby: Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, Sun Kim v. 21 i. 10 p. 2514 - 2516
- SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)by: Fengkai Zhang, Zhongming Zhao v. 21 i. 10 p. 2517 - 2519
- MIPS bacterial genomes functional annotation benchmark datasetby: Igor V. Tetko, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Gisela Fobo, Andreas Ruepp, Alexey V. Antonov, Dimitrij Surmeli, Hans-Werner Mewes v. 21 i. 10 p. 2520 - 2521
- PSLpred: prediction of subcellular localization of bacterial proteinsby: Manoj Bhasin, Aarti Garg, G. P. S. Raghava v. 21 i. 10 p. 2522 - 2524
- AutoMotif server: prediction of single residue post-translational modifications in proteinsby: Dariusz Plewczynski, Adrian Tkacz, Lucjan Stanislaw Wyrwicz, Leszek Rychlewski v. 21 i. 10 p. 2525 - 2527
- SNP discovery using advanced algorithms and neural networksby: Per Unneberg, Michael Strömberg, Fredrik Sterky v. 21 i. 10 p. 2528 - 2530
- Datamonkey: rapid detection of selective pressure on individual sites of codon alignmentsby: Sergei L. Kosakovsky Pond, Simon D. W. Frost v. 21 i. 10 p. 2531 - 2533
- FastContact: rapid estimate of contact and binding free energiesby: Carlos J. Camacho, Chao Zhang v. 21 i. 10 p. 2534 - 2536
- Protein structure topological comparison, discovery and matching serviceby: Gilleain M. Torrance, David R. Gilbert, Ioannis Michalopoulos, David R. Westhead v. 21 i. 10 p. 2537 - 2538
- CoC: a database of universally conserved residues in protein foldsby: Jason E. Donald, Isaac A. Hubner, Veronica Rotemberg, Eugene I. Shakhnovich, Leonid A. Mirny v. 21 i. 10 p. 2539 - 2540
- PSIbase: a database of Protein Structural Interactome map (PSIMAP)by: Sungsam Gong, Giseok Yoon, Insoo Jang, Dan Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, Jonghwa Bhak v. 21 i. 10 p. 2541 - 2543
- The Graphical Query Language: a tool for analysis of gene expression time-coursesby: Ivan G. Costa, Alexander Schönhuth, Alexander Schliep v. 21 i. 10 p. 2544 - 2545
- A knowledge-driven approach to cluster validity assessmentby: Nadia Bolshakova, Francisco Azuaje, Padraig Cunningham v. 21 i. 10 p. 2546 - 2547
- A web-based tool for principal component and significance analysis of microarray databy: Alexei A. Sharov, Dawood B. Dudekula, Minoru S. H. Ko v. 21 i. 10 p. 2548 - 2549
- Gene-Expression Omnibus integration and clustering Tools in SeqExpressby: John Boyle v. 21 i. 10 p. 2550 - 2551
- ADAPT: a database of affymetrix probesets and transcriptsby: Hui Sun Leong, Tim Yates, Claire Wilson, Crispin J. Miller v. 21 i. 10 p. 2552 - 2553
- ArrayCyGHt: a web application for analysis and visualization of array-CGH databy: Su Young Kim, Suk Woo Nam, Sug Hyung Lee, Won Sang Park, Nam Jin Yoo, Jung Young Lee, Yeun-Jun Chung v. 21 i. 10 p. 2554 - 2555
- Mega2: data-handling for facilitating genetic linkage and association analysesby: Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill, Daniel E. Weeks v. 21 i. 10 p. 2556 - 2557
- Protein function prediction using the Protein Link EXplorer (PLEX)by: Shailesh V. Date, Edward M. Marcotte v. 21 i. 10 p. 2558 - 2559
- Using the biological taxonomy to access biological literature with PathBinderHby: Jing Ding, K. Viswanathan, Daniel Berleant, L. Hughes, Eve Syrkin Wurtele, Daniel A. Ashlock, Julie A. Dickerson, Andy W. Fulmer, Patrick S. Schnable v. 21 i. 10 p. 2560 - 2562
- MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosisby: Pierre-Étienne Jacques, Alain L. Gervais, Mathieu Cantin, Jean-Francois Lucier, Guillaume Dallaire, Geneviève Drouin, Luc Gaudreau, Jean Goulet, Ryszard Brzezinski v. 21 i. 10 p. 2563 - 2565
- MamMiBase: a mitochondrial genome database for mammalian phylogenetic studiesby: Ana Tereza R. Vasconcelos, Ana Carolina R. Guimarães, Carlos Henrique M. Castelletti, Célia S. Caruso, Cristina Ribeiro, Fabiano Yokaichiya, Geraldo R. G. Armôa, Gislaine da Silva P. Pereira, Israel T. da Silva, Carlos G. Schrago, Adélia L. V. Fernandes, Aline R. da Silveira, André G. Carneiro, Bruno M. Carvalho, Carlos J. M. Viana, Daniel Gramkow, Franklin J. Lima, Luiz G. G. Corrêa, Maurício de A. Mudado, Pablo Nehab-Hess, Rangel de Souza, Régis L. Corrêa, Claudia A. M. Russo v. 21 i. 10 p. 2566 - 2567
- DATF: a database of Arabidopsis transcription factorsby: Anyuan Guo, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, Liping Wei, Jingchu Luo v. 21 i. 10 p. 2568 - 2569
- WebAllergen: a web server for predicting allergenic proteinsby: Tariq Riaz, Hen Ley Hor, Arun Krishnan, Francis Tang, Kuo-Bin Li v. 21 i. 10 p. 2570 - 2571
- Optimization of cDNA-AFLP experiments using genomic sequence databy: Teemu Kivioja, Mikko Arvas, Markku Saloheimo, Merja Penttilä, Esko Ukkonen v. 21 i. 11 p. 2573 - 2579
- An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genesby: Yan Zhang, Vadim N. Gladyshev v. 21 i. 11 p. 2580 - 2589
- A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10by: Daniel R. Clutterbuck, A. Leroy, M. A. O'Connell, C. A. M. Semple v. 21 i. 11 p. 2590 - 2595
- Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databasesby: Jean-François Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, François Rechenmann, Guy Perrière v. 21 i. 11 p. 2596 - 2603
- A periodicity analysis of transmembrane helicesby: Hadas Leonov, Isaiah T. Arkin v. 21 i. 11 p. 2604 - 2610
- Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structuresby: Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara v. 21 i. 11 p. 2611 - 2617
- The properties of protein family space depend on experimental designby: Victor Kunin, Sarah A. Teichmann, Martijn A. Huynen, Christos A. Ouzounis v. 21 i. 11 p. 2618 - 2622
- Promoter modeling: the case study of mammalian histone promotersby: Rajesh Chowdhary, R. Ayesha Ali, Werner Albig, Detlef Doenecke, Vladimir B. Bajic v. 21 i. 11 p. 2623 - 2628
- Determining functional specificity from protein sequencesby: Jason E. Donald, Eugene I. Shakhnovich v. 21 i. 11 p. 2629 - 2635
- A boosting approach for motif modeling using ChIP-chip databy: Pengyu Hong, X. Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, Wing Hung Wong v. 21 i. 11 p. 2636 - 2643
- Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selectionby: Zheng Rong Yang v. 21 i. 11 p. 2644 - 2650
- Genetic algorithm-based optimization of hydrophobicity tablesby: Moti Zviling, Hadas Leonov, Isaiah T. Arkin v. 21 i. 11 p. 2651 - 2656
- Identification of transcription factor binding sites with variable-order Bayesian networksby: Irad E. Ben-Gal, Ayala Shani, Andre Gohr, Jan Grau, S. Arviv, Armin Shmilovici, Stefan Posch, Ivo Grosse v. 21 i. 11 p. 2657 - 2666
- Fold recognition by combining profile-profile alignment and support vector machineby: Sangjo Han, Byung-chul Lee, Seung Taek Yu, Chan-seok Jeong, Soyoung Lee, Dongsup Kim v. 21 i. 11 p. 2667 - 2673
- A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray databy: A. L. Tarca, Janice E. K. Cooke v. 21 i. 11 p. 2674 - 2683
- A practical false discovery rate approach to identifying patterns of differential expression in microarray databy: Gregory R. Grant, Junmin Liu, Christian J. Stoeckert Jr. v. 21 i. 11 p. 2684 - 2690
- Multiclass cancer classification and biomarker discovery using GA-based algorithmsby: Jane Jijun Liu, Gene Cutler, Wuxiong Li, Zheng Pan, Sihua Peng, Timothy Hoey, Liangbiao Chen, Xuefeng Bruce Ling v. 21 i. 11 p. 2691 - 2697
- A new measure of the robustness of biochemical networksby: Bor-Sen Chen, Yu-Chao Wang, Wei-Sheng Wu, Wen-Hsiung Li v. 21 i. 11 p. 2698 - 2705
- Inferring genetic regulatory logic from expression databy: Svetlana Bulashevska, Roland Eils v. 21 i. 11 p. 2706 - 2713
- AgentCell: a digital single-cell assay for bacterial chemotaxisby: Thierry Emonet, Charles M. Macal, Michael J. North, Charles E. Wickersham, Philippe Cluzel v. 21 i. 11 p. 2714 - 2721
- Noise-induced cooperative behavior in a multicell systemby: Luonan Chen, Ruiqi Wang, Tianshou Zhou, Kazuyuki Aihara v. 21 i. 11 p. 2722 - 2729
- Correlation between gene expression profiles and protein-protein interactions within and across genomesby: Nitin Bhardwaj, Hui Lu v. 21 i. 11 p. 2730 - 2738
- Modularized learning of genetic interaction networks from biological annotations and mRNA expression databy: Phil Hyoun Lee, Doheon Lee v. 21 i. 11 p. 2739 - 2747
- MaSTerClass: a case-based reasoning system for the classification of biomedical termsby: Irena Spasic, Sophia Ananiadou, Jun-ichi Tsujii v. 21 i. 11 p. 2748 - 2758
- Literature mining and database annotation of protein phosphorylation using a rule-based systemby: Zhang-Zhi Hu, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu v. 21 i. 11 p. 2759 - 2765
- Common denominator procedure: a novel approach to gene-expression data mining for identification of phenotype-specific genesby: René Korn, Sascha Röhrig, Steffen Schulze-Kremer, Ulrich Brinkmann v. 21 i. 11 p. 2766 - 2772
- Formalizing concepts of species, sex and developmental stage in anatomical ontologiesby: Stuart Aitken v. 21 i. 11 p. 2773 - 2779
- ROBIN: a tool for genome rearrangement of block-interchangesby: Chin Lung Lu, Tsui Ching Wang, Ying Chih Lin, Chuan Yi Tang v. 21 i. 11 p. 2780 - 2782
- seq++: analyzing biological sequences with a range of Markov-related modelsby: Vincent Miele, Pierre-Yves Bourguignon, David Robelin, Grégory Nuel, Hugues Richard v. 21 i. 11 p. 2783 - 2784
- GandrKB--ontological microarray annotation and visualizationby: Daniel Schober, Ulf Leser, Martin Zenke, Jens Reich v. 21 i. 11 p. 2785 - 2786
- GOR V server for protein secondary structure predictionby: Taner Z. Sen, Robert L. Jernigan, Jean Garnier, Andrzej Kloczkowski v. 21 i. 11 p. 2787 - 2788
- MADE4: an R package for multivariate analysis of gene expression databy: Aedín C. Culhane, Jean Thioulouse, Guy Perrière, Desmond G. Higgins v. 21 i. 11 p. 2789 - 2790
- VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism databy: Albert J. Vilella, Angel Blanco-Garcia, Stephan Hutter, Julio Rozas v. 21 i. 11 p. 2791 - 2793
- POSBIOTM--NER: a trainable biomedical named-entity recognition systemby: Yu Song, Eunju Kim, Gary Geunbae Lee, Byoung-kee Yi v. 21 i. 11 p. 2794 - 2796
- Erratumby: Guillaume Koum, Augustin Yekel, Bengyella Ndifon, Frédéric Simard v. 21 i. 11 p. 2797 - 2802
- Comment on 'Evaluation of the gene-specific dye bias in cDNA microarray experiments'by: Kevin Dobbin, Joanna H. Shih, Richard Simon v. 21 i. 12 p. 2803 - 2804
- MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systemsby: Vivek Anantharaman, L. Aravind v. 21 i. 12 p. 2805 - 2811
- EGene: a configurable pipeline generation system for automated sequence analysisby: Alan M. Durham, André Y. Kashiwabara, Fernando T. G. Matsunaga, Paulo H. Ahagon, Flávia Rainone, Leonardo Varuzza, Arthur Gruber v. 21 i. 12 p. 2812 - 2813
- LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sourcesby: Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J. Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali v. 21 i. 12 p. 2814 - 2820
- Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologuesby: B. Anand, V. S. Gowri, Narayanaswamy Srinivasan v. 21 i. 12 p. 2821 - 2826
- Convergent Island Statistics: a fast method for determining local alignment score significanceby: Aleksandar Poleksic, Joseph F. Danzer, Kevin Hambly, Derek A. Debe v. 21 i. 12 p. 2827 - 2831
- A comprehensive and non-redundant database of protein domain movementsby: Guoying Qi, Richard A. Lee, Steven Hayward v. 21 i. 12 p. 2832 - 2838
- Density guided importance sampling: application to a reduced model of protein foldingby: Geraint Thomas, Richard B. Sessions, Martin J. Parker v. 21 i. 12 p. 2839 - 2843
- Prediction of protein solvent accessibility using fuzzy k-nearest neighbor methodby: Jaehyun Sim, Seung-Yeon Kim, Julian Lee v. 21 i. 12 p. 2844 - 2849
- Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfacesby: A. Selim Aytuna, Attila Gursoy, Ozlem Keskin v. 21 i. 12 p. 2850 - 2855
- Three-dimensional computation of atom depth in complex molecular structuresby: Daniele Varrazzo, Andrea Bernini, Ottavia Spiga, Arianna Ciutti, Stefano Chiellini, Vincenzo Venditti, Luisa Bracci, Neri Niccolai v. 21 i. 12 p. 2856 - 2860
- Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicatesby: Dung-Tsa Chen, James J. Chen, Seng-jaw Soong v. 21 i. 12 p. 2861 - 2866
- A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumorsby: Albert M. Levin, Debashis Ghosh, Kathleen R. Cho, Sharon L. R. Kardia v. 21 i. 12 p. 2867 - 2874
- Donuts, scratches and blanks: robust model-based segmentation of microarray imagesby: Qunhua Li, Chris Fraley, Roger Eugene Bumgarner, Ka Yee Yeung, Adrian E. Raftery v. 21 i. 12 p. 2875 - 2882
- A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiaeby: Kuang-Chi Chen, Tse-Yi Wang, Huei-Hun Tseng, Chi-Ying F. Huang, Cheng-Yan Kao v. 21 i. 12 p. 2883 - 2890
- Modeling and simulation of cancer immunoprevention vaccineby: Francesco Pappalardo, Pierluigi Lollini, F. Castiglione, Santo Motta v. 21 i. 12 p. 2891 - 2897
- Differential network expression during drug and stress responseby: Lawrence Cabusora, Electra Sutton, Andy W. Fulmer, Christian V. Forst v. 21 i. 12 p. 2898 - 2905
- Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifugeby: Florence Armand, Philipp Bucher, C. Victor Jongeneel, Edward E. Farmer v. 21 i. 12 p. 2906 - 2908
- BEST: Binding-site Estimation Suite of Toolsby: Dongsheng Che, Shane Jensen, Liming Cai, Jun S. Liu v. 21 i. 12 p. 2909 - 2911
- Visualizing profile-profile alignment: pairwise HMM logosby: Benjamin Schuster-Böckler, Alex Bateman v. 21 i. 12 p. 2912 - 2913
- MollDE: a homology modeling framework you can click withby: Adrian A. Canutescu, Roland L. Dunbrack Jr. v. 21 i. 12 p. 2914 - 2916
- Meta-DP: domain prediction meta-serverby: Harpreet Kaur Saini, Daniel Fischer v. 21 i. 12 p. 2917 - 2920
- twilight; a Bioconductor package for estimating the local false discovery rateby: Stefanie Scheid, Rainer Spang v. 21 i. 12 p. 2921 - 2922
- Stochastic reaction-diffusion simulation with MesoRDby: Johan Hattne, David Fange, Johan Elf v. 21 i. 12 p. 2923 - 2924
- STARS: statistics on inter-atomic distances and torsion angles in protein secondary structuresby: Yu Zheng, Daiwen Yang v. 21 i. 12 p. 2925 - 2926
- NodMutDB: a database for genes and mutants involved in symbiosisby: Chunhong Mao, Jing Qiu, Chunxia Wang, Trevor C. Charles, Bruno W. S. Sobral v. 21 i. 12 p. 2927 - 2929
- EMPReSS: European Mouse Phenotyping Resource for Standardized Screensby: Eain C. J. Green, Georgios V. Gkoutos, Heena V. Lad, Andrew Blake, Joseph Weekes, John M. Hancock v. 21 i. 12 p. 2930 - 2931
- Twelve C2H2 zinc-finger genes on human chromosome 19 can be each translated into the same type of protein after frameshiftsby: Shao-Wu Meng, Zhuo Zhang, Jinyan Li v. 20 i. 1 p. 1 - 4
- Identifying periodically expressed transcripts in microarray time series databy: Sofia Wichert, Konstantinos Fokianos, Korbinian Strimmer v. 20 i. 1 p. 5 - 20
- Prediction of protein subcellular locations using fuzzy k-NN methodby: Ying Huang, Yanda Li v. 20 i. 1 p. 21 - 28
- Efficient filtering methods for clustering cDNAs with spliced sequence alignmentby: Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya v. 20 i. 1 p. 29 - 39
- Protein ß-turn prediction using nearest-neighbor methodby: Saejoon Kim v. 20 i. 1 p. 40 - 44
- ClusPro: an automated docking and discrimination method for the prediction of protein complexesby: Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho v. 20 i. 1 p. 45 - 50
- Light-weight integration of molecular biological databasesby: Stephan Philippi v. 20 i. 1 p. 51 - 57
- An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknotsby: Jianhua Ruan, Gary D. Stormo, Weixiong Zhang v. 20 i. 1 p. 58 - 66
- Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomesby: O. Michael Melko, Arcady R. Mushegian v. 20 i. 1 p. 67 - 74
- MedBlast: searching articles related to a biological sequenceby: Qiang Tu, Haixu Tang, Dafu Ding v. 20 i. 1 p. 75 - 77
- Adaptive stochastic-deterministic chemical kinetic simulationsby: Karan Vasudeva, Upinder S. Bhalla v. 20 i. 1 p. 78 - 84
- VizStruct: exploratory visualization for gene expression profilingby: Li Zhang, Aidong Zhang, Murali Ramanathan v. 20 i. 1 p. 85 - 92
- A global test for groups of genes: testing association with a clinical outcomeby: Jelle J. Goeman, Sara A. van de Geer, Floor de Kort, Hans C. van Houwelingen v. 20 i. 1 p. 93 - 99
- A generalized likelihood ratio test to identify differentially expressed genes from microarray databy: Song Wang, Stewart Ethier v. 20 i. 1 p. 100 - 104
- Adjustment of systematic microarray data biasesby: Monica Benito, Joel Parker, Quan Du, Junyuan Wu, Dong Xiang, Charles M. Perou, James Stephen Marron v. 20 i. 1 p. 105 - 114
- Essentiality and damage in metabolic networksby: Ney Lemke, Fabiana Herédia, Cláudia K. Barcellos, Adriana N. dos Reis, José C. M. Mombach v. 20 i. 1 p. 115 - 119
- GIS: a biomedical text-mining system for gene information discoveryby: Jung-Hsien Chiang, Hsu-Chun Yu, Huai-Jen Hsu v. 20 i. 1 p. 120 - 121
- GRIL: genome rearrangement and inversion locatorby: Aaron Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna v. 20 i. 1 p. 122 - 124
- HOMGL - comparing genelists across species and with different accession numbersby: Nils Blüthgen, Szymon M. Kielbasa, Branka Cajavec, Hanspeter Herzel v. 20 i. 1 p. 125 - 126
- WILMA - automated annotation of protein sequencesby: Andreas Prlic, Francisco S. Domingues, Peter Lackner, Manfred J. Sippl v. 20 i. 1 p. 127 - 128
- BugView: a browser for comparing genomesby: David P. Leader v. 20 i. 1 p. 129 - 130
- The Genomic Threading Databaseby: Liam J. McGuffin, Stefano Street, Søren-Aksel Sørensen, David T. Jones v. 20 i. 1 p. 131 - 132
- PARIS: a proteomic analysis and resources indexation systemby: Juhui Wang, Christophe Caron, Michel-Yves Mistou, Christophe Gitton, Alain Trubuil v. 20 i. 1 p. 133 - 135
- TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilterby: Miklós Cserzo, Frank Eisenhaber, Birgit Eisenhaber, István Simon v. 20 i. 1 p. 136 - 137
- Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competitionby: Richard M. Bruskiewich v. 20 i. 2 p. 139 - 139
- A strategy for assembling the maize (Zea mays L.) genomeby: Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh Narayanan, Ling Guo, Daniel A. Ashlock, Patrick S. Schnable v. 20 i. 2 p. 140 - 147
- Multi-species comparative mapping in silico using the COMPASS strategyby: Lei Liu, George Gong, Yong Liu, Shreedhar Natarajan, Denis M. Larkin, Annelie Everts-van der Wind, Mark Rebeiz, Jonathan E. Beever v. 20 i. 2 p. 148 - 154
- Transposable element annotation of the rice genomeby: Nikoleta Juretic, Thomas E. Bureau, Richard M. Bruskiewich v. 20 i. 2 p. 155 - 160
- Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genomeby: Qingsong Zhu, Youping Deng, Phaneendra Vanka, Susan J. Brown, Subbaratnam Muthukrishnan, Karl J. Kramer v. 20 i. 2 p. 161 - 169
- Phylogenomic inference of protein molecular function: advances and challengesby: Kimmen Sjölander v. 20 i. 2 p. 170 - 179
- A comparative phylogenetic approach for dating whole genome duplication eventsby: Brad A. Chapman, John E. Bowers, Stefan R. Schulze, Andrew H. Paterson v. 20 i. 2 p. 180 - 185
- Prediction of locally stable RNA secondary structures for genome-wide surveysby: Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler v. 20 i. 2 p. 186 - 190
- Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship networkby: Jonathan D. Wren, Harold R. Garner v. 20 i. 2 p. 191 - 198
- Limited conformational space for early-stage protein folding simulationby: Michal Brylinski, W. Jurkowski, Leszek Konieczny, Irena Roterman v. 20 i. 2 p. 199 - 205
- Comparative evaluation of word composition distances for the recognition of SCOP relationshipsby: Susana Vinga, Rodrigo Gouveia-Oliveira, Jonas S. Almeida v. 20 i. 2 p. 206 - 215
- GAPSCORE: finding gene and protein names one word at a timeby: Jeffrey T. Chang, Hinrich Schütze, Russ B. Altman v. 20 i. 2 p. 216 - 225
- Minimal cut sets in biochemical reaction networksby: Steffen Klamt, Ernst Dieter Gilles v. 20 i. 2 p. 226 - 234
- An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experimentsby: Susmita Datta, Glen A. Satten, Dale J. Benos, Jiazeng Xia, Martin J. Heslin, Somnath Datta v. 20 i. 2 p. 235 - 242
- Graph-based clustering for finding distant relationships in a large set of protein sequencesby: Hideya Kawaji, Yoichi Takenaka, Hideo Matsuda v. 20 i. 2 p. 243 - 252
- Is cross-validation better than resubstitution for ranking genes?by: Ulisses Braga-Neto, Ronaldo Fumio Hashimoto, Edward R. Dougherty, Danh V. Nguyen, Raymond J. Carroll v. 20 i. 2 p. 253 - 258
- Formalization of mouse embryo anatomyby: Albert Burger, Duncan Davidson, Richard A. Baldock v. 20 i. 2 p. 259 - 267
- The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resourcesby: Torsten Crass, Iris Antes, Rico Basekow, Peer Bork, Christian Buning, Maik Christensen, Holger Claussen, Christian Ebeling, Peter Ernst, Valérie Gailus-Durner, Karl-Heinz Glatting, Rolf Gohla, Frank Gößling, Korbinian Grote, Karsten R. Heidtke, Alexander Herrmann, Sean O'Keeffe, O. Kießlich, Sven Kolibal, Jan O. Korbel, Thomas Lengauer, Ines Liebich, Mark van der Linden, Hannes Luz, Kathrin Meissner, Christian von Mering, Heinz-Theodor Mevissen, Hans-Werner Mewes, Holger Michael, Martin Mokrejs, Tobias Müller, Heike Pospisil, Matthias Rarey, Jens G. Reich, Ralf Schneider, Dietmar Schomburg, Steffen Schulze-Kremer, Knut Schwarzer, Ingolf Sommer, Stephan Springstubbe, Sándor Suhai, Gnanasekaran Thoppae, Martin Vingron, Jens Warfsmann, Thomas Werner, Daniel Wetzler, Edgar Wingender, Ralf Zimmer v. 20 i. 2 p. 268 - 270
- ROSO: optimizing oligonucleotide probes for microarraysby: Nancie Reymond, Hubert Charles, Laurent Duret, Federica Calevro, Guillaume Beslon, Jean-Michel Fayard v. 20 i. 2 p. 271 - 273
- LVB: parsimony and simulated annealing in the search for phylogenetic treesby: Daniel Barker v. 20 i. 2 p. 274 - 275
- PGTdb: a database providing growth temperatures of prokaryotesby: Shir-Ly Huang, Li-Cheng Wu, Han-Kuen Liang, Kuan-Ting Pan, Jorng-Tzong Horng, Ming-Tat Ko v. 20 i. 2 p. 276 - 278
- JDotter: a Java interface to multiple dotplots generated by dotterby: Ryan Brodie, Rachel L. Roper, Chris Upton v. 20 i. 2 p. 279 - 281
- FGDP: functional genomics data pipeline for automated, multiple microarray data analysesby: Jeffrey D. Grant, Luke A. Somers, Yue Zhang, Frank J. Manion, Ghislain Bidaut, Michael F. Ochs v. 20 i. 2 p. 282 - 283
- YETI: Yeast Exploration Tool Integratorby: Richard J. Orton, William I. Sellers, Dietlind L. Gerloff v. 20 i. 2 p. 284 - 285
- EST-PAGE - managing and analyzing EST databy: Lakshmi K. Matukumalli, John J. Grefenstette, Tad S. Sonstegard, Curtis P. Van Tassell v. 20 i. 2 p. 286 - 288
- APE: Analyses of Phylogenetics and Evolution in R languageby: Emmanuel Paradis, Julien Claude, Korbinian Strimmer v. 20 i. 2 p. 289 - 290
- AnaGram: protein function assignmentby: Antonio Jesús Pérez, Guillermo Thode, Oswaldo Trelles v. 20 i. 2 p. 291 - 292
- A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteinsby: Torgeir R. Hvidsten, Andriy Kryshtafovych, Henryk Jan Komorowski, Krzysztof Fidelis v. 20 i. 2 p. 293 - 293
- Pseudo-periodic partitions of biological sequencesby: Lugang Li, Renchao Jin, Poh-Lin Kok, Honghui Wan v. 20 i. 3 p. 295 - 306
- affy - analysis of Affymetrix GeneChip data at the probe levelby: Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry v. 20 i. 3 p. 307 - 315
- Hybrid simulation of cellular behaviorby: Thomas R. Kiehl, Robert M. Mattheyses, Melvin K. Simmons v. 20 i. 3 p. 316 - 322
- A benchmark for Affymetrix GeneChip expression measuresby: Leslie Cope, Rafael A. Irizarry, Harris A. Jaffee, Zhijin Wu, Terence P. Speed v. 20 i. 3 p. 323 - 331
- Model-based methods for identifying periodically expressed genes based on time course microarray gene expression databy: Yihui Luan, Hongzhe Li v. 20 i. 3 p. 332 - 339
- Functional topology in a network of protein interactionsby: Natasa Przulj, Dennis A. Wigle, Igor Jurisica v. 20 i. 3 p. 340 - 348
- An ontology for collaborative construction and analysis of cellular pathwaysby: Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz, Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay v. 20 i. 3 p. 349 - 356
- Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovisby: Zoltan Kutalik, Jacqueline Inwald, Steve V. Gordon, R. Glyn Hewinson, Philip D. Butcher, Jason Hinds, Kwang-Hyun Cho, Olaf Wolkenhauer v. 20 i. 3 p. 357 - 363
- Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypesby: Jeanne Kowalski, Charles Drake, Ronald H. Schwartz, Jonathan Powell v. 20 i. 3 p. 364 - 373
- Is cross-validation valid for small-sample microarray classification?by: Ulisses Braga-Neto, Edward R. Dougherty v. 20 i. 3 p. 374 - 380
- A graph-theoretic modeling on GO space for biological interpretation of gene clustersby: Sung Geun Lee, Jung Uk Hur, Yang Seok Kim v. 20 i. 3 p. 381 - 388
- Knowledge discovery by automated identification and ranking of implicit relationshipsby: Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, Harold R. Garner v. 20 i. 3 p. 389 - 398
- Metrics for comparing regulatory sequences on the basis of pattern countsby: Jacques van Helden v. 20 i. 3 p. 399 - 406
- Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inferenceby: Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck, Fredrik Ronquist v. 20 i. 3 p. 407 - 415
- LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequencesby: Mikael Thollesson v. 20 i. 3 p. 416 - 418
- Predicting protein secondary structure by cascade-correlation neural networksby: Matthew J. Wood, Jonathan D. Hirst v. 20 i. 3 p. 419 - 420
- SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequenceby: Manoj Bhasin, G. P. S. Raghava v. 20 i. 3 p. 421 - 423
- PIVOT: Protein Interacions VisualizatiOn Toolby: Nir Orlev, Ron Shamir, Yosef Shiloh v. 20 i. 3 p. 424 - 425
- The Jalview Java alignment editorby: Michele E. Clamp, James A. Cuff, Stephen M. Searle, Geoffrey J. Barton v. 20 i. 3 p. 426 - 427
- SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experimentsby: Henrik Hornshøj, Henrik Stengaard, Frank Panitz, Christian Bendixen v. 20 i. 3 p. 428 - 429
- Gene specific siRNA selectorby: Natasha Levenkova, Qingjuan Gu, John J. Rux v. 20 i. 3 p. 430 - 432
- VisCoSe: visualization and comparison of consensus sequencesby: Michael Spitzer, Georg Fuellen, Paul Cullen, Stefan Lorkowski v. 20 i. 3 p. 433 - 435
- HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical databy: Susanna Lamers, Scott Beason, Luke Dunlap, Robert Compton, Marco Salemi v. 20 i. 3 p. 436 - 438
- Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markersby: Tu H. Nguyen, Chunyu Liu, Elliot S. Gershon, Francis J. McMahon v. 20 i. 3 p. 439 - 443
- CHOISS for selection of single nucleotide polymorphism markers on interval regularityby: Soohyun Lee, Changwon Kang v. 20 i. 4
- RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studiesby: Elisabetta Manduchi, Gregory R. Grant, H. He, Junmin Liu, Matthew D. Mailman, A. D. Pizarro, P. L. Whetzel, Christian J. Stoeckert Jr. v. 20 i. 4
- A simple fold with variations: the pacifastin inhibitor familyby: Zoltán Gáspári, Csaba Ortutay, András Perczel v. 20 i. 4
- A multi-algorithm, multi-timescale method for cell simulationby: Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita v. 20 i. 4
- Enrichment of transcriptional regulatory sites in non-coding genomic regionby: Wen Xue, Jin Wang, Zhirong Shen, Huaiqiu Zhu v. 20 i. 4
- The PCR Suiteby: Marijke J. van Baren, Peter Heutink v. 20 i. 4
- Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptorsby: Florence Horn, Anthony L. Lau, Fred E. Cohen v. 20 i. 4
- FORTE: a profile-profile comparison tool for protein fold recognitionby: Kentaro Tomii, Yutaka Akiyama v. 20 i. 4
- AntiHunter: searching BLAST output for EST antisense transcriptsby: Giovanni Lavorgna, Luca Sessa, Alessandro Guffanti, Lelio Lassandro, Giorgio Casari v. 20 i. 4
- Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arraysby: Tzu-Ming Chu, B. S. Weir, Russell D. Wolfinger v. 20 i. 4
- Mismatch string kernels for discriminative protein classificationby: Christina S. Leslie, Eleazar Eskin, Adiel Cohen, Jason Weston, William Stafford Noble v. 20 i. 4
- Support vector machine classification on the webby: Paul Pavlidis, Ilan Wapinski, William Stafford Noble v. 20 i. 4
- FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genesby: Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo v. 20 i. 4
- ChromoWheel: a new spin on eukaryotic chromosome visualizationby: Sven Ekdahl, Erik L. L. Sonnhammer v. 20 i. 4
- Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular functionby: Daehee Hwang, George Stephanopoulos, Christina Chan v. 20 i. 4
- SaRAD: a Simple and Robust Abbreviation Dictionaryby: Eytan Adar v. 20 i. 4
- Predicting subcellular localization of proteins using machine-learned classifiersby: Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, Roman Eisner v. 20 i. 4
- GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structuresby: Yukimitsu Yabuki, Yuri Mukai, Mark B. Swindells, Makiko Suwa v. 20 i. 4
- Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thalianaby: Alex V. Kochetov, Akinori Sarai v. 20 i. 4
- Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural informationby: Shandar Ahmad, M. Michael Gromiha, Akinori Sarai v. 20 i. 4
- Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statisticsby: Olivier Bastien, Jean-Christophe Aude, Sylvaine Roy, Eric Maréchal v. 20 i. 4
- Rapid and sensitive dot-matrix methods for genome analysisby: Yue Huang, Ling Zhang v. 20 i. 4
- Tailored gene array databases: applications in mechanistic toxicologyby: Tatiana V. Karpinets, Brent D. Foy, John M. Frazier v. 20 i. 4
- Reducing the variability in cDNA microarray image processing by Bayesian inferenceby: Neil D. Lawrence, Marta Milo, Mahesan Niranjan, Penny Rashbass, Stephan Soullier v. 20 i. 4
- me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elementsby: Kevin Murphy, Towfique Raj, R. Scott Winters, Peter S. White v. 20 i. 4
- Conservation analysis of small RNA genes in Escherichia coliby: Yong Zhang, Zhihua Zhang, Lunjiang Ling, Baochen Shi, Run-Sheng Chen v. 20 i. 5 p. 599 - 603
- Extracting human protein interactions from MEDLINE using a full-sentence parserby: Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Svetlana Novichkova, Alexander Nikitin, Ilya Mazo v. 20 i. 5 p. 604 - 611
- A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome Iby: Ren Zhang, Chun-Ting Zhang v. 20 i. 5 p. 612 - 622
- Enhancing scatterplots with smoothed densitiesby: Paul H. C. Eilers, Jelle J. Goeman v. 20 i. 5 p. 623 - 628
- PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomesby: R. Lavigne, W. D. Sun, G. Volckaert v. 20 i. 5 p. 629 - 635
- Phylo-VISTA: interactive visualization of multiple DNA sequence alignmentsby: Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak v. 20 i. 5 p. 636 - 643
- Optimization models for cancer classification: extracting gene interaction information from microarray expression databy: Alexey V. Antonov, Igor V. Tetko, Michael T. Mader, Jan Budczies, Hans-Werner Mewes v. 20 i. 5 p. 644 - 652
- Disulfide connectivity prediction using recursive neural networks and evolutionary informationby: Alessandro Vullo, Paolo Frasconi v. 20 i. 5 p. 653 - 659
- Variance-stabilizing transformations for two-color microarraysby: Blythe Durbin, David M. Rocke v. 20 i. 5 p. 660 - 667
- 404 not found: the stability and persistence of URLs published in MEDLINEby: Jonathan D. Wren v. 20 i. 5 p. 668 - 672
- Comparison of various algorithms for recognizing short coding sequences of human genesby: Feng Gao, Chun-Ting Zhang v. 20 i. 5 p. 673 - 681
- Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudesby: David R. Bickel v. 20 i. 5 p. 682 - 688
- A statistical framework for combining and interpreting proteomic datasetsby: Michael A. Gilchrist, Laura A. Salter, Andreas Wagner v. 20 i. 5 p. 689 - 700
- Adplot: detection and visualization of repetitive patterns in complete genomesby: Akito Taneda v. 20 i. 5 p. 701 - 708
- Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databasesby: Pedro Romero, Peter D. Karp v. 20 i. 5 p. 709 - 717
- Genotyping of single nucleotide polymorphism using model-based clusteringby: H. Fujisawa, S. Eguchi, M. Ushijima, S. Miyata, Y. Miki, T. Muto, M. Matsuura v. 20 i. 5 p. 718 - 726
- Java-based application framework for visualization of gene regulatory region annotationsby: Hao Sun, Ramana V. Davuluri v. 20 i. 5 p. 727 - 734
- Bio-support vector machines for computational proteomicsby: Zheng Rong Yang, Kuo-Chen Chou v. 20 i. 5 p. 735 - 741
- Dominant spectral component analysis for transcriptional regulations using microarray time-series databy: Lap Kun Yeung, Lap Keung Szeto, Alan Wee-Chung Liew, Hong Yan v. 20 i. 5 p. 742 - 749
- Regression trees for regulatory element identificationby: Tu Minh Phuong, Doheon Lee, Kwang Hyung Lee v. 20 i. 5 p. 750 - 757
- STAM: simple Transmembrane Alignment Methodby: Yinon Shafrir, H. Robert Guy v. 20 i. 5 p. 758 - 769
- Predicting protein structure classes from function predictionsby: Ingolf Sommer, Jörg Rahnenführer, Francisco S. Domingues, U. de Lichtenberg, Thomas Lengauer v. 20 i. 5 p. 770 - 776
- Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experimentsby: Keith A. Baggerly, Jeffrey S. Morris, Kevin R. Coombes v. 20 i. 5 p. 777 - 785
- Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosityby: Jakob C. Mueller, Christophe Andreoli v. 20 i. 5 p. 786 - 787
- Algorithms for variable length Markov chain modelingby: Gill Bejerano v. 20 i. 5 p. 788 - 789
- CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projectsby: L. Frangeul, Philippe Glaser, C. Rusniok, C. Buchrieser, E. Duchaud, P. Dehoux, Frank Kunst v. 20 i. 5 p. 790 - 797
- In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restrictionby: Joseba Bikandi, Rosario San Millán, Aitor Rementeria, Javier Garaizar v. 20 i. 5 p. 798 - 799
- Gene Unscrambler for detangling scrambled genes in ciliatesby: Andre R. O. Cavalcanti, Laura F. Landweber v. 20 i. 5 p. 800 - 802
- ReDiT: Repeat Discrepancy Tagger-a shotgun assembly finishing aidby: Martti T. Tammi, Erik Arner, Ellen Kindlund, Björn Andersson v. 20 i. 5 p. 803 - 804
- ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux clusterby: Gernot Stocker, Dietmar Rieder, Zlatko Trajanoski v. 20 i. 5 p. 805 - 807
- Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiationby: C. Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, R. Koch, U. Schlecht, L. Hermida, Benjamin Masdoua, R. Ishii, V. Cassen, M. Yamamoto, C. Lane, M. Cherry, N. Lamb, M. Primig v. 20 i. 5 p. 808 - 811
- Alu repeat analysis in the complete human genome: trends and variations with respect to genomic compositionby: Deepak Grover, Mitali Mukerji, Pankaj Bhatnagar, Krishnamoorthy Kannan, Samir K. Brahmachari v. 20 i. 6 p. 813 - 817
- Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologsby: Ruslan Sadreyev, Nick V. Grishin v. 20 i. 6 p. 818 - 828
- ESPD: a pattern detection model underlying gene expression profilesby: Chun Tang, Aidong Zhang, Murali Ramanathan v. 20 i. 6 p. 829 - 838
- Comparative analysis of algorithms for signal quantitation from oligonucleotide microarraysby: Yoseph Barash, Elinor Dehan, Meir Krupsky, Wilbur Franklin, Marc Geraci, Nir Friedman, Naftali Kaminski v. 20 i. 6 p. 839 - 846
- Fold-specific substitution matrices for protein classificationby: R. B. Vilim, R. M. Cunningham, B. Lu, P. Kheradpour, Fred J. Stevens v. 20 i. 6 p. 847 - 853
- Gene selection for oligonucleotide array: an approach using PM probe level databy: Dung-Tsa Chen, Sue-Hwa Lin, Seng-jaw Soong v. 20 i. 6 p. 854 - 862
- Optimizing substitution matrices by separating score distributionsby: Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama v. 20 i. 6 p. 863 - 873
- Approximate geodesic distances reveal biologically relevant structures in microarray databy: Jens Nilsson, Thoas Fioretos, Mattias Höglund, Magnus Fontes v. 20 i. 6 p. 874 - 880
- On the significance of sequence alignments when using multiple scoring matricesby: Florian Frommlet, Andreas Futschik, Malgorzata Bogdan v. 20 i. 6 p. 881 - 887
- Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squaresby: Xiaohong Huang, Wei Pan, Soon Park, Xinqiang Han, Leslie W. Miller, Jennifer Hall v. 20 i. 6 p. 888 - 894
- Mapping gene ontology to proteins based on protein-protein interaction databy: Minghua Deng, Zhidong Tu, Fengzhu Sun, Ting Chen v. 20 i. 6 p. 895 - 902
- Predicting the linkage sites in glycoproteins using bio-basis function neural networkby: Zheng Rong Yang, Kuo-Chen Chou v. 20 i. 6 p. 903 - 908
- Modeling within-motif dependence for transcription factor binding site predictionsby: Qing Zhou, Jun S. Liu v. 20 i. 6 p. 909 - 916
- Gaussian mixture clustering and imputation of microarray databy: Ming Ouyang, William J. Welsh, Panos Georgopoulos v. 20 i. 6 p. 917 - 923
- External control in Markovian genetic regulatory networks: the imperfect information caseby: Aniruddha Datta, Ashish Choudhary, Michael L. Bittner, Edward R. Dougherty v. 20 i. 6 p. 924 - 930
- mdclust-exploratory microarray analysis by multidimensional clusteringby: Martin Dugas, S. Merk, S. Breit, P. Dirschedl v. 20 i. 6 p. 931 - 936
- The Hera database and its use in the characterization of endoplasmic reticulum proteinsby: M. Scott, Guoqing Lu, Michael T. Hallett, David Thomas v. 20 i. 6 p. 937 - 944
- Finding coexpressed genes in counts-based data: an improved measure with validation experimentsby: Morgan N. Price, Eleanor G. Rieffel v. 20 i. 6 p. 945 - 952
- Visualization of near-optimal sequence alignmentsby: Michael E. Smoot, Stephanie Guerlain, William R. Pearson v. 20 i. 6 p. 953 - 958
- Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling databy: Kyongbum Lee, Daehee Hwang, Tadaaki Yokoyama, George Stephanopoulos, Gregory Stephanopoulos, Martin L. Yarmush v. 20 i. 6 p. 959 - 969
- Sequence analysis and membrane partitioning energies of -helical antimicrobial peptidesby: Xing Han, Wenjun Kang v. 20 i. 6 p. 970 - 973
- SQUARE-determining reliable regions in sequence alignmentsby: Michael L. Tress, Osvaldo Graña, Alfonso Valencia v. 20 i. 6 p. 974 - 975
- GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel imagesby: Nelson Young, Zhan Chang, David S. Wishart v. 20 i. 6 p. 976 - 978
- Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontologyby: Peter N. Robinson, Andreas Wollstein, Ulrike Böhme, Brad Beattie v. 20 i. 6 p. 979 - 981
- A rapid method for illustrating features in both coding and non-coding regions of a genomeby: Ross Hall, Linda Stern v. 20 i. 6 p. 982 - 983
- Exploring genome architecture through GOV: a WWW-based gene order visualizerby: Kishore R. Sakharkar, Vincent T. K. Chow v. 20 i. 6 p. 984 - 985
- PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProtby: Andrew C. R. Martin v. 20 i. 6 p. 986 - 988
- AmpliBASE MTTM: a Mycobacterium tuberculosis diversity knowledgebaseby: Ahmed A. Majeed, Niyaz Ahmed, K. Rajender Rao, S. Ghousunnissa, Farhana Kauser, Buddhaditta Bose, Hampapathalu A. Nagarajaram, V. M. Katoch, Debby V. Cousins, Leonardo A. Sechi, Robert H. Gilman, Seyed E. Hasnain v. 20 i. 6 p. 989 - 992
- Effects of choice of DNA sequence model structure on gene identification accuracyby: Rajeev K. Azad, Mark Borodovsky v. 20 i. 7 p. 993 - 1005
- Large-scale analysis of non-synonymous coding region single nucleotide polymorphismsby: Robert J. Clifford, Michael Edmonson, Cu Nguyen, Kenneth H. Buetow v. 20 i. 7 p. 1006 - 1014
- Measuring the similarity of protein structures by means of the universal similarity metricby: Natalio Krasnogor, David A. Pelta v. 20 i. 7 p. 1015 - 1021
- Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patternsby: Adele A. Mitchell, Michael E. Zwick, Aravinda Chakravarti, David J. Cutler v. 20 i. 7 p. 1022 - 1032
- Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression databy: Jorge Lepre, John Jeremy Rice, Yuhai Tu, Gustavo Stolovitzky v. 20 i. 7 p. 1033 - 1044
- Rapid 3D protein structure database searching using information retrieval techniquesby: Zeyar Aung, Kian-Lee Tan v. 20 i. 7 p. 1045 - 1052
- Good spaced seeds for homology searchby: Kwok Pui Choi, Fanfan Zeng, Louxin Zhang v. 20 i. 7 p. 1053 - 1059
- Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarraysby: Andrew C. James, Jim G. Veitch, Ali R. Zareh, Timothy Triche v. 20 i. 7 p. 1060 - 1065
- Statistically rigorous automated protein annotationby: Werner G. Krebs, Philip E. Bourne v. 20 i. 7 p. 1066 - 1073
- Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirusby: Ramakant Sharma, Jitendra Kumar Maheshwari, Tulika Prakash, Debasis Dash, Samir K. Brahmachari v. 20 i. 7 p. 1074 - 1080
- Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thalianaby: Lida Zhang, Dejun Yuan, Shunwu Yu, Zhugang Li, Youfang Cao, Zhiqi Miao, Hongmei Qian, Kexuan Tang v. 20 i. 7 p. 1081 - 1086
- Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignmentby: Adrian Arakaki, Yang Zhang, Jeffrey Skolnick v. 20 i. 7 p. 1087 - 1096
- SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesisby: Yohei Minakuchi, Masahiro Ito, Yuji Kohara v. 20 i. 7 p. 1097 - 1109
- Confirmation of data mining based predictions of protein functionby: Ross D. King, Paul H. Wise, Amanda Clare v. 20 i. 7 p. 1110 - 1118
- Predicting rules on organization of cis-regulatory elements, taking the order of elements into accountby: Goro Terai, Toshihisa Takagi v. 20 i. 7 p. 1119 - 1128
- COMPUCELL, a multi-model framework for simulation of morphogenesisby: Jesús A. Izaguirre, R. Chaturvedi, C. Huang, Trevor Cickovski, J. Coffland, G. Thomas, G. Forgacs, Mark S. Alber, G. Hentschel, Stuart A. Newman, James A. Glazier v. 20 i. 7 p. 1129 - 1137
- Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)by: Wan K. Kim, Dan M. Bolser, Jong H. Park v. 20 i. 7 p. 1138 - 1150
- Predicting subcellular localization of proteins in a hybridization spaceby: Yu-Dong Cai, Kuo-Chen Chou v. 20 i. 7 p. 1151 - 1156
- Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locusby: Volker Brendel, Liqun Xing, Wei Zhu v. 20 i. 7 p. 1157 - 1169
- An evaluation of new criteria for CpG islands in the human genome as gene markersby: Yong Wang, Frederick C. C. Leung v. 20 i. 7 p. 1170 - 1177
- Recognizing names in biomedical texts: a machine learning approachby: GuoDong Zhou, Jie Zhang, Jian Su, Dan Shen, Chew Lim Tan v. 20 i. 7 p. 1178 - 1190
- ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphicsby: Jihoon Kim, Hee-Joon Chung, Chan Hee Park, Woong-Yang Park, Ju Han Kim v. 20 i. 7 p. 1191 - 1192
- Multiple sequence alignment in parallel on a workstation clusterby: Justin Ebedes, Amitava Datta v. 20 i. 7 p. 1193 - 1195
- CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontologyby: N. H. Shah, Nina V. Fedoroff v. 20 i. 7 p. 1196 - 1197
- Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sitesby: Han Yu, Andrew S. Yoo, Iva Greenwald v. 20 i. 7 p. 1198 - 1200
- NvAssign: protein NMR spectral assignment with NMRViewby: Nigel I. Kirby, Eugene F. DeRose, Robert E. London, Geoffrey A. Mueller v. 20 i. 7 p. 1201 - 1203
- Probabilistic inference of molecular networks from noisy data sourcesby: Ivan Iossifov, Michael Krauthammer, Carol Friedman, Vasileios Hatzivassiloglou, Joel S. Bader, Kevin P. White, Andrey Rzhetsky v. 20 i. 8 p. 1205 - 1213
- A metric model of amino acid substitutionby: Weijia Xu, Daniel P. Miranker v. 20 i. 8 p. 1214 - 1221
- Bayesian mixture model based clustering of replicated microarray databy: Mario Medvedovic, K. Y. Yeung, Roger Eugene Bumgarner v. 20 i. 8 p. 1222 - 1232
- dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity databy: Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong, Cheng Li v. 20 i. 8 p. 1233 - 1240
- Growing genetic regulatory networks from seed genesby: Ronaldo Fumio Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, Edward R. Dougherty v. 20 i. 8 p. 1241 - 1247
- Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteinsby: H. Shmuely, E. Dinitz, I. Dahan, J. Eichler, D. Fischer, B. Shaanan v. 20 i. 8 p. 1248 - 1253
- Correction of sequence-based artifacts in serial analysis of gene expressionby: Viatcheslav R. Akmaev, Clarence J. Wang v. 20 i. 8 p. 1254 - 1263
- Automated ordering of fingerprinted clonesby: Stephane Flibotte, Readman Chiu, Chris Fjell, Martin Krzywinski, Jacqueline E. Schein, Heesun Shin, Marco A. Marra v. 20 i. 8 p. 1264 - 1271
- Analysing microarray data using modular regulation analysisby: R. Keira Curtis, Martin D. Brand v. 20 i. 8 p. 1272 - 1284
- RAG: RNA-As-Graphs database-concepts, analysis, featuresby: Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, Tamar Schlick v. 20 i. 8 p. 1285 - 1291
- Prediction of Saccharomyces cerevisiae protein functional class from functional domain compositionby: Yu-Dong Cai, Andrew J. Doig v. 20 i. 8 p. 1292 - 1300
- A comparison of scoring functions for protein sequence profile alignmentby: Robert C. Edgar, Kimmen Sjölander v. 20 i. 8 p. 1301 - 1308
- COACH: profile-profile alignment of protein families using hidden Markov modelsby: Robert C. Edgar, Kimmen Sjölander v. 20 i. 8 p. 1309 - 1318
- Cellware-a multi-algorithmic software for computational systems biologyby: Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Mandar Chitre, Hao Zhu, Kishore Sakharkar v. 20 i. 8 p. 1319 - 1321
- ConSeq: the identification of functionally and structurally important residues in protein sequencesby: Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal v. 20 i. 8 p. 1322 - 1324
- 2LD, GENECOUNTING and HAP: computer programs for linkage disequilibrium analysisby: Jing Hua Zhao v. 20 i. 8 p. 1325 - 1326
- CVD: the intestinal crypt/villus in situ hybridization databaseby: Line Olsen, Morten Hansen, Claus Thorn Ekstrøm, Jesper T. Troelsen, Jørgen Olsen v. 20 i. 8 p. 1327 - 1328
- eF-site and PDBjViewer: database and viewer for protein functional sitesby: Kengo Kinoshita, Haruki Nakamura v. 20 i. 8 p. 1329 - 1330
- WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignmentsby: Flavio Mignone, David S. Horner, Graziano Pesole v. 20 i. 8 p. 1331 - 1333
- Automatic prediction of protein domains from sequence information using a hybrid learning systemby: Niranjan Nagarajan, Golan Yona v. 20 i. 9 p. 1335 - 1360
- Modeling T-cell activation using gene expression profiling and state-space modelsby: Claudia Rangel, John Angus, Zoubin Ghahramani, Maria Lioumi, Elizabeth Sotheran, Alessia Gaiba, David L. Wild, Francesco Falciani v. 20 i. 9 p. 1361 - 1372
- A hint to search for metalloproteins in gene banksby: Claudia Andreini, Ivano Bertini, Antonio Rosato v. 20 i. 9 p. 1373 - 1380
- Analysis of disturbed imagesby: Gerhard Kauer, Helmut Blöcker v. 20 i. 9 p. 1381 - 1387
- Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approachby: Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund v. 20 i. 9 p. 1388 - 1397
- PartiGene-constructing partial genomesby: John Parkinson, Alasdair Anthony, James Wasmuth, Ralf Schmid, Ann Hedley, Mark Blaxter v. 20 i. 9 p. 1398 - 1404
- Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformationby: Deepak Sharma, Biju Issac, G. P. S. Raghava, R. Ramaswamy v. 20 i. 9 p. 1405 - 1412
- PINdb: a database of nuclear protein complexes from human and yeastby: Phuong-Van Luc, Paul Tempst v. 20 i. 9 p. 1413 - 1415
- Enhanced homology searching through genome reading frame predeterminationby: Jeffrey Yuan, Bruce Bush, Alex Elbrecht, Yuan Liu, Theresa Zhang, Wenqing Zhao, Richard Blevins v. 20 i. 9 p. 1416 - 1427
- Align-m-a new algorithm for multiple alignment of highly divergent sequencesby: Ivo Van Walle, Ignace Lasters, Lode Wyns v. 20 i. 9 p. 1428 - 1435
- Analysis of variance components in gene expression databy: James J. Chen, Robert R. Delongchamp, Chen-An Tsai, Huey-miin Hsueh, Frank Sistare, Karol L. Thompson, Varsha G. Desai, James C. Fuscoe v. 20 i. 9 p. 1436 - 1446
- galaxie-CGI scripts for sequence identification through automated phylogenetic analysisby: R. Henrik Nilsson, Karl-Henrik Larsson, Björn M. Ursing v. 20 i. 9 p. 1447 - 1452
- German Conference on Bioinformatics 2003 (GCB'03)by: Werner Mewes v. 20 i. 10 p. 1481 - 1481
- Regional and time-resolved mutation patterns of the human genomeby: Peter F. Arndt, Terence Hwa v. 20 i. 10 p. 1482 - 1485
- Using convex hulls to extract interaction interfaces from known structuresby: Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park, Michael Schroeder v. 20 i. 10 p. 1486 - 1490
- Threshold extraction in metabolite concentration databy: A. Flöter, J. Nicolas, Torsten Schaub, Joachim Selbig v. 20 i. 10 p. 1491 - 1494
- Conserved RNA secondary structures in viral genomes: a surveyby: Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits v. 20 i. 10 p. 1495 - 1499
- Gene expression analysis on biochemical networks using the Potts spin modelby: Rainer König, Roland Eils v. 20 i. 10 p. 1500 - 1505
- Bifurcation analysis of the regulatory modules of the mammalian G1/S transitionby: Maciej Swat, Alexander E. Kel, Hanspeter Herzel v. 20 i. 10 p. 1506 - 1511
- Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methodsby: Alexander E. Kel, Yuri Tikunov, Nico Voss, Edgar Wingender v. 20 i. 10 p. 1512 - 1516
- New methods for joint analysis of biological networks and expression databy: Florian Sohler, Daniel Hanisch, Ralf Zimmer v. 20 i. 10 p. 1517 - 1521
- Efficient similarity search in protein structure databases by k-clique hashingby: Nils Weskamp, Daniel Kuhn, Eyke Hüllermeier, Gerhard Klebe v. 20 i. 10 p. 1522 - 1526
- Gap statistics for whole genome shotgun DNA sequencing projectsby: Michael C. Wendl, Shiaw-Pyng Yang v. 20 i. 10 p. 1527 - 1534
- Evaluation and optimization of clustering in gene expression data analysisby: A. Fazel Famili, Ganming Liu, Ziying Liu v. 20 i. 10 p. 1535 - 1545
- Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problemsby: Catherine Grasso, Christopher Lee v. 20 i. 10 p. 1546 - 1556
- BioOptimizer: a Bayesian scoring function approach to motif discoveryby: Shane T. Jensen, Jun S. Liu v. 20 i. 10 p. 1557 - 1564
- A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignmentsby: John P. Dekker, Anthony Fodor, Richard W. Aldrich, Gary Yellen v. 20 i. 10 p. 1565 - 1572
- Evaluating the predictability of conformational switching in RNAby: Björn Voss, Carsten Meyer, Robert Giegerich v. 20 i. 10 p. 1573 - 1582
- An object model and database for functional genomicsby: Andrew Jones, Ela Hunt, Jonathan M. Wastling, Angel Pizarro, Christian J. Stoeckert Jr. v. 20 i. 10 p. 1583 - 1590
- A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequencesby: Yongmei Ji, Xing Xu, Gary D. Stormo v. 20 i. 10 p. 1603 - 1611
- Protein backbone angle prediction with machine learning approachesby: Rui Kuang, Christina S. Leslie, An-Suei Yang v. 20 i. 10 p. 1612 - 1621
- Development of joint application strategies for two microbial gene findersby: Alice C. McHardy, Alexander Goesmann, Alfred Pühler, Folker Meyer v. 20 i. 10 p. 1622 - 1631
- Common structural patterns in human genesby: Aubrey Hill, Eric Sorscher v. 20 i. 10 p. 1632 - 1635
- QDist-quartet distance between evolutionary treesby: Thomas Mailund, Christian N. S. Pedersen v. 20 i. 10 p. 1636 - 1637
- Application of the GA/KNN method to SELDI proteomics databy: Leping Li, David M. Umbach, Paul Terry, Jack A. Taylor v. 20 i. 10 p. 1638 - 1640
- VARAN: a web server for Variability Analysis of DNA microarray experimentsby: G. Golfier, M. Tran Dang, L. Dauphinot, E. Graison, J. Rossier, M.-C. Potier v. 20 i. 10 p. 1641 - 1643
- Amplicon: software for designing PCR primers on aligned DNA sequencesby: Simon N. Jarman v. 20 i. 10 p. 1644 - 1645
- OBIYagns: a grid-based biochemical simulator with a parameter estimatorby: Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya v. 20 i. 10 p. 1646 - 1648
- SeqExpress: desktop analysis and visualization tool for gene expression experimentsby: John Boyle v. 20 i. 10 p. 1649 - 1650
- matchprobes: a Bioconductor package for the sequence-matching of microarray probe elementsby: Wolfgang Huber, Robert Gentleman v. 20 i. 10 p. 1651 - 1652
- Mathematical characterization of three-dimensional gene expression patternsby: Luciano da Fontoura Costa, M. S. Barbosa, Edson Tadeu Monteiro Manoel, Johannes Streicher, Gerd B. Müller v. 20 i. 11 p. 1653 - 1662
- Mixture models for assessing differential expression in complex tissues using microarray databy: Debashis Ghosh v. 20 i. 11 p. 1663 - 1669
- Decoupling dynamical systems for pathway identification from metabolic profilesby: Eberhard O. Voit, Jonas S. Almeida v. 20 i. 11 p. 1670 - 1681
- Protein homology detection using string alignment kernelsby: Hiroto Saigo, Jean-Philippe Vert, Nobuhisa Ueda, Tatsuya Akutsu v. 20 i. 11 p. 1682 - 1689
- Fuzzy J-Means and VNS methods for clustering genes from microarray databy: Nabil Belacel, Miroslava Cuperlovic-Culf, Mark Laflamme, Rodney Ouellette v. 20 i. 11 p. 1690 - 1701
- Why neural networks should not be used for HIV-1 protease cleavage site predictionby: Thorsteinn S. Rögnvaldsson, Liwen You v. 20 i. 11 p. 1702 - 1709
- Primer design using genetic algorithmby: Jain-Shing Wu, Chungnan Lee, Chien-Chang Wu, Yow-Ling Shiue v. 20 i. 11 p. 1710 - 1717
- Sight: automating genomic data-mining without programming skillsby: Audrius Meskauskas, Frank Lehmann-Horn, Karin Jurkat-Rott v. 20 i. 11 p. 1718 - 1720
- An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experimentsby: R. S. Anderssen, Y. Wu, R. Dolferus, I. Saunders v. 20 i. 11 p. 1721 - 1727
- Robust PCA and classification in biosciencesby: Mia Hubert, Sanne Engelen v. 20 i. 11 p. 1728 - 1736
- Improving false discovery rate estimationby: Stan Pounds, Cheng Cheng v. 20 i. 11 p. 1737 - 1745
- Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifsby: N. Kashtan, S. Itzkovitz, R. Milo, U. Alon v. 20 i. 11 p. 1746 - 1758
- Omic space: coordinate-based integration and analysis of genomic phenomic interactionsby: Tetsuro Toyoda, Akiyoshi Wada v. 20 i. 11 p. 1759 - 1765
- Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weightsby: Fenghai Duan, Heping Zhang v. 20 i. 11 p. 1766 - 1771
- Normalization of single-channel DNA array data by principal component analysisby: Radka Stoyanova, Troy D. Querec, Truman R. Brown, Christos Patriotis v. 20 i. 11 p. 1772 - 1784
- MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteinsby: Chittibabu Guda, Eoin Fahy, Shankar Subramaniam v. 20 i. 11 p. 1785 - 1794
- A general computational model of mitochondrial metabolism in a whole organelle scaleby: Katsuyuki Yugi, Masaru Tomita v. 20 i. 11 p. 1795 - 1796
- GeneCluster 2.0: an advanced toolset for bioarray analysisby: Michael Reich, K. Ohm, Michael Angelo, Pablo Tamayo, Jill P. Mesirov v. 20 i. 11 p. 1797 - 1798
- HMMGEP: clustering gene expression data using hidden Markov modelsby: Xinglai Ji, Yuan Yuan, Jesse Li-Ling, Yanda Li, Zhirong Sun v. 20 i. 11 p. 1799 - 1800
- Structural exon database, SEDB, mapping exon boundaries on multiple protein structuresby: Chesley M. Leslin, Alex Abyzov, Valentin A. Ilyin v. 20 i. 11 p. 1801 - 1803
- Genomic data visualization on the Webby: Wei Wu, William Stafford Noble v. 20 i. 11 p. 1804 - 1805
- TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignmentsby: Iain Milne, Frank Wright, Glenn Rowe, David F. Marshall, Dirk Husmeier, Gráinne McGuire v. 20 i. 11 p. 1806 - 1807
- FunMap: functional mapping of complex traitsby: Chang-Xing Ma, Rongling Wu, George Casella v. 20 i. 11 p. 1808 - 1811
- Visualization for genomics: the Microbial Genome Viewerby: Robert Kerkhoven, Frank H. J. van Enckevort, Jos Boekhorst, Douwe Molenaar, Roland J. Siezen v. 20 i. 11 p. 1812 - 1814
- CisML: an XML-based format for sequence motif detection softwareby: Peter M. Haverty, Zhiping Weng v. 20 i. 11 p. 1815 - 1817
- A Web-based design center for vector-based siRNA and siRNA cassetteby: Luquan Wang, Forest Y. Mu v. 20 i. 11 p. 1818 - 1820
- New Leadership for Bioinformaticsby: Alex Bateman, Alfonso Valencia v. 20 i. 12 p. 1821 - 1821
- A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteinsby: Thijs Beuming, Harel Weinstein v. 20 i. 12 p. 1822 - 1835
- Haplotypes histories as pathways of recombinationsby: Nadia El-Mabrouk, Damian Labuda v. 20 i. 12 p. 1836 - 1841
- Haplotype reconstruction from genotype data using Imperfect Phylogenyby: Eran Halperin, Eleazar Eskin v. 20 i. 12 p. 1842 - 1849
- Multiple-sequence functional annotation and the generalized hidden Markov phylogenyby: Jon D. McAuliffe, Lior Pachter, Michael I. Jordan v. 20 i. 12 p. 1850 - 1860
- Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutationby: Danny Barash v. 20 i. 12 p. 1861 - 1869
- Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graphby: Hong-Wu Ma, Xue-Ming Zhao, Ying-Jin Yuan, An-Ping Zeng v. 20 i. 12 p. 1870 - 1876
- Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite databy: Eduardo D. Sontag, Anatoly Kiyatkin, Boris N. Kholodenko v. 20 i. 12 p. 1877 - 1886
- Simultaneous search for multiple QTL using the global optimization algorithm DIRECTby: Kajsa Ljungberg, Sverker Holmgren, Örjan Carlborg v. 20 i. 12 p. 1887 - 1895
- A comparison of cluster analysis methods using DNA methylation databy: Kimberly D. Siegmund, Peter W. Laird, Ite A. Laird-Offringa v. 20 i. 12 p. 1896 - 1904
- Supervised cluster analysis for microarray data based on multivariate Gaussian mixtureby: Yi Qu, Shizhong Xu v. 20 i. 12 p. 1905 - 1913
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- Gene annotation from scientific literature using mappings between keyword systemsby: Antonio Jesús Pérez, Carolina Perez-Iratxeta, Peer Bork, Guillermo Thode, Miguel A. Andrade v. 20 i. 13 p. 2084 - 2091
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- The DISOPRED server for the prediction of protein disorderby: Jonathan J. Ward, Liam J. McGuffin, Kevin Bryson, Bernard F. Buxton, David T. Jones v. 20 i. 13 p. 2138 - 2139
- Identifying multiple alignment regions satisfying simple formulas and patternsby: Nikola Stojanovic, Ken Dewar v. 20 i. 13 p. 2140 - 2142
- Web-based kinetic modelling using JWS Onlineby: Brett G. Olivier, Jacky L. Snoep v. 20 i. 13 p. 2143 - 2144
- STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfacesby: Adauto L. Mancini, Roberto H. Higa, Adilton G. Oliveira, Fabiana Dominiquini, Paula R. Kuser, Michel E. B. Yamagishi, Roberto C. Togawa, Goran Neshich v. 20 i. 13 p. 2145 - 2147
- TIP: protein backtranslation aided by genetic algorithmsby: Andrés Moreira, Alejandro Maass v. 20 i. 13 p. 2148 - 2149
- F2CS: FSSP to CATH and SCOP prediction serverby: Gad Getz, Alina Starovolsky, Eytan Domany v. 20 i. 13 p. 2150 - 2152
- Ligand Depot: a data warehouse for ligands bound to macromoleculesby: Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, John D. Westbrook v. 20 i. 13 p. 2153 - 2155
- Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray databy: Ritu Pandey, Raghavendra K. Guru, David W. Mount v. 20 i. 13 p. 2156 - 2158
- Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics techniciansby: Pavel A. Pevzner v. 20 i. 14 p. 2159 - 2161
- Protein isoelectric point as a predictor for increased crystallization screening efficiencyby: Katherine A. Kantardjieff, Bernhard Rupp v. 20 i. 14 p. 2162 - 2168
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- Performance of an iterated T-HMM for homology detectionby: Bin Qian, Richard A. Goldstein v. 20 i. 14 p. 2175 - 2180
- Probabilistic nucleotide assembling method for sequencing by hybridizationby: Takaho A. Endo v. 20 i. 14 p. 2181 - 2188
- Extraction of fluorescent cell puncta by adaptive fuzzy segmentationby: Tuan D. Pham, Denis I. Crane, Tuan H. Tran, Tam H. Nguyen v. 20 i. 14 p. 2189 - 2196
- An examination of the conservation of surface patch polarity for proteinsby: H. P. Shanahan, Janet M. Thornton v. 20 i. 14 p. 2197 - 2204
- Design and implementation of a mosquito database through an entomological ontologyby: Guillaume Koum, Augustin Yekel, Bengyella Ndifon, Frédéric Simard v. 20 i. 14 p. 2205 - 2211
- A database for management of gene expression data in situby: Ekaterina Poustelnikova, Andrei Pisarev, Maxim Blagov, Maria Samsonova, John Reinitz v. 20 i. 14 p. 2212 - 2221
- Alignment of RNA base pairing probability matricesby: Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler v. 20 i. 14 p. 2222 - 2227
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- Spot shape modelling and data transformations for microarraysby: Claus Thorn Ekstrøm, Søren Bak, Charlotte Kristensen, Mats Rudemo v. 20 i. 14 p. 2270 - 2278
- Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveysby: Edward Susko, Andrew J. Roger v. 20 i. 14 p. 2279 - 2287
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- Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry databy: Alejandro Heredia-Langner, William R. Cannon, Kenneth D. Jarman, Kristin H. Jarman v. 20 i. 14 p. 2296 - 2304
- ACID: a database for microarray clone informationby: Markus Ringnér, Srinivas Veerla, Samuel Andersson, Johan Staaf, Jari Häkkinen v. 20 i. 14 p. 2305 - 2306
- GeConT: gene context analysisby: R. Ciria, C. Abreu-Goodger, E. Morett, E. Merino v. 20 i. 14 p. 2307 - 2308
- MuSiC: a tool for multiple sequence alignment with constraintsby: Yin-Te Tsai, Yen Pin Huang, Ching Ta Yu, Chin Lung Lu v. 20 i. 14 p. 2309 - 2311
- SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genomeby: Todd J. Dolinsky, P. M. J. Burgers, Kevin Karplus, Nathan A. Baker v. 20 i. 14 p. 2312 - 2314
- PedSplit: pedigree management for stratified analysisby: M. B. Lanktree, L. VanderBeek, F. M. Macciardi, J. L. Kennedy v. 20 i. 14 p. 2315 - 2316
- Bellerophon: a program to detect chimeric sequences in multiple sequence alignmentsby: Thomas Huber, Geoffrey Faulkner, Philip Hugenholtz v. 20 i. 14 p. 2317 - 2319
- MedPost: a part-of-speech tagger for bioMedical textby: Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur v. 20 i. 14 p. 2320 - 2321
- Drawing phylogenetic trees in LATEX and Microsoft Wordby: George Savva, Jenn Conn, Jo L. Dicks v. 20 i. 14 p. 2322 - 2323
- BioMercator: integrating genetic maps and QTL towards discovery of candidate genesby: Anne Arcade, Aymeric Labourdette, Matthieu Falque, Brigitte Mangin, Fabien Chardon, Alain Charcosset, Johann Joets v. 20 i. 14 p. 2324 - 2326
- Pelican: pedigree editor for linkage computer analysisby: Frank Dudbridge, Tim Carver, Gary W. Williams v. 20 i. 14 p. 2327 - 2328
- INCA: synonymous codon usage analysis and clustering by means of self-organizing mapby: Fran Supek, Kristian Vlahovicek v. 20 i. 14 p. 2329 - 2330
- AliasServer: a web server to handle multiple aliases used to refer to proteinsby: Florian Iragne, Aurélien Barré, Nicolas Goffard, Antoine de Daruvar v. 20 i. 14 p. 2331 - 2332
- SAD - a normalized structural alignment database: improving sequence-structure alignmentsby: Brian Marsden, Ruben Abagyan v. 20 i. 15 p. 2333 - 2344
- Proteins associated with diseases show enhanced sequence correlation between charged residuesby: Ruxandra I. Dima, D. Thirumalai v. 20 i. 15 p. 2345 - 2354
- Supertree algorithms for ancestral divergence dates and nested taxaby: Charles Semple, Philip Daniel, Wim Hordijk, Roderic D. M. Page, Mike A. Steel v. 20 i. 15 p. 2355 - 2360
- An online database for the detection of novel archaeal sequences in human ESTsby: Neil F. W. Saunders, Paul M. G. Curmi, Ricardo Cavicchioli v. 20 i. 15 p. 2361 - 2362
- BAPS 2: enhanced possibilities for the analysis of genetic population structureby: Jukka Corander, Patrik Waldmann, Pekka Marttinen, Mikko J. Sillanpää v. 20 i. 15 p. 2363 - 2369
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- Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein familiesby: Ricardo Núñez Miguel v. 20 i. 15 p. 2380 - 2389
- GEPIS - quantitative gene expression profiling in normal and cancer tissuesby: Yan Zhang, David A. Eberhard, Gretchen D. Frantz, Patrick Dowd, Thomas D. Wu, Yan Zhou, Colin Watanabe, Shiuh-Ming Luoh, Paul Polakis, Kenneth J. Hillan, William I. Wood, Zemin Zhang v. 20 i. 15 p. 2390 - 2398
- PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer designby: Paul C. Boutros, Allan B. Okey v. 20 i. 15 p. 2399 - 2400
- Algorithms for sequence analysis via mutagenesisby: Jonathan M. Keith, Peter Adams, Darryn E. Bryant, Duncan A. E. Cochran, Gita H. Lala, Keith R. Mitchelson v. 20 i. 15 p. 2401 - 2410
- Explicit formulation of different receptor-G-protein interactions and effector regulationby: Jyrki P. Kukkonen v. 20 i. 15 p. 2411 - 2420
- How independent are the appearances of n-mers in different genomes?by: Yuriy Fofanov, Yi Luo, Charles Katili, Jim Wang, Yuri Belosludtsev, Thomas Powdrill, Chetan Belapurkar, Viacheslav Fofanov, Tong-Bin Li, Sergey Chumakov, B. Montgomery Pettitt v. 20 i. 15 p. 2421 - 2428
- A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expressionby: Tao Li, Chengliang Zhang, Mitsunori Ogihara v. 20 i. 15 p. 2429 - 2437
- Analysis of longitudinal metabolomics databy: Jeroen J. Jansen, Huub C. J. Hoefsloot, Hans F. M. Boelens, Jan van der Greef, Age K. Smilde v. 20 i. 15 p. 2438 - 2446
- Metabolite fingerprinting: detecting biological features by independent component analysisby: Matthias Scholz, S. Gatzek, A. Sterling, Oliver Fiehn, Joachim Selbig v. 20 i. 15 p. 2447 - 2454
- YAdumper: extracting and translating large information volumes from relational databases to structured flat filesby: José María Fernández, Alfonso Valencia v. 20 i. 15 p. 2455 - 2457
- An interactive triple-helical collagen builderby: Jan K. Rainey, M. Cynthia Goh v. 20 i. 15 p. 2458 - 2459
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- Pedro: a configurable data entry tool for XMLby: Kevin L. Garwood, Chris F. Taylor, Kai J. Runte, Andy Brass, Stephen G. Oliver, Norman W. Paton v. 20 i. 15 p. 2463 - 2465
- HPID: The Human Protein Interaction Databaseby: Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong, Jong Park v. 20 i. 15 p. 2466 - 2470
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- The SRS 3D module: integrating structures, sequences and featuresby: Seán I. O'Donoghue, Joachim E. W. Meyer, Andrea Schafferhans, Karsten Fries v. 20 i. 15 p. 2476 - 2478
- Data mining in bioinformatics using Wekaby: Eibe Frank, Mark Hall, Lenard E. Trigg, Geoffrey Holmes, Ian H. Witten v. 20 i. 15 p. 2479 - 2481
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- Sfixem - graphical sequence feature display in Javaby: Alistair M. Chalk, Martin Wennerberg, Erik L. L. Sonnhammer v. 20 i. 15 p. 2488 - 2490
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- Analyzing time series gene expression databy: Ziv Bar-Joseph v. 20 i. 16 p. 2493 - 2503
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- Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptorby: Dominique Tessier, Benjamin Bardiaux, Colette Larré, Yves Popineau v. 20 i. 16 p. 2509 - 2512
- Which is better for cDNA-microarray-based classification: ratios or direct intensitiesby: Sanju Attoor, Edward R. Dougherty, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent v. 20 i. 16 p. 2513 - 2520
- A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditionsby: Delong Liu, Clarice R. Weinberg, Shyamal D. Peddada v. 20 i. 16 p. 2521 - 2528
- Efficient combination of multiple word models for improved sequence comparisonby: Xiaoqiu Huang, Liang Ye, Hui-Hsien Chou, I-Hsuan Yang, Kun-Mao Chao v. 20 i. 16 p. 2529 - 2533
- Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarraysby: Jinwook Seo, Marina Bakay, Yi-Wen Chen, Sara Hilmer, Ben Shneiderman, Eric P. Hoffman v. 20 i. 16 p. 2534 - 2544
- Class discovery and classification of tumor samples using mixture modeling of gene expression data - a unified approachby: Roxana Alexandridis, Shili Lin, Mark Irwin v. 20 i. 16 p. 2545 - 2552
- Identification of DNA regulatory motifs using Bayesian variable selectionby: Mahlet G. Tadesse, Marina Vannucci, Pietro Lió v. 20 i. 16 p. 2553 - 2561
- A mixture model-based strategy for selecting sets of genes in multiclass response microarray experimentsby: Philippe Broët, Alex Lewin, Sylvia Richardson, Cyril Dalmasso, Henri Magdelenat v. 20 i. 16 p. 2562 - 2571
- Predicting allergenic proteins using wavelet transformby: Kuo-Bin Li, Praveen Issac, Arun Krishnan v. 20 i. 16 p. 2572 - 2578
- Genome wide identification and classification of alternative splicing based on EST databy: Shobhit Gupta, Dorothea Zink, Bernhard Korn, Martin Vingron, Stefan A. Haas v. 20 i. 16 p. 2579 - 2585
- Incremental generation of summarized clustering hierarchy for protein family analysisby: Chien-Yu Chen, Yen-Jen Oyang, Hsueh-Fen Juan v. 20 i. 16 p. 2586 - 2596
- Distribution of information in biomedical abstracts and full-text publicationsby: Martijn J. Schuemie, Marc Weeber, Bob J. A. Schijvenaars, Erik M. van Mulligen, C. Christiaan van der Eijk, Rob Jelier, Barend Mons, Jan A. Kors v. 20 i. 16 p. 2597 - 2604
- A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profilesby: Feng Luo, Latifur Khan, Farokh B. Bastani, I-Ling Yen, Jizhong Zhou v. 20 i. 16 p. 2605 - 2617
- GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology termsby: Marcel Smid, Lambert C. J. Dorssers v. 20 i. 16 p. 2618 - 2625
- A statistical framework for genomic data fusionby: Gert R. G. Lanckriet, Tijl De Bie, Nello Cristianini, Michael I. Jordan, William Stafford Noble v. 20 i. 16 p. 2626 - 2635
- THEA: ontology-driven analysis of microarray databy: Claude Pasquier, F. Girardot, K. Jevardat de Fombelle, R. Christen v. 20 i. 16 p. 2636 - 2643
- Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathwayby: Harm van Bakel, Martijn A. Huynen, Cisca Wijmenga v. 20 i. 16 p. 2644 - 2655
- SCA db: spinocerebellar ataxia candidate gene databaseby: Y.-F. Liu, U.-C. Yang v. 20 i. 16 p. 2656 - 2661
- DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutantsby: Koji Kyoda, Kotaro Baba, Shuichi Onami, Hiroaki Kitano v. 20 i. 16 p. 2662 - 2675
- An efficient algorithm for optimizing whole genome alignment with noiseby: Prudence W. H. Wong, Tak Wah Lam, N. Lu, Hing-Fung Ting, Siu-Ming Yiu v. 20 i. 16 p. 2676 - 2684
- Correcting log ratios for signal saturation in cDNA microarraysby: Lori E. Dodd, Edward L. Korn, Lisa M. McShane, G. V. R. Chandramouli, Eric Y. Chuang v. 20 i. 16 p. 2685 - 2693
- A mixture model for estimating the local false discovery rate in DNA microarray analysisby: J. G. Liao, Yong Lin, Zachariah E. Selvanayagam, Weichung Joe Shih v. 20 i. 16 p. 2694 - 2701
- Exhaustive whole-genome tandem repeats searchby: Arun Krishnan, Francis Tang v. 20 i. 16 p. 2702 - 2710
- Mining gene expression data for positive and negative co-regulated gene clustersby: Liping Ji, Kian-Lee Tan v. 20 i. 16 p. 2711 - 2718
- Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replicationby: Nicolas Omont, François Képès v. 20 i. 16 p. 2719 - 2725
- The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray databy: Robert Mansourian, David M. Mutch, Nicolas Antille, Jerome Aubert, Paul Fogel, Jean-Marc Le Goff, Julie Moulin, Anton Petrov, Andreas Rytz, Johannes J. Voegel, Matthew-Alan Roberts v. 20 i. 16 p. 2726 - 2737
- Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscuraby: Yonatan H. Grad, Frederick P. Roth, Marc S. Halfon, George M. Church v. 20 i. 16 p. 2738 - 2750
- A neural network method for prediction of ?-turn types in proteins using evolutionary informationby: Harpreet Kaur, G. P. S. Raghava v. 20 i. 16 p. 2751 - 2758
- Mining gene expression data based on template theoryby: Zheng Rong Yang v. 20 i. 16 p. 2759 - 2766
- ICBS: a database of interactions between protein chains mediated by ?-sheet formationby: Yimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, Pierre Baldi v. 20 i. 16 p. 2767 - 2777
- Faster cyclic loess: normalizing RNA arrays via linear modelsby: Karla V. Ballman, Diane E. Grill, Ann L. Oberg, Terry M. Therneau v. 20 i. 16 p. 2778 - 2786
- BacTregulators: a database of transcriptional regulators in bacteria and archaeaby: Manuel Martínez-Bueno, Antonio J. Molina-Henares, Eduardo Pareja, Juan L. Ramos, Raquel Tobes v. 20 i. 16 p. 2787 - 2791
- Qxpak: a versatile mixed model application for genetical genomics and QTL analysesby: M. Pérez-Enciso, I. Misztal v. 20 i. 16 p. 2792 - 2798
- Regulatory motif finding by logic regressionby: Sündüz Keles, Mark van der Laan, Chris Vulpe v. 20 i. 16 p. 2799 - 2811
- STAR: an algorithm to Search for Tandem Approximate Repeatsby: Olivier Delgrange, Eric Rivals v. 20 i. 16 p. 2812 - 2820
- A statistical framework for the design of microarray experiments and effective detection of differential gene expressionby: Shu-Dong Zhang, Timothy W. Gant v. 20 i. 16 p. 2821 - 2828
- MathSBML: a package for manipulating SBML-based biological modelsby: Bruce E. Shapiro, Michael Hucka, Andrew Finney, John Doyle v. 20 i. 16 p. 2829 - 2831
- A System for Automated Bacterial (genome) Integrated Annotation - SABIAby: Luiz G. P. Almeida, Roger Paixão, Rangel C. Souza, Gisele C. da Costa, Frank J. A. Barrientos, M. Trindade dos Santos, Darcy F. de Almeida, Ana Tereza R. Vasconcelos v. 20 i. 16 p. 2832 - 2833
- Dblox: a genome-wide test for ancient segmental duplicationby: Robert Friedman, Vikram Ekollu, John R. Rose, Austin L. Hughes v. 20 i. 16 p. 2834 - 2835
- ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequencesby: Eisuke Chikayama, Atsushi Kurotani, Yutaka Kuroda, Shigeyuki Yokoyama v. 20 i. 16 p. 2836 - 2838
- GDPC: connecting researchers with multiple integrated data sourcesby: Terry M. Casstevens, Edward S. Buckler v. 20 i. 16 p. 2839 - 2840
- PaVESy: Pathway Visualization and Editing Systemby: Alexander Lüdemann, Daniel Weicht, Joachim Selbig, Joachim Kopka v. 20 i. 16 p. 2841 - 2844
- The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functionsby: Sandra Barth, Markus Fischer, Rolf D. Schmid, Jürgen Pleiss v. 20 i. 16 p. 2845 - 2847
- RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasetsby: Fulvio Lazzarato, Giuliana Franceschinis, M. Botta, F. Cordero, Raffaele Calogero v. 20 i. 16 p. 2848 - 2850
- Gene-Ontology-based clustering of gene expression databy: Boris Adryan, Reinhard Schuh v. 20 i. 16 p. 2851 - 2852
- ASIAN: a website for network inferenceby: Sachiyo Aburatani, Kousuke Goto, Shigeru Saito, Masaki Fumoto, Akira Imaizumi, Nobuyoshi Sugaya, Hiroo Murakami, Makihiko Sato, Hiroyuki Toh, Katsuhisa Horimoto v. 20 i. 16 p. 2853 - 2856
- A collaborative database of inbred mouse strain characteristicsby: Stephen C. Grubb, Gary A. Churchill, Molly A. Bogue v. 20 i. 16 p. 2857 - 2859
- TargetDB: a target registration database for structural genomics projectsby: Li Chen, Rose Oughtred, Helen M. Berman, John D. Westbrook v. 20 i. 16 p. 2860 - 2862
- Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assembliesby: W. H. Lee, V. B. Vega v. 20 i. 16 p. 2863 - 2864
- LUCY2: an interactive DNA sequence quality trimming and vector removal toolby: Song Li, Hui-Hsien Chou v. 20 i. 16 p. 2865 - 2866
- SWAPSC: sliding window analysis procedure to detect selective constraintsby: Mario A. Fares v. 20 i. 16 p. 2867 - 2868
- ClutrFree: cluster tree visualization and interpretationby: Ghislain Bidaut, Michael F. Ochs v. 20 i. 16 p. 2869 - 2871
- Rainbow: a toolbox for phylogenetic supertree construction and analysisby: D. Chen, Oliver Eulenstein, David Fernández-Baca v. 20 i. 16 p. 2872 - 2873
- Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistryby: Robert N. Goldberg, Yadu B. Tewari, Talapady N. Bhat v. 20 i. 16 p. 2874 - 2877
- TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-findersby: William H. Majoros, Mihaela Pertea, Steven Salzberg v. 20 i. 16 p. 2878 - 2879
- FigSearch: a figure legend indexing and classification systemby: Fang Liu, Tor-Kristian Jenssen, Vegard Nygaard, John Sack, Eivind Hovig v. 20 i. 16 p. 2880 - 2882
- GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computersby: P. D'Addabbo, L. Lenzi, F. Facchin, R. Casadei, S. Canaider, L. Vitale, F. Frabetti, P. Carinci, M. Zannotti, P. Strippoli v. 20 i. 16 p. 2883 - 2885
- CoPS: Comprehensive Peptide Signature Databaseby: Tulika Prakash, Mamta Khandelwal, Dipayan Dasgupta, Debasis Dash, Samir K. Brahmachari v. 20 i. 16 p. 2886 - 2888
- Command line tool for calculating theoretical MS spectra for given sequencesby: Andreas M. Boehm, Florian Grosse-Coosmann, Albert Sickmann v. 20 i. 16 p. 2889 - 2891
- Picky: oligo microarray design for large genomesby: Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, Patrick S. Schnable v. 20 i. 17 p. 2893 - 2902
- Letter to the Editorby: Lisa M. Schilling, Jonathan D. Wren, Robert P. Dellavalle v. 20 i. 17 p. 2903 - 2903
- Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteinsby: Neeraj Pandey, Mythily Ganapathi, Kaushal Kumar, Dipayan Dasgupta, Sushanta Kumar Das Sutar, Debasis Dash v. 20 i. 17 p. 2904 - 2910
- Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequencesby: Eric Bonnet, Jan Wuyts, Pierre Rouzé, Yves Van de Peer v. 20 i. 17 p. 2911 - 2917
- A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networksby: Xiaobo Zhou, Xiaodong Wang, Ranadip Pal, Ivan Ivanov, Michael L. Bittner, Edward R. Dougherty v. 20 i. 17 p. 2918 - 2927
- Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditionsby: Sven Rahmann, Christine Gräfe v. 20 i. 17 p. 2928 - 2933
- Reconstruction of gene networks using Bayesian learning and manipulation experimentsby: Iosifina Pournara, Lorenz Wernisch v. 20 i. 17 p. 2934 - 2942
- Bayesian integrated functional analysis of microarray databy: Madhuchhanda Bhattacharjee, Colin C. Pritchard, Peter S. Nelson, Elja Arjas v. 20 i. 17 p. 2943 - 2953
- A spline function approach for detecting differentially expressed genes in microarray data analysisby: Wenqing He v. 20 i. 17 p. 2954 - 2963
- Transmembrane proteins in the Protein Data Bank: identification and classificationby: Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon v. 20 i. 17 p. 2964 - 2972
- EST clustering error evaluation and correctionby: Ji-Ping Wang, Bruce Lindsay, James Leebens-Mack, Liying Cui, Kerr Wall, Webb C. Miller, Claude W. dePamphilis v. 20 i. 17 p. 2973 - 2984
- Supervised machine learning techniques for the classification of metabolic disorders in newbornsby: Christian Baumgartner, Christian Böhm, D. Baumgartner, G. Marini, K. Weinberger, B. Olgemöller, B. Liebl, A. A. Roscher v. 20 i. 17 p. 2985 - 2996
- Visualizations for taxonomic and phylogenetic treesby: Cynthia Sims Parr, Bongshin Lee, Dana Campbell, Benjamin B. Bederson v. 20 i. 17 p. 2997 - 3004
- Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificatesby: Jörn Lewin, Armin O. Schmitt, Péter Adorján, Thomas Hildmann 0002, Christian Piepenbrock v. 20 i. 17 p. 3005 - 3012
- Protein complex prediction via cost-based clusteringby: A. D. King, Natasa Przulj, Igor Jurisica v. 20 i. 17 p. 3013 - 3020
- Biologically valid linear factor models of gene expressionby: Mark Girolami, Rainer Breitling v. 20 i. 17 p. 3021 - 3033
- Sample classification from protein mass spectrometry, by 'peak probability contrasts'by: Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Scott Soltys, Gongyi Shi, Albert Koong, Quynh-Thu Le v. 20 i. 17 p. 3034 - 3044
- Taverna: a tool for the composition and enactment of bioinformatics workflowsby: Thomas M. Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Martin Senger, R. Mark Greenwood, Tim Carver, Kevin Glover, Matthew R. Pocock, Anil Wipat, Peter Li v. 20 i. 17 p. 3045 - 3054
- Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programmingby: Pål Sætrom v. 20 i. 17 p. 3055 - 3063
- A comparative method for identification of gene structures and alternatively spliced variantsby: Trees-Juen Chuang, Feng-Chi Chen, Meng-Yuan Chou v. 20 i. 17 p. 3064 - 3079
- Developing optimal non-linear scoring function for protein designby: Changyu Hu II, Xiang Li, Jie Liang v. 20 i. 17 p. 3080 - 3098
- Comparison of probabilistic combination methods for protein secondary structure predictionby: Yan Liu, Jaime G. Carbonell, Judith Klein-Seetharaman, Vanathi Gopalakrishnan v. 20 i. 17 p. 3099 - 3107
- Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytesby: A. Hsiao, D. S. Worrall, J. M. Olefsky, Shankar Subramaniam v. 20 i. 17 p. 3108 - 3127
- Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimensby: Glen A. Satten, Somnath Datta, Hercules Moura, Adrian R. Woolfitt, Maria da G. Carvalho, George M. Carlone, Barun K. De, Antonis Pavlopoulos, John R. Barr v. 20 i. 17 p. 3128 - 3136
- Constrained clusters of gene expression profiles with pathological featuresby: Jun Sese, Yukinori Kurokawa, Morito Monden, Kikuya Kato, Shinichi Morishita v. 20 i. 17 p. 3137 - 3145
- A statistical method for identifying differential gene-gene co-expression patternsby: Yinglei Lai, Baolin Wu, Liang Chen, Hongyu Zhao v. 20 i. 17 p. 3146 - 3155
- The UniMarker (UM) method for synteny mapping of large genomesby: Ben-Yang Liao, Yu-Jung Chang, Jan-Ming Ho, Ming-Jing Hwang v. 20 i. 17 p. 3156 - 3165
- Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studiesby: J. Wang, Kevin R. Coombes, W. Edward Highsmith, M. J. Keating, Lynne V. Abruzzo v. 20 i. 17 p. 3166 - 3178
- Prediction of phosphorylation sites using SVMsby: Jong-Hun Kim, Juyoung Lee, Bermseok Oh, Kuchan Kimm, InSong Koh v. 20 i. 17 p. 3179 - 3184
- Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reductionby: Nathalie Pochet, Frank De Smet, Johan A. K. Suykens, Bart De Moor v. 20 i. 17 p. 3185 - 3195
- Normalization of microarray data using a spatial mixed model analysis which includes splinesby: David Baird, Peter Johnstone, Theresa Wilson v. 20 i. 17 p. 3196 - 3205
- BioRAT: extracting biological information from full-length papersby: David P. A. Corney, Bernard F. Buxton, William B. Langdon, David T. Jones v. 20 i. 17 p. 3206 - 3213
- Computational prediction of RNA editing sitesby: Ralf Bundschuh v. 20 i. 17 p. 3214 - 3220
- A model-based optimization framework for the inference on gene regulatory networks from DNA array databy: Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, Vassily Hatzimanikatis v. 20 i. 17 p. 3221 - 3235
- UniProt archiveby: Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, Rolf Apweiler v. 20 i. 17 p. 3236 - 3237
- Bio-Mirror project for public bio-data distributionby: Don Gilbert, Yoshihiro Ugawa, Markus Buchhorn, Tin Wee Tan, Akira Mizushima, Hyun-chul Kim, Kilnam Chon, Seyeon Weon, Juncai Ma, Yoshihiro Ichiyanagi, Der-Ming Liou, Somnuk Keretho, Suhaimi Napis v. 20 i. 17 p. 3238 - 3240
- GOLDsurfer: three dimensional display of linkage disequilibriumby: Fredrik Pettersson, Oskar Jonsson, Lon R. Cardon v. 20 i. 17 p. 3241 - 3243
- lga972: a cross-platform application for optimizing LD studies using a genetic algorithmby: Jaime R. Robles, Edwin J. C. G. van den Oord v. 20 i. 17 p. 3244 - 3245
- Java Treeview - extensible visualization of microarray databy: Alok J. Saldanha v. 20 i. 17 p. 3246 - 3248
- An entity tagger for recognizing acquired genomic variations in cancer literatureby: Ryan T. McDonald, R. Scott Winters, Mark Mandel, Yang Jin, Peter S. White, Fernando C. N. Pereira v. 20 i. 17 p. 3249 - 3251
- Automatic annotation of organellar genomes with DOGMAby: Stacia K. Wyman, Robert K. Jansen, Jeffrey L. Boore v. 20 i. 17 p. 3252 - 3255
- CTRD: a fast applet for computing signed translocation distance between genomesby: WangSen Feng, Lusheng Wang, Daming Zhu v. 20 i. 17 p. 3256 - 3257
- TMRPres2D: high quality visual representation of transmembrane protein modelsby: Ioannis C. Spyropoulos, Theodore Liakopoulos, Pantelis G. Bagos, Stavros J. Hamodrakas v. 20 i. 17 p. 3258 - 3260
- QuickJoin - fast neighbour-joining tree reconstructionby: Thomas Mailund, Christian N. S. Pedersen v. 20 i. 17 p. 3261 - 3262
- SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assaysby: Tianhua Niu, Zhenjun Hu v. 20 i. 17 p. 3263 - 3265
- The CRASSS plug-in for integrating annotation data with hierarchical clustering resultsby: Eugen C. Buehler, Jeffrey R. Sachs, Kui Shao, Ansuman Bagchi, Lyle H. Ungar v. 20 i. 17 p. 3266 - 3269
- BioSilico: an integrated metabolic database systemby: Bo Kyeng Hou, Jin Sik Kim, Ji Hoon Jun, Dong-Yup Lee, Yong Wook Kim, Sujin Chae, Mira Roh, Yong-Ho In, Sang Yup Lee v. 20 i. 17 p. 3270 - 3272
- POINT: a database for the prediction of protein-protein interactions based on the orthologous interactomeby: Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G. Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, Chi-Ying F. Huang v. 20 i. 17 p. 3273 - 3276
- PTGL - a web-based database application for protein topologiesby: Patrick May, Stefan Barthel, Ina Koch v. 20 i. 17 p. 3277 - 3279
- HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markersby: M. Bahlo, Lei Xing, C. R. Wilkinson v. 20 i. 17 p. 3280 - 3283
- A web portal for classification of expression data using maximal margin linear programmingby: Alexey V. Antonov, Igor V. Tetko, Volodymyr V. Prokopenko, Denis Kosykh, Hans-Werner Mewes v. 20 i. 17 p. 3284 - 3285
- Phan3D: design of biological phantoms in 3D electron microscopyby: J. R. Bilbao-Castro, C. O. S. Sorzano, Inmaculada García, José-Jesús Fernández v. 20 i. 17 p. 3286 - 3288
- BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domainsby: Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek v. 20 i. 17 p. 3289 - 3291
- A computational search for box C/D snoRNA genes in the Drosophila melanogaster genomeby: M. C. Accardo, E. Giordano, S. Riccardo, F. A. Digilio, Giovanni Iazzetti, Raffaele Calogero, M. Furia v. 20 i. 18 p. 3293 - 3301
- Preferred in vivo ubiquitination sitesby: André Catic, Cal T. Collins, George M. Church, Hidde L. Ploegh v. 20 i. 18 p. 3302 - 3307
- Accuracy improvement for identifying translation initiation sites in microbial genomesby: Huai-Qiu Zhu, Gang-Qing Hu, Zheng-Qing Ouyang, Jin Wang, Zhen-Su She v. 20 i. 18 p. 3308 - 3317
- Effects of pooling mRNA in microarray class comparisonsby: Joanna H. Shih, Aleksandra M. Michalowska, Kevin Dobbin, Yumei Ye, Ting Hu Qiu, Jeffrey E. Green v. 20 i. 18 p. 3318 - 3325
- MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanksby: Marco Masseroli, Andrea Stella, Natalia Meani, Myriam Alcalay, Francesco Pinciroli v. 20 i. 18 p. 3326 - 3335
- DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteriaby: Yong Wang, Frederick C. C. Leung v. 20 i. 18 p. 3336 - 3345
- Conserved network motifs allow protein-protein interaction predictionby: István Albert, Réka Albert v. 20 i. 18 p. 3346 - 3352
- A graph-theoretic approach to testing associations between disparate sources of functional genomics databy: Raji Balasubramanian, Thomas LaFramboise, Denise Scholtens, Robert Gentleman v. 20 i. 18 p. 3353 - 3362
- Reducing storage requirements for biological sequence comparisonby: Michael Roberts, Wayne Hayes, Brian Hunt, Stephen M. Mount, James Yorke v. 20 i. 18 p. 3363 - 3369
- Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parserby: Daniel McDonald, Hsinchun Chen, Hua Su, Byron Marshall v. 20 i. 18 p. 3370 - 3378
- A software program combining sequence motif searches with keywords for finding repeats containing DNA sequencesby: Mehmet Bilgen, Mehmet Karaca, A. Naci Onus, Ayse Gül Ince v. 20 i. 18 p. 3379 - 3386
- An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolitesby: Vitaly A. Selivanov, Joaquim Puigjaner, Antonio Sillero, Josep J. Centelles, Antonio Ramos-Montoya, Paul W.-N. Lee, Marta Cascante v. 20 i. 18 p. 3387 - 3397
- Mining HIV protease cleavage data using genetic programming with a sum-product functionby: Zheng Rong Yang, Andrew R. Dalby, Jing Qiu v. 20 i. 18 p. 3398 - 3405
- Dimension reduction methods for microarrays with application to censored survival databy: Lexin Li, Hongzhe Li v. 20 i. 18 p. 3406 - 3412
- Analysis of array CGH data: from signal ratio to gain and loss of DNA regionsby: Philippe Hupé, Nicolas Stransky, Jean-Paul Thiery, François Radvanyi, Emmanuel Barillot v. 20 i. 18 p. 3413 - 3422
- Gene selection using a two-level hierarchical Bayesian modelby: Kyounghwa Bae, Bani K. Mallick v. 20 i. 18 p. 3423 - 3430
- Limited agreement among three global gene expression methods highlights the requirement for non-global validationby: Peter M. Haverty, Li-Li Hsiao, Steven R. Gullans, Ulla Hansen, Zhiping Weng v. 20 i. 18 p. 3431 - 3441
- Data exploration tools for the Gene Ontology databaseby: Elizabeth Shoop, Paulo Casaes, Getiria Onsongo, Lisa Lesnett, Erla Osk Petursdottir, Edward Kofi Yeboah Donkor, Dennis Tkach, Michael Cosimini v. 20 i. 18 p. 3442 - 3454
- A probabilistic measure for alignment-free sequence comparisonby: Tuan D. Pham, Johannes Zuegg v. 20 i. 18 p. 3455 - 3461
- ORFcurator: molecular curation of genes and gene clusters in prokaryotic organismsby: Jeffrey A. Rosenfeld, Indra N. Sarkar, Paul J. Planet, David H. Figurski, Rob DeSalle v. 20 i. 18 p. 3462 - 3465
- Systematic analysis of snake neurotoxins' functional classification using a data warehousing approachby: Joyce Phui Yee Siew, Asif M. Khan, Paul T. J. Tan, Judice L. Y. Koh, Seng Hong Seah, Chuay Yeng Koo, Siaw Ching Chai, Arunmozhiarasi Armugam, Vladimir Brusic, Kandiah Jeyaseelan v. 20 i. 18 p. 3466 - 3480
- DIVAA: analysis of amino acid diversity in multiple aligned protein sequencesby: Diane J. Rodi, Suneeta Mandava, Lee Makowski v. 20 i. 18 p. 3481 - 3489
- Predicting GPCR-G-protein coupling using hidden Markov modelsby: Kodangattil R. Sreekumar, You-Ping Huang, Mark H. Pausch, Kamalakar Gulukota v. 20 i. 18 p. 3490 - 3499
- Exploring protein fold space by secondary structure prediction using data distribution method on Grid platformby: Soojin Lee, Min-Kyu Cho, Jin-Won Jung, Jai-Hoon Kim, Weontae Lee v. 20 i. 18 p. 3500 - 3507
- Modeling interactome: scale-free or geometric?by: Natasa Przulj, Derek G. Corneil, Igor Jurisica v. 20 i. 18 p. 3508 - 3515
- Comparative analysis of methods for representing and searching for transcription factor binding sitesby: Robert Osada, Elena Zaslavsky, Mona Singh v. 20 i. 18 p. 3516 - 3525
- Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modelingby: Anton Yuryev, Jianping Huang, Kathryn E. Scott, Jennifer Kuebler, Miriam Donaldson, Michael S. Phillips 0002, Mark Pohl, Michael T. Boyce-Jacino v. 20 i. 18 p. 3526 - 3532
- Accurate detection of aneuploidies in array CGH and gene expression microarray databy: Chad L. Myers, Maitreya J. Dunham, Sun-Yuan Kung, Olga G. Troyanskaya v. 20 i. 18 p. 3533 - 3543
- The 'subsequent artificial neural network' (SANN) approach might bring more classificatory power to ANN-based DNA microarray analysesby: Roland Linder, Dawn Dew, Holger Sudhoff, Dirk Theegarten, Klaus Remberger, Siegfried J. Pöppl, Mathias Wagner II v. 20 i. 18 p. 3544 - 3552
- The Baumgartner-Wei?-Schindler test for the detection of differentially expressed genes in replicated microarray experimentsby: Markus Neuháuser II, Roswitha Senske v. 20 i. 18 p. 3553 - 3564
- Discovery of meaningful associations in genomic data using partial correlation coefficientsby: Alberto de la Fuente, Nan Bing, Ina Hoeschele, Pedro Mendes v. 20 i. 18 p. 3565 - 3574
- Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serumby: Markus Anderle II, Sushmita Roy, Hua Lin, Christopher Becker, Keith Joho v. 20 i. 18 p. 3575 - 3582
- BagBoosting for tumor classification with gene expression databy: Marcel Dettling v. 20 i. 18 p. 3583 - 3593
- Advances to Bayesian network inference for generating causal networks from observational biological databy: Jing Yu, V. Anne Smith, Paul P. Wang, Alexander J. Hartemink, Erich D. Jarvis v. 20 i. 18 p. 3594 - 3603
- Discovering patterns to extract protein-protein interactions from full textsby: Minlie Huang, Xiaoyan Zhu, Yu Hao, Donald G. Payan, Kunbin Qu, Ming Li v. 20 i. 18 p. 3604 - 3612
- Training HMM structure with genetic algorithm for biological sequence analysisby: Kyoung-Jae Won, Adam Prügel-Bennett, Anders Krogh v. 20 i. 18 p. 3613 - 3619
- Highly specific prediction of phosphorylation sites in proteinsby: Matthias Koenig, Niels Grabe v. 20 i. 18 p. 3620 - 3627
- Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprintingby: Jim Samuelsson, Daniel Dalevi, Fredrik Levander, Thorsteinn S. Rögnvaldsson v. 20 i. 18 p. 3628 - 3635
- Breakpoint identification and smoothing of array comparative genomic hybridization databy: Kees Jong, Elena Marchiori, Gerrit Meijer, Aad van der Vaart, Bauke Ylstra v. 20 i. 18 p. 3636 - 3637
- SARGE: a tool for creation of putative genetic networksby: O. J. Shaw, Colin Harwood, L. Jason Steggles, Anil Wipat v. 20 i. 18 p. 3638 - 3640
- Importing MAGE-ML format microarray data into BioConductorby: Steffen Durinck, Joke Allemeersch, Vincent Carey, Yves Moreau, Bart De Moor v. 20 i. 18 p. 3641 - 3642
- DAGchainer: a tool for mining segmental genome duplications and syntenyby: Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven Salzberg v. 20 i. 18 p. 3643 - 3646
- CSB.DB: a comprehensive systems-biology databaseby: Dirk Steinhauser, Björn Usadel, Alexander Lüdemann, Oliver Thimm, Joachim Kopka v. 20 i. 18 p. 3647 - 3651
- PLPMDB: Pyridoxal-5'-phosphate dependent enzymes mutants databaseby: Paolo Di Giovine v. 20 i. 18 p. 3652 - 3653
- VisRD--visual recombination detectionby: Kristoffer Forslund, Daniel H. Huson, Vincent Moulton v. 20 i. 18 p. 3654 - 3655
- DNMAD: web-based diagnosis and normalization for microarray databy: Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte v. 20 i. 18 p. 3656 - 3658
- MedlineR: an open source library in R for Medline literature data miningby: Simon M. Lin, Patrick McConnell, Kimberly F. Johnson, Jennifer Shoemaker v. 20 i. 18 p. 3659 - 3661
- Interactive gene-order comparison for multiple small genomesby: Aaron Kaluszka, Cynthia Gibas v. 20 i. 18 p. 3662 - 3664
- CRH_Server: an online comparative and radiation hybrid mapping server for the canine genomeby: Christophe Hitte, Thomas Derrien, Catherine André, Elaine A. Ostrander, Francis Galibert v. 20 i. 18 p. 3665 - 3667
- EC_oligos: automated and whole-genome primer design for exons within one or between two genomesby: Shaolin Liu, Nicholas A. Tinker, Stephen J. Molnar, Diane E. Mather v. 20 i. 18 p. 3668 - 3669
- GenePicker: replicate analysis of Affymetrix gene expression microarraysby: Giacomo Finocchiaro, Paola Parise, Simone P. Minardi, Myriam Alcalay, Heiko Mueller v. 20 i. 18 p. 3670 - 3672
- SelSim: a program to simulate population genetic data with natural selection and recombinationby: Chris C. A. Spencer, Graham Coop v. 20 i. 18 p. 3673 - 3675
- DNAfan: a software tool for automated extraction and analysis of user-defined sequence regionsby: Andreas Gisel, Maria Panetta, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Cecilia Saccone, Graziano Pesole v. 20 i. 18 p. 3676 - 3679
- The JigCell Model Builder and Run Managerby: Marc Vass, Nicholas Allen, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson v. 20 i. 18 p. 3680 - 3681
- CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence databy: Peter F. Hallin, David Ussery v. 20 i. 18 p. 3682 - 3686
- Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression databy: Nicholas Knowlton, Igor Dozmorov, Michael Centola v. 20 i. 18 p. 3687 - 3690
- GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray databy: Chia-Chin Wu, Hsuan-Cheng Huang, Hsueh-Fen Juan, Shui-Tein Chen v. 20 i. 18 p. 3691 - 3693
- ViTO: tool for refinement of protein sequence-structure alignmentsby: Vincent Catherinot, Gilles Labesse v. 20 i. 18 p. 3694 - 3696
- PCOAT: positional correlation analysis using multiple methodsby: Yuan Qi, Nick V. Grishin v. 20 i. 18 p. 3697 - 3699
- Ontologies for Behaviorby: Peter E. Midford v. 20 i. 18 p. 3700 - 3701
- CLANS: a Java application for visualizing protein families based on pairwise similarityby: Tancred Frickey, Andrei Lupas v. 20 i. 18 p. 3702 - 3704
- limmaGUI: A graphical user interface for linear modeling of microarray databy: James M. Wettenhall, Gordon K. Smyth v. 20 i. 18 p. 3705 - 3706
- NMRb: a web-site repository for raw NMR datasetsby: Jean-Luc Pons, Therese E. Malliavin, D. Tramesel, Marc-André Delsuc v. 20 i. 18 p. 3707 - 3709
- GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genesby: Elizabeth I. Boyle, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, J. Michael Cherry, Gavin Sherlock v. 20 i. 18 p. 3710 - 3715
- A metric model of amino acid substitutionby: Weijia Xu, Daniel P. Miranker v. 20 i. 18 p. 3716 - 3716
- Growth in Bioinformaticsby: Chris Sander v. 19 i. 1 p. 1 - 1
- Wavelets in bioinformatics and computational biology: state of art and perspectivesby: Pietro Lió v. 19 i. 1 p. 2 - 9
- Novel organelle-targeting signals in viral proteinsby: K. V. Krishna Mohan, C. D. Atreya v. 19 i. 1 p. 10 - 13
- Reconstruction of DNA sequencing by hybridizationby: Ji-Hong Zhang, Ling-Yun Wu, Xiang-Sun Zhang v. 19 i. 1 p. 14 - 21
- A divide-and-conquer approach to fragment assemblyby: Hasan H. Otu, Khalid Sayood v. 19 i. 1 p. 22 - 29
- Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing mapsby: João Aires-de-Sousa, Luisa Aires-de-Sousa v. 19 i. 1 p. 30 - 36
- Genetic algorithms applied to multi-class prediction for the analysis of gene expression databy: C. H. Ooi, Patrick Tan v. 19 i. 1 p. 37 - 44
- Evolutionary algorithms for finding optimal gene sets in microarray predictionby: J. M. Deutsch v. 19 i. 1 p. 45 - 52
- Analysis of whole-genome microarray replicates using mixed modelsby: Lorenz Wernisch, Sharon L. Kendall, Shamit Soneji, Andreas Wietzorrek, Tanya Parish, Jason Hinds, Philip D. Butcher, Neil G. Stoker v. 19 i. 1 p. 53 - 61
- Prediction of biologically significant components from microarray data: Independently Consistent Expression Discriminator (ICED)by: Rahul Bijlani, Yinhe Cheng, David A. Pearce, Andrew I. Brooks, Mitsunori Ogihara v. 19 i. 1 p. 62 - 70
- Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patientsby: Jinyan Li, Huiqing Liu, James R. Downing, Allen Eng-Juh Yeoh, Limsoon Wong v. 19 i. 1 p. 71 - 78
- Mining gene expression databases for association rulesby: Chad Creighton, Samir Hanash v. 19 i. 1 p. 79 - 86
- MADGE: scalable distributed data management software for cDNA microarraysby: Richard A. McIndoe, Aaron Lanzen, Kimberly Hurtz v. 19 i. 1 p. 87 - 89
- Gene selection: a Bayesian variable selection approachby: Kyeong Eun Lee, Naijun Sha, Edward R. Dougherty, Marina Vannucci, Bani K. Mallick v. 19 i. 1 p. 90 - 97
- Predicting HIV drug resistance with neural networksby: Sorin Draghici, R. Brian Potter v. 19 i. 1 p. 98 - 107
- Finding the common structure shared by two homologous RNAsby: Olivier Perriquet, Hélène Touzet, Max Dauchet v. 19 i. 1 p. 108 - 116
- Search for structural similarity in proteinsby: Jacek Leluk, Leszek Konieczny, Irena Roterman v. 19 i. 1 p. 117 - 124
- Whole-proteome interaction miningby: Joel R. Bock, David A. Gough v. 19 i. 1 p. 125 - 134
- Protein Structures and Information Extraction from Biological Texts: The PASTA Systemby: Robert J. Gaizauskas, George Demetriou, Peter J. Artymiuk, Peter Willett v. 19 i. 1 p. 135 - 143
- Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populationsby: C. Carleos, F. Rodriguez, H. Lamelas, J. A. Baro v. 19 i. 1 p. 144 - 148
- Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traitsby: S. Purcell, Stacey S. Cherny, P. C. Sham v. 19 i. 1 p. 149 - 150
- MAVG: locating non-overlapping maximum average segments in a given sequenceby: Yaw-Ling Lin, Xiaoqiu Huang, Tao Jiang, Kun-Mao Chao v. 19 i. 1 p. 151 - 152
- An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequencesby: T. De Oliveira, R. Miller, M. Tarin, S. Cassol v. 19 i. 1 p. 153 - 154
- An extensible application for assembling annotation for genomic databy: Jianhua Zhang, Vincent Carey, Robert Gentleman v. 19 i. 1 p. 155 - 156
- Microarray data assemblerby: Ramswamy Anbazhagan v. 19 i. 1 p. 157 - 158
- XdomView: protein domain and exon position visualizationby: Gopalan Vivek, Tin Wee Tan, Shoba Ranganathan v. 19 i. 1 p. 159 - 160
- InterPreTS: protein Interaction Prediction through Tertiary Structureby: Patrick Aloy, Robert B. Russell v. 19 i. 1 p. 161 - 162
- ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Informationby: Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E. Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal v. 19 i. 1 p. 163 - 164
- ModView, visualization of multiple protein sequences and structuresby: Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Linda McMahan, Andrej Sali v. 19 i. 1 p. 165 - 166
- Detection of hydrogen-bond signature patterns in protein familiesby: Tejasvini Prasad, M. N. Prathima, Nagasuma Chandra v. 19 i. 1 p. 167 - 168
- Computational, experimental analysis reveals a novel Src family kinase in the C. elegans genomeby: Akhilesh Pandey, Suraj Peri, Colin Thacker, Chery A. Whipple, John J. Collins, Matthias Mann v. 19 i. 2 p. 169 - 172
- Chemometric Modelling based on 2D-Fluorescence Spectra without a Calibration Measurementby: D. Solle, D. Geissler, E. Stärk, T. Scheper, B. Hitzmann v. 19 i. 2 p. 173 - 177
- A study of accuracy, precision in oligonucleotide arrays: extracting more signal at large concentrationsby: Felix Naef, Nicholas D. Socci, Marcelo Magnasco v. 19 i. 2 p. 178 - 184
- A comparison of normalization methods for high density oligonucleotide array data based on variance and biasby: Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed v. 19 i. 2 p. 185 - 193
- Combinatorial image analysis of DNA microarray featuresby: Chris A. Glasbey, P. Ghazal v. 19 i. 2 p. 194 - 203
- An associative analysis of gene expression array databy: Igor Dozmorov, Michael Centola v. 19 i. 2 p. 204 - 211
- Rank order metrics for quantifying the association of sequence features with gene regulationby: Neil D. Clarke, Joshua A. Granek v. 19 i. 2 p. 212 - 218
- Gene finding with a hidden Markov model of genome structure and evolutionby: Jakob Skou Pedersen, Jotun Hein v. 19 i. 2 p. 219 - 227
- A generalized global alignment algorithmby: Xiaoqiu Huang, Kun-Mao Chao v. 19 i. 2 p. 228 - 233
- A naive Bayes model to predict coupling between seven transmembrane domain receptors, and G-proteinsby: Jack Cao, Rosemarie Panetta, Shiyi Yue, Alain Steyaert, Michele Young-Bellido, Sultan Ahmad v. 19 i. 2 p. 234 - 240
- Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)by: Iwei Yeh, Peter D. Karp, Natalya Fridman Noy, Russ B. Altman v. 19 i. 2 p. 241 - 248
- Positional candidate gene selection from livestock EST databases using Gene Ontologyby: Gregory P. Harhay, John W. Keele v. 19 i. 2 p. 249 - 255
- Fractional populations in multiple gene inheritanceby: Myung-Hoon Chung, Chul Koo Kim, Kyun Nahm v. 19 i. 2 p. 256 - 260
- FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux mapsby: Steffen Klamt, Jörg Stelling, Martin Ginkel, Ernst Dieter Gilles v. 19 i. 2 p. 261 - 269
- Reconstruction of metabolic networks from genome data and analysis of their global structure for various organismsby: Hongwu Ma, An-Ping Zeng v. 19 i. 2 p. 270 - 277
- A task framework for the web interface W2Hby: Peter Ernst, Karl-Heinz Glatting, Sándor Suhai v. 19 i. 2 p. 278 - 282
- QuickLIMS: facilitating the data management for DNA-microarray fabricationby: Felix Kokocinski, Gunnar Wrobel, Meinhard Hahn, Peter Lichter v. 19 i. 2 p. 283 - 284
- An efficient algorithm for minimal primer set selectionby: Ming-Hua Hsieh, Wei-Che Hsu, Sung-Kay Chiu, Chi-Meng Tzeng v. 19 i. 2 p. 285 - 286
- Efficient selective screening of haplotype tag SNPsby: Xiayi Ke, Lon R. Cardon v. 19 i. 2 p. 287 - 288
- Simulating haplotype blocks in the human genomeby: David Posada, Carsten Wiuf v. 19 i. 2 p. 289 - 290
- Pedstrip: extracting a maximal subset of available, unrelated individuals from a pedigreeby: Jeremy M. R. Martin, Lan J. Mackay, Christopher J. Rawlings v. 19 i. 2 p. 291 - 292
- AVA: visual analysis of gene expression microarray databy: Yihua Zhou, Jingdong Liu v. 19 i. 2 p. 293 - 294
- Matrix2png: a utility for visualizing matrix databy: Paul Pavlidis, William Stafford Noble v. 19 i. 2 p. 295 - 296
- SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignmentsby: Lusheng Wang, Ying Xu 0002 v. 19 i. 2 p. 297 - 298
- RnaViz 2: an improved representation of RNA secondary structureby: Peter De Rijk, Jan Wuyts, Rupert De Wachter v. 19 i. 2 p. 299 - 300
- r8s: inferring absolute rates of molecular evolution, divergence times in the absence of a molecular clockby: Michael J. Sanderson v. 19 i. 2 p. 301 - 302
- Chimera: construction of chimeric sequences for phylogenetic analysisby: Jack A. M. Leunissen v. 19 i. 2 p. 303 - 304
- G-language Genome Analysis Environment: a workbench for nucleotide sequence data miningby: Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita v. 19 i. 2 p. 305 - 306
- A profile hidden Markov model for signal peptides generated by HMMERby: Zemin Zhang, William I. Wood v. 19 i. 2 p. 307 - 308
- MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC moleculesby: Kunde Ramamoorthy Govindarajan, Pandjassarame Kangueane, Tin Wee Tan, Shoba Ranganathan v. 19 i. 2 p. 309 - 310
- TopDraw: a sketchpad for protein structure topology cartoonsby: Charles S. Bond v. 19 i. 2 p. 311 - 321
- DPX: for the analysis of the protein coreby: Alessandro Pintar, Oliviero Carugo, Sándor Pongor v. 19 i. 2 p. 313 - 314
- ARIA: automated NOE assignment and NMR structure calculationby: Jens P. Linge, Michael Habeck, Wolfgang Rieping, Michael Nilges v. 19 i. 2 p. 315 - 316
- Visualization and analysis of protein interactionsby: Byong-Hyon Ju, Byungkyu Park, Jong H. Park, Kyungsook Han v. 19 i. 2 p. 317 - 318
- FORRepeats: detects repeats on entire chromosomes and between genomesby: Arnaud Lefebvre, Thierry Lecroq, H. Dauchel, Joël Alexandre v. 19 i. 3 p. 319 - 326
- Towards a computational model for -1 eukaryotic frameshifting sitesby: Michaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset, Michel Termier v. 19 i. 3 p. 327 - 335
- Genetic Network Analyzer: qualitative simulation of genetic regulatory networksby: Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page v. 19 i. 3 p. 336 - 344
- `Hybrid Protein Model' for optimally defining 3D protein structure fragmentsby: Alexandre G. de Brevern, Serge A. Hazout v. 19 i. 3 p. 345 - 353
- Discovering well-ordered folding patterns in nucleotide sequencesby: Shu-Yun Le, Jih-H. Chen, Danielle Konings, Jacob V. Maizel v. 19 i. 3 p. 354 - 361
- LTR_STRUC: a novel search and identification program for LTR retrotransposonsby: Eugene M. McCarthy, John F. McDonald v. 19 i. 3 p. 362 - 367
- Identifying differentially expressed genes using false discovery rate controlling proceduresby: Anat Reiner, Daniel Yekutieli, Yoav Benjamini v. 19 i. 3 p. 368 - 375
- Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactionsby: Lance W. Hahn, Marylyn D. Ritchie, Jason H. Moore v. 19 i. 3 p. 376 - 382
- GenePath: a system for automated construction of genetic networks from mutant databy: Blaz Zupan, Janez Demsar, Ivan Bratko, Peter Juvan, John A. Halter, Adam Kuspa, Gad Shaulsky v. 19 i. 3 p. 383 - 389
- SimiTri-visualizing similarity relationships for groups of sequencesby: John Parkinson, Mark Blaxter v. 19 i. 3 p. 390 - 395
- A literature-based method for assessing the functional coherence of a gene groupby: Soumya Raychaudhuri, Russ B. Altman v. 19 i. 3 p. 396 - 401
- Identification of key concepts in biomedical literature using a modified Markov heuristicby: W. H. Majoros, G. M. Subramanian, M. D. Yandell v. 19 i. 3 p. 402 - 407
- The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networksby: Sudhir Sivakumaran, Sridhar Hariharaputran, Jyoti Mishra, Upinder S. Bhalla v. 19 i. 3 p. 408 - 415
- cMap: the comparative genetic map viewerby: Zhiwei Fang, Mary L. Polacco, S. Chen, Steven G. Schroeder, D. Hancock, Hector Sanchez-Villeda, Edward H. Coe v. 19 i. 3 p. 416 - 417
- IslandPath: aiding detection of genomic islands in prokaryotesby: William Hsiao, Ivan Wan, Steven J. Jones, Fiona S. L. Brinkman v. 19 i. 3 p. 418 - 420
- Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNPby: Gary Barker, Jacqueline Batley, Helen O'Sullivan, Keith J. Edwards, David Edwards v. 19 i. 3 p. 421 - 422
- MELINA: motif extraction from promoter regions of potentially co-regulated genesby: Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai v. 19 i. 3 p. 423 - 424
- AltAVisT: Comparing alternative multiple sequence alignmentsby: Burkhard Morgenstern, Sachin Goel, Alexander Sczyrba, Andreas W. M. Dress v. 19 i. 3 p. 425 - 426
- PCMA: fast and accurate multiple sequence alignment based on profile consistencyby: Jimin Pei, Ruslan Sadreyev, Nick V. Grishin v. 19 i. 3 p. 427 - 428
- PDP: protein domain parserby: Nickolai Alexandrov, Ilya N. Shindyalov v. 19 i. 3 p. 429 - 430
- pathSCOUTTM: exploration and analysis of biochemical pathwaysby: E. Minch, M. de Rinaldis, S. Weiss v. 19 i. 3 p. 431 - 432
- KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray databy: Tetsuro Toyoda, Akihiko Konagaya v. 19 i. 3 p. 433 - 434
- Modeling biological systems using Dynetica-a simulator of dynamic networksby: Lingchong You, Apirak Hoonlor, John Yin v. 19 i. 3 p. 435 - 436
- GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphsby: Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya v. 19 i. 3 p. 437 - 438
- WiGID: wireless genome information databaseby: Björn M. Ursing v. 19 i. 3 p. 439 - 440
- Wrapping up BLAST and other applications for use on Unix clustersby: Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey v. 19 i. 3 p. 441 - 442
- Can transcriptome size be estimated from SAGE catalogs?by: Michael D. Stern, Sergey V. Anisimov, Kenneth R. Boheler v. 19 i. 4 p. 443 - 448
- An information theoretic approach for analyzing temporal patterns of gene expressionby: Jyotsna Kasturi, Raj Acharya, Murali Ramanathan v. 19 i. 4 p. 449 - 458
- Comparisons and validation of statistical clustering techniques for microarray gene expression databy: Susmita Datta, Somnath Datta v. 19 i. 4 p. 459 - 466
- A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcriptionby: Daniel Johansson, Petter Lindgren, Anders Berglund v. 19 i. 4 p. 467 - 473
- Clustering of time-course gene expression data using a mixed-effects model with B-splinesby: Yihui Luan, Hongzhe Li v. 19 i. 4 p. 474 - 482
- Estimating the diversity of peptide populations from limited sequence databy: Lee Makowski, Alexei Soares v. 19 i. 4 p. 483 - 489
- Statistical alignment based on fragment insertion and deletion modelsby: Dirk Metzler v. 19 i. 4 p. 490 - 499
- MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segmentsby: Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio v. 19 i. 4 p. 500 - 505
- Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structuresby: Mounir Errami, Christophe Geourjon, Gilbert Deléage v. 19 i. 4 p. 506 - 512
- Alignment-free sequence comparison-a reviewby: Susana Vinga, Jonas S. Almeida v. 19 i. 4 p. 513 - 523
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsby: Michael Hucka, Andrew Finney, H. M. Sauro, H. Bolouri, John C. Doyle, H. Kitano, Adam P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, I. I. Goryanin, W. J. Hedley, T. Charles Hodgman, J. H. Hofmeyr, P. J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang v. 19 i. 4 p. 524 - 531
- Subnetwork hierarchies of biochemical pathwaysby: Petter Holme, Mikael Huss, Hawoong Jeong v. 19 i. 4 p. 532 - 538
- PopHist: inferring population history from the spectrum of allele frequenciesby: Stephen Wooding v. 19 i. 4 p. 539 - 540
- 3MOTIF: visualizing conserved protein sequence motifs in the protein structure databaseby: Steven P. Bennett, Craig G. Nevill-Manning, Douglas L. Brutlag v. 19 i. 4 p. 541 - 542
- IS: a web-site for intron statisticsby: Endre Barta, László Kaján, Sándor Pongor v. 19 i. 4 p. 543 - 543
- Protein family annotation in a multiple alignment viewerby: Jason M. Johnson, Keith Mason, Ciamac Cyrus Moallemi, Hualin Xi, Shyamal Somaroo, Enoch S. Huang v. 19 i. 4 p. 544 - 545
- The European Bioinformatics Institute web site: a new viewby: Rodrigo Lopez, Stephen Robinson, Asif Kibria, Nicola Harte, Gulam Patel, Rob Harper, Emmanuel Quevillon, Ville Silventoinen, Kimmo Kallio, Petteri Jokinen v. 19 i. 4 p. 546 - 547
- Triplet repeats in human genome: distribution and their association with genes and other genomic regionsby: Subbaya Subramanian, Vamsi M. Madgula, Ranjan George, Rakesh K. Mishra, Madhusudhan W. Pandit, Chanderashekar S. Kumar, Lalji Singh v. 19 i. 5 p. 549 - 552
- Automatic analysis of DNA microarray images using mathematical morphologyby: Jesús Angulo, Jean Serra v. 19 i. 5 p. 553 - 562
- Effective dimension reduction methods for tumor classification using gene expression databy: A. Antoniadis, S. Lambert-Lacroix, F. Leblanc v. 19 i. 5 p. 563 - 570
- PCA disjoint models for multiclass cancer analysis using gene expression databy: Silvio Bicciato, A. Luchini, Carlo Di Bello v. 19 i. 5 p. 571 - 578
- Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genomeby: Gernot G. Presting v. 19 i. 5 p. 579 - 586
- The fuzzy polynucleotide space: basic propertiesby: Angela Torres, Juan J. Nieto v. 19 i. 5 p. 587 - 592
- The Z curve database: a graphic representation of genome sequencesby: Chun-Ting Zhang, Ren Zhang, Hong-Yu Ou v. 19 i. 5 p. 593 - 599
- The estimation of relative site variability among aligned homologous protein sequencesby: David S. Horner, Graziano Pesole v. 19 i. 5 p. 600 - 606
- Greedy mixture learning for multiple motif discovery in biological sequencesby: Konstantinos Blekas, Dimitrios I. Fotiadis, Aristidis Likas v. 19 i. 5 p. 607 - 617
- How Bayes tests of molecular phylogenies compare with frequentist approachesby: Stéphane Aris-Brosou v. 19 i. 5 p. 618 - 624
- MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distanceby: Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin v. 19 i. 5 p. 625 - 634
- Prediction of human protein function according to Gene Ontology categoriesby: Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak v. 19 i. 5 p. 635 - 642
- Dynamic modeling of genetic networks using genetic algorithm and S-systemby: Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita v. 19 i. 5 p. 643 - 650
- TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasetsby: Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush v. 19 i. 5 p. 651 - 652
- DigiNorthern, digital expression analysis of query genes based on ESTsby: Jianxin Wang, Ping Liang v. 19 i. 5 p. 653 - 654
- Gene expression data preprocessingby: Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo v. 19 i. 5 p. 655 - 656
- Engene: the processing and exploratory analysis of gene expression databy: Jorge García de la Nava, Daniel Franco Santaella, Jesús Cuenca Alba, José María Carazo, Oswaldo Trelles, Alberto D. Pascual-Montano v. 19 i. 5 p. 657 - 658
- MatArray: a Matlab toolbox for microarray databy: David Venet v. 19 i. 5 p. 659 - 660
- TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcriptsby: Stefano Toppo, Nicola Cannata, Paolo Fontana, Chiara Romualdi, Paolo Laveder, Emanuela Bertocco, Gerolamo Lanfranchi, Giorgio Valle v. 19 i. 5 p. 661 - 662
- MENDB: a database of polymorphic loci from natural populationsby: K. Livingstone, L. Rieseberg v. 19 i. 5 p. 663 - 664
- MHCBN: a comprehensive database of MHC binding and non-binding peptidesby: Manoj Bhasin, Harpreet Singh, G. P. S. Raghava v. 19 i. 5 p. 665 - 666
- GPCR-GRAPA-LIB-a refined library of hidden Markov Models for annotating GPCRsby: Ron Shigeta, Melissa S. Cline, Guoying Liu, Michael A. Siani-Rose v. 19 i. 5 p. 667 - 668
- PedNavigator: a pedigree drawing servlet for large and inbred populationsby: Gianmaria Mancosu, Giuseppe Ledda, Paola M. Melis v. 19 i. 5 p. 669 - 670
- TreeSAAP: Selection on Amino Acid Properties using phylogenetic treesby: Steve Woolley, Justin Johnson, Matthew J. Smith, Keith A. Crandall, David A. McClellan v. 19 i. 5 p. 671 - 672
- DomCut: prediction of inter-domain linker regions in amino acid sequencesby: Mikita Suyama, Osamu Ohara v. 19 i. 5 p. 673 - 674
- ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic databaseby: Andrew Kossenkov, Frank J. Manion, Eugene Korotkov, Thomas D. Moloshok, Michael F. Ochs v. 19 i. 5 p. 675 - 676
- Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulationsby: Bruce E. Shapiro, Andre Levchenko, Elliot M. Meyerowitz, Barbara J. Wold, Eric Mjolsness v. 19 i. 5 p. 677 - 678
- Open Bioinformaticsby: D. Curtis Jamison v. 19 i. 6 p. 679 - 680
- Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and functionby: Subbaya Subramanian, Rakesh K. Mishra, Lalji Singh v. 19 i. 6 p. 681 - 685
- Directed indices for exploring gene expression databy: Michael LeBlanc, Charles Kooperberg, Thomas M. Grogan, Thomas P. Miller v. 19 i. 6 p. 686 - 693
- Statistical tests for identifying differentially expressed genes in time-course microarray experimentsby: Taesung Park, Sung-Gon Yi, Seungmook Lee, Seung Yeoun Lee, Dong-Hyun Yoo, Jun-Ik Ahn, Yong-Sung Lee v. 19 i. 6 p. 694 - 703
- Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegansby: Atsushi Kajita, Masayuki Yamamura, Yuji Kohara v. 19 i. 6 p. 704 - 716
- Evaluation of annotation strategies using an entire genome sequenceby: Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, Vassilis J. Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros J. Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis v. 19 i. 6 p. 717 - 726
- Automated generation and refinement of protein signatures: case study with G-protein coupled receptorsby: Michael I. Sadowski, John Howard Parish v. 19 i. 6 p. 727 - 734
- Protein structure comparison by probability-based matching of secondary structure elementsby: Edward S. C. Shih, Ming-Jing Hwang v. 19 i. 6 p. 735 - 741
- A segment alignment approach to protein comparisonby: Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik v. 19 i. 6 p. 742 - 749
- Using multiple interdependency to separate functional from phylogenetic correlations in protein alignmentsby: Elisabeth R. M. Tillier, Thomas W. H. Lui v. 19 i. 6 p. 750 - 755
- Construction of reliable protein-protein interaction networks with a new interaction generality measureby: Rintaro Saito, Harukazu Suzuki, Yoshihide Hayashizaki v. 19 i. 6 p. 756 - 763
- Feature selection and transduction for prediction of molecular bioactivity for drug designby: Jason Weston, Fernando Pérez-Cruz, Olivier Bousquet, Olivier Chapelle, André Elisseeff, Bernhard Schölkopf v. 19 i. 6 p. 764 - 771
- Client-Server environment for high-performance gene expression data analysisby: Alexander Sturn, Bernhard Mlecnik, Roland Pieler, Johannes Rainer, Thomas Truskaller, Zlatko Trajanoski v. 19 i. 6 p. 772 - 773
- GAAS: Gene Array Analyzer Software for management, analysis and visualization of gene expression databy: Marco Masseroli, Pietro Cerveri, P. G. Pelicci, Myriam Alcalay v. 19 i. 6 p. 774 - 775
- AFLPinSilico, simulating AFLP fingerprintsby: Stephane Rombauts, Yves Van de Peer, Pierre Rouzé v. 19 i. 6 p. 776 - 777
- PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applicationsby: Kyungjoon Lee, Isaac S. Kohane, Atul J. Butte v. 19 i. 6 p. 778 - 779
- Perfect phylogeny haplotyper: haplotype inferral using a tree modelby: Ren Hua Chung, Dan Gusfield v. 19 i. 6 p. 780 - 781
- Phylogenetic Web Profilerby: Philip Wong, Grigory Kolesov, Dmitrij Frishman, Walid A. Houry v. 19 i. 6 p. 782 - 783
- EPPS: mining the COG database by an extended phylogenetic patterns searchby: Klaus Reichard, Michael Kaufmann v. 19 i. 6 p. 784 - 785
- Java editor for biological pathwaysby: Elmar Trost, Hubert Hackl, Michael Maurer, Zlatko Trajanoski v. 19 i. 6 p. 786 - 787
- GoFish finds genes with combinations of Gene Ontology attributesby: Gabriel F. Berriz, James V. White, Oliver D. King, Frederick P. Roth v. 19 i. 6 p. 788 - 789
- RECSIM and INDSTATS: probabilities of identity in general genealogiesby: Polixeni Dimitropoulou, Chris Cannings v. 19 i. 6 p. 790 - 791
- Interpreting peptide mass spectra by VEMSby: R. Matthiesen, M. Lundsgaard, K. G. Welinder, G. Bauw v. 19 i. 6 p. 792 - 793
- Meta, Metan and Cyber Serversby: Alfonso Valencia v. 19 i. 7 p. 795 - 795
- Selection of Oligonucleotide Probes for Protein Coding Sequencesby: Xiaowei Wang, Brian Seed v. 19 i. 7 p. 796 - 802
- Statistical Design of Reverse Dye Microarraysby: Kevin Dobbin, Joanna H. Shih, Richard Simon v. 19 i. 7 p. 803 - 810
- SamCluster: An Integrated Scheme for Automatic Discovery of Sample Classes Using Gene Expression Profileby: Li Wuju, Ming Fan, Momiao Xiong v. 19 i. 7 p. 811 - 817
- Robust Cluster Analysis of Microarray Gene Expression Data with the Number of Clusters Determined Biologicallyby: David R. Bickel v. 19 i. 7 p. 818 - 824
- Non-linear Normalization and Background Correction in One-channel CDNA Microarray Studiesby: David Edwards v. 19 i. 7 p. 825 - 833
- Gene Selection and Clustering for Time-course and Dose-response Microarray Experiments Using Order-restricted Inferenceby: Shyamal D. Peddada, Edward K. Lobenhofer, Leping Li, Cynthia A. Afshari, Clarice R. Weinberg, David M. Umbach v. 19 i. 7 p. 834 - 841
- Reconstructing the Temporal Ordering of Biological Samples Using Microarray Databy: Paul M. Magwene, Paul Lizardi, Junhyong Kim v. 19 i. 7 p. 842 - 850
- ALES: Cell Lineage Analysis and Mapping of Developmental Eventsby: Volker Braun, Ricardo B. R. Azevedo, Markus Gumbel, Paul-Michael Agapow, Armand M. Leroi, Hans-Peter Meinzer v. 19 i. 7 p. 851 - 858
- MuGeN: Simultaneous Exploration of Multiple Genomes and Computer Analysis Resultsby: Mark Hoebeke, Pierre Nicolas, Philippe Bessières v. 19 i. 7 p. 859 - 864
- A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Predictionby: Sverker Edvardsson, Paul P. Gardner, Anthony M. Poole, Michael D. Hendy, David Penny, Vincent Moulton v. 19 i. 7 p. 865 - 873
- Improvement of the GenTHREADER Method for Genomic Fold Recognitionby: Liam J. McGuffin, David T. Jones v. 19 i. 7 p. 874 - 881
- Towards Optimal Views of Proteinsby: Oscar Sverud, Robert M. MacCallum v. 19 i. 7 p. 882 - 888
- R/qtl: QTL Mapping in Experimental Crossesby: Karl W. Broman, Hao Wu, Saunak Sen, Gary A. Churchill v. 19 i. 7 p. 889 - 890
- GeneMerge - Post-genomic Analysis, Data Mining, and Hypothesis Testingby: Cristian I. Castillo-Davis, Daniel L. Hartl v. 19 i. 7 p. 891 - 892
- MARAN: Normalizing Micro-array Databy: Kristof Engelen, Bert Coessens, Kathleen Marchal, Bart De Moor v. 19 i. 7 p. 893 - 894
- Do Current Sequence Analysis Algorithms Disclose Multifunctional (moonlighting) Proteins?by: Antonio Gómez, Nuria Domedel, Juan Cedano, Jaume Piñol, Enrique Querol v. 19 i. 7 p. 895 - 896
- BioEditor - Simplifying Macromolecular Structure Annotationby: Peng Yang, Paul A. Craig, David Goodsell, Philip E. Bourne v. 19 i. 7 p. 897 - 898
- SCide: Identification of Stabilization Centers in Proteinsby: Zsuzsanna Dosztányi, Csaba Magyar, Gábor E. Tusnády, István Simon v. 19 i. 7 p. 899 - 900
- BioQuery: An Object Framework for Building Queries to Biomedical Databasesby: James M. Brundege, Christopher Dubay v. 19 i. 7 p. 901 - 902
- IPPRED: Server for Proteins Interactions Inferenceby: Nicolas Goffard, Virginie Garcia, Florian Iragne, Alexis Groppi, Antoine de Daruvar v. 19 i. 7 p. 903 - 904
- Inference of Transcriptional Regulation Relationships from Gene Expression Databy: Andrew T. Kwon, Holger H. Hoos, Raymond T. Ng v. 19 i. 8 p. 905 - 912
- FPV: Fast Protein Visualization Using Java 3DTMby: Tolga Can, Yujun Wang, Yuan-Fang Wang, Jianwen Su v. 19 i. 8 p. 913 - 922
- Integrative Approach for Computationally Inferring Protein Domain Interactionsby: See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan v. 19 i. 8 p. 923 - 929
- Pathways Database System: An Integrated System for Biological Pathwaysby: Larkshmi Krishnamurthy, Joseph H. Nadeau, Gultekin Özsoyoglu, Z. Meral Özsoyoglu, Greg Schaeffer, Murat Tasan, Wanhong Xu v. 19 i. 8 p. 930 - 937
- Terminology-driven Mining of Biomedical Literatureby: Goran Nenadic, Irena Spasic, Sophia Ananiadou v. 19 i. 8 p. 938 - 943
- Corrected Small-sample Estimation of the Bayes Errorby: Marcel Brun, David Sabbagh, Seungchan Kim, Edward R. Dougherty v. 19 i. 8 p. 944 - 951
- Computation Method to Identify Differential Allelic Gene Expression and Novel Imprinted Genesby: Howard H. Yang, Ying Hu, Michael Edmonson, Kenneth Buetow, Maxwell P. Lee v. 19 i. 8 p. 952 - 955
- Microarray Standard Data Set and Figures of Merit for Comparing Data Processing Methods and Experiment Designsby: Yudong D. He, Hongyue Dai, Eric E. Schadt, Guy Cavet, Stephen W. Edwards, Sergey B. Stepaniants, Sven Duenwald, Robert Kleinhanz, Allan R. Jones, Daniel D. Shoemaker, Roland B. Stoughton v. 19 i. 8 p. 956 - 965
- Approximate Variance-stabilizing Transformations for Gene-expression Microarray Databy: David M. Rocke, Blythe Durbin v. 19 i. 8 p. 966 - 972
- Fuzzy C-means Method for Clustering Microarray Databy: Doulaye Dembélé, Philippe Kastner v. 19 i. 8 p. 973 - 980
- Mining HIV Dynamics Using Independent Component Analysisby: Sorin Draghici, Frank Graziano, Samira Kettoola, Ishwar K. Sethi, George Towfic v. 19 i. 8 p. 981 - 986
- Codon Pairs in the Genome of Escherichia Coliby: Svetlana Boycheva, Georgi Chkodrov, Ivan Ivanov v. 19 i. 8 p. 987 - 998
- Generating Consensus Sequences from Partial Order Multiple Sequence Alignment Graphsby: Christopher Lee v. 19 i. 8 p. 999 - 1008
- ProPred1: Prediction of Promiscuous MHC Class-I Binding Sitesby: Harpreet Singh, G. P. S. Raghava v. 19 i. 8 p. 1009 - 1014
- 3D-Jury: A Simple Approach to Improve Protein Structure Predictionsby: Krzysztof Ginalski, Arne Elofsson, Daniel Fischer, Leszek Rychlewski v. 19 i. 8 p. 1015 - 1018
- Observing and Interpreting Correlations in Metabolic Networksby: Ralph E. Steuer, Jürgen Kurths, Oliver Fiehn, Wolfram Weckwerth v. 19 i. 8 p. 1019 - 1026
- Hierarchical Analysis of Dependency in Metabolic Networksby: Julien Gagneur, David B. Jackson, Georg Casari v. 19 i. 8 p. 1027 - 1034
- Zerg: A Very Fast BLAST Parser Libraryby: Apuã C. M. Paquola, Abimael A. Machado, Eduardo M. Reis, Aline M. Da Silva, Sergio Verjovski-Almeida v. 19 i. 8 p. 1035 - 1036
- Visual Representation of Database Search Results: The RHIMS Plotby: David M. A. Martin, Pamela Hill, Geoffrey J. Barton, Andrew J. Flavell v. 19 i. 8 p. 1037 - 1038
- ACGT - A Comparative Genomics Toolby: Tao Xie, Leroy E. Hood v. 19 i. 8 p. 1039 - 1040
- Ligand-Info, Searching for Similar Small Compounds Using Index Profilesby: Marcin von Grotthuss, Jakub Pas, Leszek Rychlewski v. 19 i. 8 p. 1041 - 1042
- CAP: Conformation Angles Package - Displaying the Conformation Angles of Side Chains in Proteinsby: S. S. Sheik, Prasanna Sundararajan, V. Shanthi, Krishna Sekar v. 19 i. 8 p. 1043 - 1044
- New Analytical Techniques for the Interpretation of Microarray Databy: Colin Campbell v. 19 i. 9 p. 1045 - 1045
- Modified Nonparametric Approaches to Detecting Differentially Expressed Genes in Replicated Microarray Experimentsby: Yanli Zhao, Wei Pan v. 19 i. 9 p. 1046 - 1054
- Statistical Adjustment of Signal Censoring in Gene Expression Experimentsby: Ernst Wit, John McClure v. 19 i. 9 p. 1055 - 1060
- Boosting for Tumor Classification with Gene Expression Databy: Marcel Dettling, Peter Bühlmann v. 19 i. 9 p. 1061 - 1069
- K-ary Clustering with Optimal Leaf Ordering for Gene Expression Databy: Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi Jaakkola v. 19 i. 9 p. 1070 - 1078
- Coupled Two-way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Databy: Gad Getz, Hilah Gal, Itai Kela, Daniel A. Notterman, Eytan Domany v. 19 i. 9 p. 1079 - 1089
- Bagging to Improve the Accuracy of A Clustering Procedureby: Sandrine Dudoit, Jane Fridlyand v. 19 i. 9 p. 1090 - 1099
- Simultaneous Gene Clustering and Subset Selection for Sample Classification Via MDLby: Rebecka Jörnsten, Bin Yu v. 19 i. 9 p. 1100 - 1109
- Novel Clustering Algorithm for Microarray Expression Data in A Truncated SVD Spaceby: David Horn, Inon Axel v. 19 i. 9 p. 1110 - 1115
- Learning Rule-based Models of Biological Process from Gene Expression Time Profiles Using Gene Ontologyby: Torgeir R. Hvidsten, Astrid Lægreid, Henryk Jan Komorowski v. 19 i. 9 p. 1116 - 1123
- Gene Interaction in DNA Microarray Data Is Decomposed by Information Geometric Measureby: Hiroyuki Nakahara, Shin-ichi Nishimura, Masato Inoue, Gen Hori, Shun-ichi Amari v. 19 i. 9 p. 1124 - 113
- Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Databy: Yoonkyung Lee, Cheol-Koo Lee v. 19 i. 9 p. 1132 - 1139
- eXPatGen: Generating Dynamic Expression Patterns for the Systematic Evaluation of Analytical Methodsby: Dennis J. Michaud, Adam G. Marsh, Prasad S. Dhurjati v. 19 i. 9 p. 1140 - 1146
- A Statistical Problem for Inference to Regulatory Structure from Associations of Gene Expression Measurements with Microarraysby: Tianjiao Chu, Clark Glymour, Richard Scheines, Peter Spirtes v. 19 i. 9 p. 1147 - 1152
- Coupled Two-way Clustering Serverby: Gad Getz, Eytan Domany v. 19 i. 9 p. 1153 - 1154
- RASCAL: Rapid Scanning and Correction of Multiple Sequence Alignmentsby: Julie D. Thompson, Jean-Claude Thierry, Olivier Poch v. 19 i. 9 p. 1155 - 1161
- The Small-world Dynamics of Tree Networks and Data Mining in Phyloinformaticsby: William H. Piel, Michael J. Sanderson, Michael J. Donoghue v. 19 i. 9 p. 1162 - 1168
- Modular Modeling of Cellular Systems with ProMoT/Divaby: Martin Ginkel, Andreas Kremling, Torsten Nutsch, R. Rehner, Ernst Dieter Gilles v. 19 i. 9 p. 1169 - 1176
- Genescript: DNA Sequence Annotation Pipelineby: Alexander K. Hudek, Joseph Cheung, Andrew P. Boright, Stephen W. Scherer v. 19 i. 9 p. 1177 - 1178
- A Survey of the Predictive Toxicology Challenge 2000-2001by: Christoph Helma, Stefan Kramer v. 19 i. 10 p. 1179 - 1182
- Statistical Evaluation of the Predictive Toxicology Challenge 2000-2001by: Hannu Toivonen, Ashwin Srinivasan, Ross D. King, Stefan Kramer, Christoph Helma v. 19 i. 10 p. 1183 - 1193
- Putting the Predictive Toxicology Challenge Into Perspective: Reflections on the Resultsby: Romualdo Benigni, Alessandro Giuliani v. 19 i. 10 p. 1194 - 1200
- Toxicology Analysis by Means of the JSM-methodby: V. G. Blinova, D. A. Dobrynin, V. K. Finn, S. O. Kuznetsov, E. S. Pankratova v. 19 i. 10 p. 1201 - 1207
- Characteristic Substructures and Properties in Chemical Carcinogens Studied by the Cascade Modelby: Takashi Okada v. 19 i. 10 p. 1208 - 1215
- Pyranose Oxidase Identified as A Member of the GMC Oxidoreductase Familyby: Mario Albrecht, Thomas Lengauer v. 19 i. 10 p. 1216 - 1220
- Fast Sequence Clustering Using A Suffix Array Algorithmby: Ketil Malde, Eivind Coward, Inge Jonassen v. 19 i. 10 p. 1221 - 1226
- A Bayesian Network Approach to Operon Predictionby: Joseph Bockhorst, Mark Craven, David Page, Jude W. Shavlik, Jeremy D. Glasner v. 19 i. 10 p. 1227 - 1235
- Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of P-valuesby: Stan Pounds, Stephan W. Morris v. 19 i. 10 p. 1236 - 1242
- A Mathematical Programming Approach for Gene Selection and Tissue Classificationby: Minghe Sun, Momiao Xiong v. 19 i. 10 p. 1243 - 1251
- Graphical Methods for Class Prediction Using Dimension Reduction Techniques on DNA Microarray Databy: Efstathia Bura, Ruth M. Pfeiffer v. 19 i. 10 p. 1252 - 1258
- Unsupervised Feature Selection Via Two-way Ordering in Gene Expression Analysisby: Chris H. Q. Ding v. 19 i. 10 p. 1259 - 1266
- Local Structure Prediction with Local Structure-based Sequence Profilesby: An-Suei Yang, Lu-yong Wang v. 19 i. 10 p. 1267 - 1274
- Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotationby: Phillip W. Lord, Robert D. Stevens, Andy Brass, Carole A. Goble v. 19 i. 10 p. 1275 - 1283
- A Comparison of Parametric Versus Permutation Methods with Applications to General and Temporal Microarray Gene Expression Databy: Ronghui Xu, Xiaochun Li v. 19 i. 10 p. 1284 - 1289
- The DynDom Database of Protein Domain Motionsby: Richard A. Lee, Moe Razaz, Steven Hayward v. 19 i. 10 p. 1290 - 1291
- TableView: Portable Genomic Data Visualizationby: James E. Johnson, Martina V. Stromvik, Kevin A. T. Silverstein, John A. Crow, Elizabeth Shoop, Ernest F. Retzel v. 19 i. 10 p. 1292 - 1293
- Longest Biased Interval and Longest Non-negative Sum Intervalby: Lloyd Allison v. 19 i. 10 p. 1294 - 1295
- GeneComber: Combining Outputs of Gene Prediction Programs for Improved Resultsby: Sohrab P. Shah, Graham P. McVicker, Alan K. Mackworth, Sanja Rogic, B. F. Francis Ouellette v. 19 i. 10 p. 1296 - 1297
- Calculation of Helix Packing Angles in Protein Structuresby: James A. R. Dalton, Ioannis Michalopoulos, David R. Westhead v. 19 i. 10 p. 1298 - 1299
- HaploBlockFinder: Haplotype Block Analysesby: Kun Zhang, Li Jin v. 19 i. 10 p. 1300 - 1301
- A Comparison of Physical Mapping Algorithms Based on the Maximum Likelihood Modelby: Jinling Huang, Suchendra M. Bhandarkar v. 19 i. 11 p. 1303 - 1310
- Design and Assessment of A Fast Algorithm for Identifying Specific Probes for Human and Mouse Genesby: Pei-chin Chang, Konan Peck v. 19 i. 11 p. 1311 - 1317
- ESTprep: Preprocessing CDNA Sequence Readsby: Todd E. Scheetz, Nishank Trivedi, Chad A. Roberts, Tamara Kucaba, Brian Berger, Natalie L. Robinson, Clayton L. Birkett, Allen J. Gavin, Brian O'Leary, Terry A. Braun, Maria F. Bonaldo, John P. Robinson, Val C. Sheffield, Marcelo Bento Soares, Thomas L. Casavant v. 19 i. 11 p. 1318 - 1324
- New Normalization Methods for CDNA Microarray Databy: Dale L. Wilson, Michael J. Buckley, Chris A. Helliwell, I. W. Wilson v. 19 i. 11 p. 1325 - 1332
- On the Use of Permutation in and the Performance of A Class of Nonparametric Methods to Detect Differential Gene Expressionby: Wei Pan v. 19 i. 11 p. 1333 - 1340
- Quantitative Quality Control in Microarray Experiments and the Application in Data Filtering, Normalization and False Positive Rate Predictionby: Xujing Wang, Martin J. Hessner, Yan Wu, Nirupma Pati, Soumitra Ghosh v. 19 i. 11 p. 1341 - 1347
- Noise Sampling Method: An ANOVA Approach Allowing Robust Selection of Differentially Regulated Genes Measured by DNA Microarraysby: Sorin Draghici, Olga Kulaeva, Bruce Hoff, Anton Petrov, Soheil Shams, Michael A. Tainsky v. 19 i. 11 p. 1348 - 1359
- Estimation of Transformation Parameters for Microarray Databy: Blythe Durbin, David M. Rocke v. 19 i. 11 p. 1360 - 1367
- Exact Significance Levels for the Maximum 2 Method of Detecting Recombinationby: Mark Spencer v. 19 i. 11 p. 1368 - 1370
- Computational Analysis of Stop Codon Readthrough in D.melanogasterby: Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita v. 19 i. 11 p. 1371 - 1380
- Identifying Property Based Sequence Motifs in Protein Families and Superfamilies: Application to DNase-1 Related Endonucleasesby: Venkatarajan S. Mathura, Catherine H. Schein, Werner Braun v. 19 i. 11 p. 1381 - 1390
- Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithmby: Hongyu Zhang v. 19 i. 11 p. 1391 - 1396
- Increased Coverage Obtained by Combination of Methods for Protein Sequence Database Searchingby: Caleb Webber, Geoffrey J. Barton v. 19 i. 11 p. 1397 - 1403
- SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Modelsby: Robert C. Edgar, Kimmen Sjölander v. 19 i. 11 p. 1404 - 1411
- GeneTRACE - Reconstruction of Gene Content of Ancestral Speciesby: Victor Kunin, Christos A. Ouzounis v. 19 i. 11 p. 1412 - 1416
- MeKE: Discovering the Functions of Gene Products from Biomedical Literature Via Sentence Alignmentby: Jung-Hsien Chiang, Hsu-Chun Yu v. 19 i. 11 p. 1417 - 1422
- The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networksby: Hong-Wu Ma, An-Ping Zeng v. 19 i. 11 p. 1423 - 1430
- An Adjustable-threshold Algorithm for the Identification of Objects in Three-dimensional Imagesby: Artem L. Ponomarev, Ronald L. Davis v. 19 i. 11 p. 1431 - 1435
- Which Genetic Loci Have Greater Population Assignment Power?by: Michael A. Banks, Will Eichert, Jeffrey B. Olsen v. 19 i. 11 p. 1436 - 1438
- Processing Quantitative Real-time RT-PCR Databy: Perikles Simon Q-Gene v. 19 i. 11 p. 1439 - 1440
- GABI-Kat SimpleSearch: A Flanking Sequence Tag (FST) Database for the Identification of T-DNA Insertion Mutants in Arabidopsis Thalianaby: Yong Li, Mario G. Rosso, Nicolai Strizhov, Prisca Viehoever, Bernd Weisshaar v. 19 i. 11 p. 1441 - 1442
- 2HAPI: A Microarray Data Analysis Systemby: J. Lynn Fink, Scott Drewes, Hiren Patel, John B. Welsh, Daniel R. Masys, Jacques Corbeil, Michael Gribskov v. 19 i. 11 p. 1443 - 1445
- POAVIZ: A Partial Order Multiple Sequence Alignment Visualizerby: Catherine Grasso, Michael Quist, Kevin Ke, Christopher Lee v. 19 i. 11 p. 1446 - 1448
- Genome Visualization Made Fast and Simpleby: René Gibson, Douglas R. Smith v. 19 i. 11 p. 1449 - 1450
- COmplete GENome Tracking (COGENT): A Flexible Data Environment for Computational Genomicsby: Paul Janssen, Anton J. Enright, Benjamin Audit, Ildefonso Cases, Leon Goldovsky, Nicola Harte, Victor Kunin, Christos A. Ouzounis v. 19 i. 11 p. 1451 - 1452
- The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfacesby: T. B. Fischer, K. V. Arunachalam, D. Bailey, V. Mangual, S. Bakhru, R. Russo, D. Huang, M. Paczkowski, V. Lalchandani, C. Ramachandra, B. Ellison, S. Galer, J. Shapley, E. Fuentes, J. Tsai v. 19 i. 11 p. 1453 - 1454
- PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1by: Christian Weinel, Maria D. Ermolaeva, Christos A. Ouzounis v. 19 i. 12 p. 1457 - 1460
- Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNAby: T. Z. DeSantis, I. Dubosarskiy, S. R. Murray, G. L. Andersen v. 19 i. 12 p. 1461 - 1468
- A comparison of statistical methods for analysis of high density oligonucleotide array databy: Dilip Rajagopalan v. 19 i. 12 p. 1469 - 1476
- Differential expression in SAGE: accounting for normal between-library variationby: Keith A. Baggerly, Li Deng, Jeffrey S. Morris, C. Marcelo Aldaz v. 19 i. 12 p. 1477 - 1483
- Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautionsby: Ray L. Somorjai, B. Dolenko, Richard Baumgartner v. 19 i. 12 p. 1484 - 1491
- Serial BLAST searchingby: Ian Korf v. 19 i. 12 p. 1492 - 1496
- Greedy method for inferring tandem duplication historyby: Louxin Zhang, Bin Ma, Lusheng Wang, Ying Xu 0002 v. 19 i. 12 p. 1497 - 1504
- A hidden Markov model for progressive multiple alignmentby: Ari Löytynoja, Michel C. Milinkovitch v. 19 i. 12 p. 1505 - 1513
- Molecular evaluation using in silico protein interaction profilesby: Yoshiharu Hayashi, Katsuyoshi Sakaguchi, Mime Kobayashi, Masaki Kobayashi, Yo Kikuchi, Eiichiro Ichiishi v. 19 i. 12 p. 1514 - 1523
- Identification of functional links between genes using phylogenetic profilesby: Jie Wu, Simon Kasif, Charles DeLisi v. 19 i. 12 p. 1524 - 1530
- Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignmentsby: David Mittelman, Ruslan Sadreyev, Nick V. Grishin v. 19 i. 12 p. 1531 - 1539
- Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformationsby: Bala Krishnamoorthy, Alexander Tropsha v. 19 i. 12 p. 1540 - 1548
- Rapid classification of a protein fold family using a statistical analysis of dipolar couplingsby: Homayoun Valafar, James H. Prestegard v. 19 i. 12 p. 1549 - 1555
- Pandit: a database of protein and associated nucleotide domains with inferred treesby: Simon Whelan, Paul I. W. de Bakker, Nick Goldman v. 19 i. 12 p. 1556 - 1563
- Evaluation of ontology development tools for bioinformaticsby: Patrick Lambrix, Manal Habbouche, Marta Pérez v. 19 i. 12 p. 1564 - 1571
- MrBayes 3: Bayesian phylogenetic inference under mixed modelsby: Fredrik Ronquist, John P. Huelsenbeck v. 19 i. 12 p. 1572 - 1574
- AGenDA: homology-based gene predictionby: Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern v. 19 i. 12 p. 1575 - 1577
- RankGene: identification of diagnostic genes based on expression databy: Yang Su, T. M. Murali, Vladimir Pavlovic, Michael Schaffer, Simon Kasif v. 19 i. 12 p. 1578 - 1579
- UniFrag and GenomePrimer: selection of primers for genome-wide production of unique ampliconsby: Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Jan Kok, Oscar P. Kuipers v. 19 i. 12 p. 1580 - 1582
- GenoMap, a circular genome data viewerby: Naoki Sato, Shigeki Ehira v. 19 i. 12 p. 1583 - 1584
- ClustalW-MPI: ClustalW analysis using distributed and parallel computingby: Kuo-Bin Li v. 19 i. 12 p. 1585 - 1586
- ESTWeb: bioinformatics services for EST sequencing projectsby: Apuã C. M. Paquola, Milton Y. Nishyiama Jr., Eduardo M. Reis, Aline M. Da Silva, Sergio Verjovski-Almeida v. 19 i. 12 p. 1587 - 1588
- PISCES: a protein sequence culling serverby: Guoli Wang, Roland L. Dunbrack Jr. v. 19 i. 12 p. 1589 - 1591
- Digital extractor: analysis of digital differential display outputby: Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen v. 19 i. 12 p. 1592 - 1593
- Digital extractor: analysis of digital differential display outputby: Stephen F. Madden, Barry O'Donovan, Simon J. Furney, Hugh R. Brady, Guenole C. M. Silvestre, Peter P. Doran v. 19 i. 12 p. 1594 - 1595
- A comparative analysis of HGSC and Celera human genome assemblies and gene setsby: Shuyu Li, Gene Cutler, Jane Jijun Liu, Timothy Hoey, Liangbiao Chen, Peter G. Schultz, Jia yu Liao, Xuefeng Bruce Ling v. 19 i. 13 p. 1597 - 1605
- ddbRNA: detection of conserved secondary structures in multiple alignmentsby: Diego di Bernardo, Thomas Down, Tim J. P. Hubbard v. 19 i. 13 p. 1606 - 1611
- Diametrical clustering for identifying anti-correlated gene clustersby: Inderjit S. Dhillon, Edward M. Marcotte, Usman Roshan v. 19 i. 13 p. 1612 - 1619
- The effect of replication on gene expression microarray experimentsby: Paul Pavlidis, Qinghong Li, William Stafford Noble v. 19 i. 13 p. 1620 - 1627
- Statistical significance analysis of longitudinal gene expression databy: Xu Guo, Huilin Qi, Catherine M. Verfaillie, Wei Pan v. 19 i. 13 p. 1628 - 1635
- Comparison of statistical methods for classification of ovarian cancer using mass spectrometry databy: Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn Stone, David Ward, Kenneth Williams, Hongyu Zhao v. 19 i. 13 p. 1636 - 1643
- An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysisby: Jonathan A. Barker, Janet M. Thornton v. 19 i. 13 p. 1644 - 1649
- Secondary structure prediction with support vector machinesby: J. J. Ward, Liam J. McGuffin, Bernard F. Buxton, David T. Jones v. 19 i. 13 p. 1650 - 1655
- Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairsby: Keun-Joon Park, Minoru Kanehisa v. 19 i. 13 p. 1656 - 1663
- PRECIS: Protein reports engineered from concise information in SWISS-PROTby: Alex Mitchell, Jacqueline Renée Reich, Terri K. Attwood v. 19 i. 13 p. 1664 - 1671
- Comparison of sequence masking algorithms and the detection of biased protein sequence regionsby: David P. Kreil, Christos A. Ouzounis v. 19 i. 13 p. 1672 - 1681
- Consensus alignment for reliable framework prediction in homology modelingby: Jahnavi C. Prasad, Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho v. 19 i. 13 p. 1682 - 1691
- PathMiner: predicting metabolic pathways by heuristic searchby: D. C. McShan, S. Rao, Imran Shah v. 19 i. 13 p. 1692 - 1698
- MedScan, a natural language processing engine for MEDLINE abstractsby: Svetlana Novichkova, Sergei Egorov, Nikolai Daraselia v. 19 i. 13 p. 1699 - 1706
- Intergenic sequence inspector: searching and identifying bacterial RNAsby: Christophe Pichon, Brice Felden v. 19 i. 13 p. 1707 - 1709
- Detecting putative orthologsby: D. P. Wall, H. B. Fraser, A. E. Hirsh v. 19 i. 13 p. 1710 - 1711
- GFPE: gene-finding program evaluationby: Jian Wang, Eileen Kraemer v. 19 i. 13 p. 1712 - 1713
- CGH-Plotter: MATLAB toolbox for CGH-data analysisby: Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi v. 19 i. 13 p. 1714 - 1715
- SignalViewer: analyzing microarray imagesby: R. J. Laws, T. L. Bergemann, F. Quiaoit, L. P. Zhao v. 19 i. 13 p. 1716 - 1717
- FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysisby: Robert J. Blick, Andrew T. Revel, Eric J. Hansen v. 19 i. 13 p. 1718 - 1719
- ESTAP-an automated system for the analysis of EST databy: Chunhong Mao, John C. Cushman, Gregory D. May, Jennifer W. Weller v. 19 i. 13 p. 1720 - 1722
- ProSAT: functional annotation of protein 3D structuresby: Razif R. Gabdoulline, René Hoffmann, Florian Leitner, Rebecca C. Wade v. 19 i. 13 p. 1723 - 1725
- CRANN: detecting adaptive evolution in protein-coding DNA sequencesby: C. J. Creevey, James O. McInerney v. 19 i. 13 p. 1726 - 1726
- E-Cell 2: Multi-platform E-Cell simulation systemby: Koichi Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, Fumihiko Miyoshi, Y. Naito, Yoichi Nakayama, Masaru Tomita v. 19 i. 13 p. 1727 - 1729
- Web-based exchange of biochemical informationby: Sinan Güler, Andreas Eberhart, Isabel Rojas v. 19 i. 13 p. 1730 - 1731
- STRING: finding tandem repeats in DNA sequencesby: Valerio Parisi, Valeria De Fonzo, Filippo Aluffi-Pentini v. 19 i. 14 p. 1733 - 1738
- Designing hardware for protein sequence analysisby: Alessandro Marongiu, Paolo Palazzari, Vittorio Rosato v. 19 i. 14 p. 1739 - 1740
- Characterizing proteolytic cleavage site activity using bio-basis function neural networksby: Rebecca Thomson, T. Charles Hodgman, Zheng Rong Yang, Austin K. Doyle v. 19 i. 14 p. 1741 - 1747
- Recognizing the fold of a protein structureby: Andrew Harrison, Frances M. G. Pearl, Ian Sillitoe, Tim Slidel, Richard Mott, Janet M. Thornton, Christine A. Orengo v. 19 i. 14 p. 1748 - 1759
- DDBASE2.0: updated domain database with improved identification of structural domainsby: A. Vinayagam, J. Shi, G. Pugalenthi, B. Meenakshi, Tom L. Blundell, R. Sowdhamini v. 19 i. 14 p. 1760 - 1764
- Examining the independent binding assumption for binding of peptide epitopes to MHC-I moleculesby: Björn Peters, Weiwei Tong, John Sidney, Alessandro Sette, Zhiping Weng v. 19 i. 14 p. 1765 - 1772
- Haplotype inference by maximum parsimonyby: Lusheng Wang, Ying Xu 0002 v. 19 i. 14 p. 1773 - 1780
- Identification and quantification of disease-related gene clustersby: Gábor Firneisz, Idit Zehavi, Csaba Vermes, Anita Hanyecz, Joshua A. Frieman, Tibor T. Glant v. 19 i. 14 p. 1781 - 1786
- CLICK and EXPANDER: a system for clustering and visualizing gene expression databy: Roded Sharan, Adi Maron-Katz, Ron Shamir v. 19 i. 14 p. 1787 - 1799
- New algorithms for multi-class cancer diagnosis using tumor gene expression signaturesby: Adil M. Bagirov, Brent Ferguson, Sasha Ivkovic, G. Saunders, John Yearwood v. 19 i. 14 p. 1800 - 1807
- Transformation and normalization of oligonucleotide microarray databy: Sue C. Geller, Jeff P. Gregg, Paul Hagerman, David M. Rocke v. 19 i. 14 p. 1817 - 1823
- Automatic registration of microarray images. I. Rectangular gridby: Vitaly L. Galinsky v. 19 i. 14 p. 1824 - 1831
- Automatic registration of microarray images. II. Hexagonal gridby: Vitaly L. Galinsky v. 19 i. 14 p. 1832 - 1836
- The design of Jemboss: a graphical user interface to EMBOSSby: Tim Carver, Alan J. Bleasby v. 19 i. 14 p. 1837 - 1843
- An XML message broker framework for exchange and integration of microarray databy: Donny Tjandra, Stephen T. C. Wong, Weimin Shen, Brian Pulliam, Elaine Yu, Laura Esserman v. 19 i. 14 p. 1844 - 1845
- A tool-kit for cDNA microarray and promoter analysisby: N. H. Shah, D. C. King, P. N. Shah, Nina V. Fedoroff v. 19 i. 14 p. 1846 - 1848
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- The UAB Proteomics Databaseby: Aubrey E. Hill, Helen Kim v. 19 i. 16 p. 2149 - 2151
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- Early bioinformatics: the birth of a discipline - a personal viewby: Christos A. Ouzounis, Alfonso Valencia v. 19 i. 17 p. 2176 - 2190
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- A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein functionby: Vidhya Gomathi Krishnan, David R. Westhead v. 19 i. 17 p. 2199 - 2209
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- In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulonby: Ivan Erill, Marcos Escribano, Susana Campoy, Jordi Barbé v. 19 i. 17 p. 2225 - 2236
- Parametric alignment of ordered treesby: Lusheng Wang, Jianyun Zhao v. 19 i. 17 p. 2237 - 2245
- A simple and efficient algorithm for gene selection using sparse logistic regressionby: Shirish Krishnaj Shevade, S. Sathiya Keerthi v. 19 i. 17 p. 2246 - 2253
- Normality of oligonucleotide microarray data and implications for parametric statistical analysesby: Peter J. Giles, David Kipling v. 19 i. 17 p. 2254 - 2262
- Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity predictionby: Irini A. Doytchinova, Darren R. Flower v. 19 i. 17 p. 2263 - 2270
- Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networksby: Dirk Husmeier v. 19 i. 17 p. 2271 - 2282
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- GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genomeby: Jason S. Iacovoni v. 19 i. 17 p. 2316 - 2318
- BioWareDB: the biomedical software and database search engineby: M. W. Matthiessen v. 19 i. 17 p. 2319 - 2320
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- BLAST++: BLASTing queries in batchesby: Hao Wang, Beng Chin Ooi, Kian-Lee Tan, Twee-Hee Ong, Lei Zhou v. 19 i. 17 p. 2323 - 2324
- libsequence: a C++ class library for evolutionary genetic analysisby: Kevin Thornton v. 19 i. 17 p. 2325 - 2327
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- ModLoop: automated modeling of loops in protein structuresby: András Fiser, Andrej Sali v. 19 i. 18 p. 2500 - 2501
- Characterizing gene sets with FuncAssociateby: Gabriel F. Berriz, Oliver D. King, Barbara Bryant, Chris Sander, Frederick P. Roth v. 19 i. 18 p. 2502 - 2504
- The Journal Bioinformatics, key medium for computational biologyby: Chris Sander v. 18 i. 1 p. 1 - 2
- ZTR: a new format for DNA sequence trace databy: James K. Bonfield, Rodger Staden v. 18 i. 1 p. 3 - 10
- A fast top-down method for constructing reliable radiation hybrid frameworksby: Trond H. Bø, Inge Jonassen, Ingvar Eidhammer, Carsten Helgesen v. 18 i. 1 p. 11 - 18
- A Bayesian framework for combining gene predictionsby: Vladimir Pavlovic, Ashutosh Garg, Simon Kasif v. 18 i. 1 p. 19 - 27
- PlantSat: a specialized database for plant satellite repeatsby: Jirí Macas, Tibor Mészáros, Marcela Nouzová v. 18 i. 1 p. 28 - 35
- Calculating the SNP-effective sample size from an alignmentby: Bernhard Haubold, Thomas Wiehe v. 18 i. 1 p. 36 - 38
- Tumor classification by partial least squares using microarray gene expression databy: Danh V. Nguyen, David M. Rocke v. 18 i. 1 p. 39 - 50
- Linear modes of gene expression determined by independent component analysisby: Wolfram Liebermeister v. 18 i. 1 p. 51 - 60
- Extracting transcriptional events from temporal gene expression patterns during Dictyostelium developmentby: R. Sásik, N. Iranfar, Terence Hwa, W. F. Loomis v. 18 i. 1 p. 61 - 66
- Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phaseby: Christian Siehs, Rainer Oberbauer, Gert Mayer, Arno Lukas, Bernd Mayer v. 18 i. 1 p. 67 - 76
- Tolerating some redundancy significantly speeds up clustering of large protein databasesby: Weizhong Li, Lukasz Jaroszewski, Adam Godzik v. 18 i. 1 p. 77 - 82
- Improved database searches for orthologous sequences by conditioning on outgroup sequencesby: Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields v. 18 i. 1 p. 83 - 91
- Automated ortholog inference from phylogenetic trees and calculation of orthology reliabilityby: Christian E. V. Storm, Erik L. L. Sonnhammer v. 18 i. 1 p. 92 - 99
- Integrated gene and species phylogenies from unaligned whole genome protein sequencesby: Gary W. Stuart, Karen Moffett, Steve Baker v. 18 i. 1 p. 100 - 108
- TreeWiz: interactive exploration of huge treesby: Ursula Rost, Erich Bornberg-Bauer v. 18 i. 1 p. 109 - 114
- A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence timesby: Tae-Kun Seo, Jeffrey L. Thorne, Masami Hasegawa, Hirohisa Kishino v. 18 i. 1 p. 115 - 123
- PathFinder: reconstruction and dynamic visualization of metabolic pathwaysby: Alexander Goesmann, Martin Haubrock, Folker Meyer, Jörn Kalinowski, Robert Giegerich v. 18 i. 1 p. 124 - 129
- The Binding Database: data management and interface designby: Xi Chen, Yuhmei Lin, Ming Liu, Michael K. Gilson v. 18 i. 1 p. 130 - 139
- Concept and prototype of protein-ligand docking simulator with force feedback technologyby: Hiroshi Nagata, Hiroshi Mizushima, Hiroshi Tanaka v. 18 i. 1 p. 140 - 146
- Classifying G-protein coupled receptors with support vector machinesby: Rachel Karchin, Kevin Karplus, David Haussler v. 18 i. 1 p. 147 - 159
- Machine learning of functional class from phenotype databy: Amanda Clare, Ross D. King v. 18 i. 1 p. 160 - 166
- Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networksby: Sabine Dietmann, Cornelius Frömmel v. 18 i. 1 p. 167 - 174
- SACS-Self-maintaining database of antibody crystal structure informationby: Lee C. Allcorn, Andrew C. R. Martin v. 18 i. 1 p. 175 - 181
- Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequencesby: Darrell Conklin, Inge Jonassen, Rein Aasland, William R. Taylor v. 18 i. 1 p. 182 - 189
- Physics-based gene identification: proof of concept for Plasmodium falciparumby: Edouard Yeramian, Serge Bonnefoy, Gordon Langsley v. 18 i. 1 p. 190 - 193
- Trev: a DNA trace editor and viewerby: James K. Bonfield, Kathryn F. Beal, Matthew J. Betts, Rodger Staden v. 18 i. 1 p. 194 - 195
- Locating probable genes using Fourier transform approachby: Biju Issac, Harpreet Singh, Harpreet Kaur, G. P. S. Raghava v. 18 i. 1 p. 196 - 197
- Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promotersby: Vladimir B. Bajic, Seng Hong Seah, Allen Chong, Guanglan Zhang, Judice L. Y. Koh, Vladimir Brusic v. 18 i. 1 p. 198 - 199
- LigBase: a database of families of aligned ligand binding sites in known protein sequences and structuresby: Ashley C. Stuart, Valentin A. Ilyin, Andrej Sali v. 18 i. 1 p. 200 - 201
- Using biplots to interpret gene expression patterns in plantsby: Scott Chapman, Peer Schenk, Kemal Kazan, John Manners v. 18 i. 1 p. 202 - 204
- CIT: identification of differentially expressed clusters of genes from microarray databy: Daniel R. Rhodes, Jeremy C. Miller, Brian B. Haab, Kyle A. Furge v. 18 i. 1 p. 205 - 206
- Genesis: cluster analysis of microarray databy: Alexander Sturn, John Quackenbush, Zlatko Trajanoski v. 18 i. 1 p. 207 - 208
- PCSB-a program collection for structural biology and biophysical chemistryby: A. Hofmann, A. Wlodawer v. 18 i. 1 p. 209 - 210
- DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectraby: A. Lobley, Lee Whitmore, B. A. Wallace v. 18 i. 1 p. 211 - 212
- Geno3D: automatic comparative molecular modelling of proteinby: Christophe Combet, Martin Jambon, Gilbert Deléage, Christophe Geourjon v. 18 i. 1 p. 213 - 214
- Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchiaby: D. R. Forsdyke v. 18 i. 1 p. 215 - 217
- Erratum: Evaluation of methods for the prediction of membrane spanning regionsby: Steffen Möller, Michael D. R. Croning, Rolf Apweiler v. 18 i. 1 p. 218 - 218
- Beyond the central dogmaby: Steven Henikoff v. 18 i. 2 p. 223 - 225
- A Bayesian approach to discriminate between alternative DNA sequence segmentationsby: Dirk Husmeier, Frank Wright v. 18 i. 2 p. 226 - 234
- A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosisby: Marc Sebban, I. Mokrousov, N. Rastogi, C. Sola v. 18 i. 2 p. 235 - 243
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- Adjustments and measures of differential expression for microarray databy: A. Tsodikov, A. Szabo, D. Jones v. 18 i. 2 p. 251 - 260
- Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networksby: Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang v. 18 i. 2 p. 261 - 274
- Mixture modelling of gene expression data from microarray experimentsby: Debashis Ghosh, Arul M. Chinnaiyan v. 18 i. 2 p. 275 - 286
- Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modelingby: Hiroyuki Toh, Katsuhisa Horimoto v. 18 i. 2 p. 287 - 297
- Extensive feature detection of N-terminal protein sorting signalsby: Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano v. 18 i. 2 p. 298 - 305
- Predicting reliable regions in protein sequence alignmentsby: Melissa S. Cline, Richard Hughey, Kevin Karplus v. 18 i. 2 p. 306 - 314
- Models@Home: distributed computing in bioinformatics using a screensaver based approachby: Elmar Krieger, Gert Vriend v. 18 i. 2 p. 315 - 318
- A cluster validity framework for genome expression databy: Francisco Azuaje v. 18 i. 2 p. 319 - 320
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- Tclass: tumor classification system based on gene expression profileby: Li Wuju, Momiao Xiong v. 18 i. 2 p. 325 - 326
- CGO: utilizing and integrating gene expression microarray data in clinical research and data managementby: Klaus Bumm, Mingzhong Zheng, Clyde Bailey, Fenghuang Zhan, M. Chiriva-Internati, Paul Eddlemon, Julian Terry, Bart Barlogie, John D. Shaughnessy Jr. v. 18 i. 2 p. 327 - 328
- ISEApeaks: an Excel platform for GeneScan and Immunoscope data retrieval, management and analysisby: A. Collette, A. Six v. 18 i. 2 p. 329 - 330
- INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Samplingby: Gert Thijs, Yves Moreau, Frank De Smet, Janick Mathys, Magali Lescot, Stephane Rombauts, Pierre Rouzé, Bart De Moor, Kathleen Marchal v. 18 i. 2 p. 331 - 332
- PROMO: detection of known transcription regulatory elements using species-tailored searchesby: Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Núñez, Javier Martínez, M. Mar Albà v. 18 i. 2 p. 333 - 334
- GenomePixelizer-a visualization program for comparative genomics within and between speciesby: A. Kozik, E. Kochetkova, R. Michelmore v. 18 i. 2 p. 335 - 336
- Generating samples under a Wright-Fisher neutral model of genetic variationby: Richard R. Hudson v. 18 i. 2 p. 337 - 338
- QTL Express: mapping quantitative trait loci in simple and complex pedigreesby: George Seaton, Chris S. Haley, Sara A. Knott, Mike Kearsey, Peter M. Visscher v. 18 i. 2 p. 339 - 340
- PATRI-paternity inference using genetic databy: J. Signorovitch, R. Nielsen v. 18 i. 2 p. 341 - 342
- Translation initiation start prediction in human cDNAs with high accuracyby: Artemis G. Hatzigeorgiou v. 18 i. 2 p. 343 - 350
- Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniaeby: Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar v. 18 i. 2 p. 351 - 361
- Structure motif discovery and mining the PDBby: Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, William R. Taylor v. 18 i. 2 p. 362 - 367
- The EBI SRS server-recent developmentsby: Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold v. 18 i. 2 p. 368 - 373
- Interactive InterPro-based comparisons of proteins in whole genomesby: Alexander Kanapin, Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Thomas M. Oinn, Isabelle Phan, Florence Servant, Evgeni M. Zdobnov v. 18 i. 2 p. 374 - 375
- Bioinformatics and the theoretical foundations of molecular biologyby: Christos A. Ouzounis v. 18 i. 3 p. 377 - 378
- Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPsby: Martti T. Tammi, Erik Arner, Tom Britton, Björn Andersson v. 18 i. 3 p. 379 - 388
- Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matricesby: Mattias Wahde, Gregory T. Klus, Michael L. Bittner, Yidong Chen, Zoltan Szallasi v. 18 i. 3 p. 389 - 394
- An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkersby: G. Ball, Shahid Mian, F. Holding, R. O. Allibone, J. Lowe, S. Ali, G. Li, S. McCardle, I. O. Ellis, C. Creaser, R. C. Rees v. 18 i. 3 p. 395 - 404
- Analysis of matched mRNA measurements from two different microarray technologiesby: Winston Patrick Kuo, Tor-Kristian Jenssen, Atul J. Butte, Lucila Ohno-Machado, Isaac S. Kohane v. 18 i. 3 p. 405 - 412
- A mixture model-based approach to the clustering of microarray expression databy: Geoffrey J. McLachlan, R. W. Bean, David Peel v. 18 i. 3 p. 413 - 422
- Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysisby: Kurt Fellenberg, Nicole C. Hauser, Benedikt Brors, Jörg D. Hoheisel, Martin Vingron v. 18 i. 3 p. 423 - 433
- JenPep: a database of quantitative functional peptide data for immunologyby: Martin J. Blythe, Irini A. Doytchinova, Darren R. Flower v. 18 i. 3 p. 434 - 439
- PatternHunter: faster and more sensitive homology searchby: Bin Ma, John Tromp, Ming Li v. 18 i. 3 p. 440 - 445
- D-ASSIRC: distributed program for finding sequence similarities in genomesby: Pierre Vincens, Anne Badel-Chagnon, Cécile André, Serge A. Hazout v. 18 i. 3 p. 446 - 451
- Multiple sequence alignment using partial order graphsby: Christopher Lee, Catherine Grasso, Mark F. Sharlow v. 18 i. 3 p. 452 - 464
- The complexity of comparing reaction systemsby: Mark Ettinger v. 18 i. 3 p. 465 - 469
- STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithmby: Andrzej M. Kierzek v. 18 i. 3 p. 470 - 481
- Long-range control of expression in yeastby: Heikki Mannila, Anne Patrikainen, Jouni K. Seppänen, Juha Kere v. 18 i. 3 p. 482 - 483
- Assembly of fingerprint contigs: parallelized FPCby: S. R. Ness, W. Terpstra, Martin Krzywinski, M. A. Marra, S. J. M. Jones v. 18 i. 3 p. 484 - 485
- OligoArray: genome-scale oligonucleotide design for microarraysby: Jean-Marie Rouillard, Christopher J. Herbert, Michael Zuker v. 18 i. 3 p. 486 - 487
- ProbeMatchDB-a web database for finding equivalent probes across microarray platforms and speciesby: Pinglang Wang, Fei Ding, Hsienyuan Chiang, Robert C. Thompson, Stanley J. Watson, Fan Meng v. 18 i. 3 p. 488 - 489
- GeneANOVA-gene expression analysis of varianceby: Gilles Didier, Pierre Brézellec, Elisabeth Remy, Alain Hénaut v. 18 i. 3 p. 490 - 491
- GRIMM: genome rearrangements web serverby: Glenn Tesler v. 18 i. 3 p. 492 - 493
- MaxBench: evaluation of sequence and structure comparison methodsby: Raphael Leplae, Tim J. P. Hubbard v. 18 i. 3 p. 494 - 495
- CASA: a server for the critical assessment of protein sequence alignment accuracyby: Robel Y. Kahsay, Guoli Wang, Nataraj Dongre, Guang R. Gao, Roland L. Dunbrack Jr. v. 18 i. 3 p. 496 - 497
- BetaTPred: prediction of beta-TURNS in a protein using statistical algorithmsby: Harpreet Kaur, G. P. S. Raghava v. 18 i. 3 p. 498 - 499
- DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein familyby: Xun Gu, Kent Vander Velden v. 18 i. 3 p. 500 - 501
- TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computingby: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler v. 18 i. 3 p. 502 - 504
- From Sequence to Biology: The Impact on Bioinformaticsby: Rainer Fuchs v. 18 i. 4 p. 505 - 506
- Compensation for nucleotide bias in a genome by representation as a discrete channel with noiseby: Mark Schreiber, Chris Brown v. 18 i. 4 p. 507 - 512
- Distribution patterns of over-represented k-mers in non-coding yeast DNAby: Steven Hampson, Dennis F. Kibler, Pierre Baldi v. 18 i. 4 p. 513 - 528
- Construction of optimal quality control for oligo arraysby: Charles J. Colbourn, Alan C. H. Ling, Martin Tompa v. 18 i. 4 p. 529 - 535
- Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning treesby: Ying Xu, Victor Olman, Dong Xu v. 18 i. 4 p. 536 - 545
- A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experimentsby: Wei Pan v. 18 i. 4 p. 546 - 554
- Binary analysis and optimization-based normalization of gene expression databy: Ilya Shmulevich, Wei Zhang v. 18 i. 4 p. 555 - 565
- Application of Bayesian Decomposition for analysing microarray databy: Thomas D. Moloshok, R. R. Klevecz, Jeffrey D. Grant, Frank J. Manion, W. F. Speier IV, Michael F. Ochs v. 18 i. 4 p. 566 - 575
- Making sense of microarray data distributionsby: David C. Hoyle, Magnus Rattray, Ray Jupp, Andy Brass v. 18 i. 4 p. 576 - 584
- Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcriptsby: Dov Greenbaum, Ronald Jansen, Mark Gerstein v. 18 i. 4 p. 585 - 596
- TranScout: prediction of gene expression regulatory proteins from their sequencesby: Daniel Aguilar, Baldomero Oliva, Francesc X. Avilés, Enrique Querol v. 18 i. 4 p. 597 - 607
- Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfacesby: Shigeki Mitaku, Takatsugu Hirokawa, Toshiyuki Tsuji v. 18 i. 4 p. 608 - 616
- An HMM model for coiled-coil domains and a comparison with PSSM-based predictionsby: Mauro Delorenzi, Terence P. Speed v. 18 i. 4 p. 617 - 625
- The SWIB and the MDM2 domains are homologous and share a common foldby: Riccardo Bennett-Lovsey, Sarah E. Hart, Hiroki Shirai, Kenji Mizuguchi v. 18 i. 4 p. 626 - 630
- CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequencesby: Loïc Ponger, Dominique Mouchiroud v. 18 i. 4 p. 631 - 633
- TROLL-Tandem Repeat Occurrence Locatorby: Adalberto T. Castelo, Wellington Martins, Guang R. Gao v. 18 i. 4 p. 634 - 636
- Advanced pairwise structure alignments of proteins and analysis of conformational changesby: Maria Elena Ochagavia, Jean Richelle, Shoshana J. Wodak v. 18 i. 4 p. 637 - 640
- DOLOP-database of bacterial lipoproteinsby: M. Madan Babu, K. Sankaran v. 18 i. 4 p. 641 - 643
- Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpertby: Filippo Rusconi, Maya Belghazi v. 18 i. 4 p. 644 - 645
- PATH: a task for the inference of phylogeniesby: Coral del Val, Peter Ernst, Rüdiger Bräuning, Karl-Heinz Glatting, Sándor Suhai v. 18 i. 4 p. 646 - 647
- Information Concept in Biologyby: Ken Nishikawa v. 18 i. 5 p. 649 - 651
- A heuristic managing errors for DNA sequencingby: Jacek Blazewicz, Piotr Formanowicz, Frédéric Guinand, Marta Kasprzak v. 18 i. 5 p. 652 - 660
- PGAAS: a prokaryotic genome assembly assistant systemby: Zhou Yu, Tao Li, Jindong Zhao, Jingchu Luo v. 18 i. 5 p. 661 - 665
- The generation of long telomere overhangs in human cells: a model and its implicationby: Yu-hua Hao, Zheng Tan v. 18 i. 5 p. 666 - 671
- Detecting cryptically simple protein sequences using the SIMPLE algorithmby: M. Mar Albà, Roman A. Laskowski, John M. Hancock v. 18 i. 5 p. 672 - 678
- Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexityby: Olga G. Troyanskaya, Ora Arbell, Yair Koren, Gad M. Landau, Alexander Bolshoy v. 18 i. 5 p. 679 - 688
- Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positionsby: Nela Zavaljevski, Fred J. Stevens, Jaques Reifman v. 18 i. 5 p. 689 - 696
- Characterization of the folding degree of proteinsby: Ernesto Estrada v. 18 i. 5 p. 697 - 704
- Extraction of knowledge on protein-protein interaction by association rule discoveryby: T. Oyama, K. Kitano, Kenji Satou, T. Ito v. 18 i. 5 p. 705 - 714
- Evaluation of computational metabolic-pathway predictions for Helicobacter pyloriby: Suzanne M. Paley, Peter D. Karp v. 18 i. 5 p. 715 - 724
- Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patternsby: Jinyan Li, Limsoon Wong v. 18 i. 5 p. 725 - 734
- Adaptive quality-based clustering of gene expression profilesby: Frank De Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, Yves Moreau v. 18 i. 5 p. 735 - 746
- Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clusteringby: Daniel Bozinov, Jörg Rahnenführer v. 18 i. 5 p. 747 - 756
- Xdigitise: visualization of hybridization experimentsby: Wasco Wruck, Huw Griffiths, Matthias Steinfath, Hans Lehrach, Uwe Radelof, John O'Brien v. 18 i. 5 p. 757 - 760
- Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictionsby: Wei Zhu, Volker Brendel v. 18 i. 5 p. 761 - 762
- EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment databaseby: Vincent Lombard, E. B. Camon, Helen E. Parkinson, Pascal Hingamp, Guenter Stoesser, Nicole Redaschi v. 18 i. 5 p. 763 - 764
- BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf clusterby: Jeffrey D. Grant, Roland L. Dunbrack Jr., Frank J. Manion, Michael F. Ochs v. 18 i. 5 p. 765 - 766
- ENDscript: a workflow to display sequence and structure informationby: Patrice Gouet, Emmanuel Courcelle v. 18 i. 5 p. 767 - 768
- The Sulfinator: predicting tyrosine sulfation sites in protein sequencesby: Flavio Monigatti, Elisabeth Gasteiger, Amos Bairoch, Eva Jung v. 18 i. 5 p. 769 - 770
- GP3: GenePix post-processing program for automated analysis of raw microarray databy: M. R. Fielden, R. G. Halgren, E. Dere, T. R. Zacharewski v. 18 i. 5 p. 771 - 773
- A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesisby: Mary E. Edgerton, Ronald C. Taylor, John I. Powell, Lawrence Hunter, Richard Simon, Edison T. Liu v. 18 i. 5 p. 774 - 775
- Exon discovery by genomic sequence alignmentby: Burkhard Morgenstern, Oliver Rinner, Saïd Abdeddaïm, Dirk Haase, Klaus F. X. Mayer, Andreas W. M. Dress, Hans-Werner Mewes v. 18 i. 6 p. 777 - 787
- A Bayesian network model for protein fold and remote homologue recognitionby: A. Raval, Zoubin Ghahramani, David L. Wild v. 18 i. 6 p. 788 - 801
- Confidence measures for protein fold recognitionby: Ingolf Sommer, Alexander Zien, Niklas von Öhsen, Ralf Zimmer, Thomas Lengauer v. 18 i. 6 p. 802 - 812
- Visualizing metabolic activity on a genome-wide scaleby: A. C. M. Luyf, J. de Gast, Antoine H. C. van Kampen v. 18 i. 6 p. 813 - 818
- NETASA: neural network based prediction of solvent accessibilityby: Shandar Ahmad, M. Michael Gromiha v. 18 i. 6 p. 819 - 824
- Modelling biological processes using workflow and Petri Net modelsby: Mor Peleg, Iwei Yeh, Russ B. Altman v. 18 i. 6 p. 825 - 837
- Adaptive algorithm of automated annotationby: A. M. Leontovich, L. I. Brodsky, V. A. Drachev, V. K. Nikolaev v. 18 i. 6 p. 838 - 844
- A novel approach to local reliability of sequence alignmentsby: Maximilian Schlosshauer, Mattias Ohlsson v. 18 i. 6 p. 847 - 854
- The chemical organization of signaling interactionsby: Upinder S. Bhalla v. 18 i. 6 p. 855 - 863
- Hybrid alignment: high-performance with universal statisticsby: Yi-Kuo Yu, Ralf Bundschuh, Terence Hwa v. 18 i. 6 p. 864 - 872
- SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database sizeby: Eldar Giladi, Michael G. Walker, James Ze Wang, Wayne Volkmuth v. 18 i. 6 p. 873 - 877
- Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic-glycine motifby: Ehud Gazit v. 18 i. 6 p. 880 - 883
- AiO, combining DNA/protein programs and oligo-managementby: Christiaan Karreman v. 18 i. 6 p. 884 - 885
- Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN)by: Matthew J. Gonzales, Jonathan M. Dugan, Robert W. Shafer v. 18 i. 6 p. 886 - 887
- Arrayplot for visualization and normalization of cDNA microarray databy: Philippe Marc, Claude Jacq v. 18 i. 6 p. 888 - 889
- MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markersby: Florian Burckhardt v. 18 i. 6 p. 890 - 891
- BAOBAB: a Java editor for large phylogenetic treesby: J. Dutheil, N. Galtier v. 18 i. 6 p. 892 - 893
- DMLE+: Bayesian linkage disequilibrium gene mappingby: Jeff P. Reeve, Bruce Rannala v. 18 i. 6 p. 894 - 895
- Bioinformatics in structural genomics - Editorialby: Burkhard Rost, Barry Honig, Alfonso Valencia v. 18 i. 7 p. 897 - 897
- Selecting targets for structural determination by navigating in a graph of protein familiesby: Elon Portugaly, Ilona Kifer, Michal Linial v. 18 i. 7 p. 899 - 907
- Clustering of proximal sequence space for the identification of protein familiesby: Federico Abascal, Alfonso Valencia v. 18 i. 7 p. 908 - 921
- Target space for structural genomics revisitedby: Jinfeng Liu, Burkhard Rost v. 18 i. 7 p. 922 - 933
- About the use of protein modelsby: Manuel C. Peitsch v. 18 i. 7 p. 934 - 938
- Ligand-induced changes in the binding sites of proteinsby: Xavier Fradera, Xavier de la Cruz, Carlos H. T. P. Silva, Jose Luis Gelpí, F. Javier Luque, Modesto Orozco v. 18 i. 7 p. 939 - 948
- A bioinformatic strategy to rapidly characterize cDNA librariesby: G. Charles Ostermeier, David J. Dix, Stephen A. Krawetz v. 18 i. 7 p. 949 - 952
- Quantitative assessment of filter-based cDNA microarrays: gene expression profiles of human T-lymphoma cell linesby: J. M. Dodson, P. T. Charles, D. A. Stenger, J. J. Pancrazio v. 18 i. 7 p. 953 - 960
- Deriving quantitative conclusions from microarray expression databy: Adam B. Olshen, Ajay N. Jain v. 18 i. 7 p. 961 - 970
- Comparative genomics study of inverted repeats in bacteriaby: Fabrizio Lillo, Salvatore Basile, Rosario N. Mantegna v. 18 i. 7 p. 971 - 979
- CX, an algorithm that identifies protruding atoms in proteinsby: Alessandro Pintar, Oliviero Carugo, Sándor Pongor v. 18 i. 7 p. 980 - 984
- Calculations of protein volumes: sensitivity analysis and parameter databaseby: Jerry Tsai, Mark Gerstein v. 18 i. 7 p. 985 - 995
- PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathwaysby: Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk v. 18 i. 7 p. 996 - 1003
- Determining a unique defining DNA sequence for yeast species using hashing techniquesby: Jan-Jaap Wesselink, Beatriz de la Iglesia, Stephen A. James, Jo L. Dicks, Ian N. Roberts, Victor J. Rayward-Smith v. 18 i. 7 p. 1004 - 1010
- TangleSolve: topological analysis of site-specific recombinationby: Yuki Saka, Mariel Vázquez v. 18 i. 7 p. 1011 - 1012
- CaGE: Cardiac gene expression knowledgebaseby: Michael Bober, Kevin Wiehe, Christina Yung, Tugba Onal Suzek, Matthew Lin, William Baumgartner Jr., Raimond L. Winslow v. 18 i. 7 p. 1013 - 1014
- CS-PSeq-Gen: Simulating the evolution of protein sequence under constraintsby: Pierre Tufféry v. 18 i. 7 p. 1015 - 1016
- SNAPper: gene order predicts gene functionby: Grigory Kolesov, Hans-Werner Mewes, Dmitrij Frishman v. 18 i. 7 p. 1017 - 1019
- Why are complementary DNA strands symmetric?by: Pierre-François Baisnée, Steven Hampson, Pierre Baldi v. 18 i. 8 p. 1021 - 1033
- Improving gene recognition accuracy by combining predictions from two gene-finding programsby: Sanja Rogic, B. F. Francis Ouellette, Alan K. Mackworth v. 18 i. 8 p. 1034 - 1045
- Computational identification of putative programmed translational frameshift sitesby: Atul A. Shah, Michael C. Giddings, Jasmin B. Parvaz, Raymond F. Gesteland, John F. Atkins, Ivaylo P. Ivanov v. 18 i. 8 p. 1046 - 1053
- Mapping physiological states from microarray expression measurementsby: Gregory Stephanopoulos, Daehee Hwang, William A. Schmitt, Jatin Misra, George Stephanopoulos v. 18 i. 8 p. 1054 - 1063
- A conditional density error model for the statistical analysis of microarray databy: Brad Love, David R. Rank, Sharron G. Penn, David A. Jenkins, Russell S. Thomas v. 18 i. 8 p. 1064 - 1072
- Analysis of expression profile using fuzzy adaptive resonance theoryby: Shuta Tomida, Taizo Hanai, Hiroyuki Honda, Takeshi Kobayashi v. 18 i. 8 p. 1073 - 1083
- Protein motif extraction with neuro-fuzzy optimizationby: Bill C. H. Chang, Saman K. Halgamuge v. 18 i. 8 p. 1084 - 1090
- Probabilistic alignment of motifs with sequencesby: Pedro Gonnet, Frédérique Lisacek v. 18 i. 8 p. 1091 - 1101
- Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matricesby: Nicola Cannata, Stefano Toppo, Chiara Romualdi, Giorgio Valle v. 18 i. 8 p. 1102 - 1108
- Prediction of Golgi Type II membrane proteins based on their transmembrane domainsby: Zheng Yuan, Rohan D. Teasdale v. 18 i. 8 p. 1109 - 1115
- A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene familiesby: Tal Pupko, Itsik Pe'er, Masami Hasegawa, Dan Graur, Nir Friedman v. 18 i. 8 p. 1116 - 1123
- Tagging gene and protein names in biomedical textby: Lorraine K. Tanabe, W. John Wilbur v. 18 i. 8 p. 1124 - 1132
- Neural network predicts sequence of TP53 gene based on DNA chipby: Jeppe S. Spicker, Friedrik Wikman, Ming-Lan Lu, Carlos Cordon-Cardo, Christopher Workman, Torben F. Ørntoft, Søren Brunak, Steen Knudsen v. 18 i. 8 p. 1133 - 1134
- TFBS: Computational framework for transcription factor binding site analysisby: Boris Lenhard, Wyeth W. Wasserman v. 18 i. 8 p. 1135 - 1136
- ShiftDetector: detection of shift mutationsby: Eyal Seroussi, Micha Ron, Darek Kedra v. 18 i. 8 p. 1137 - 1138
- MArray: analysing single, replicated or reversed microarray experimentsby: Junbai Wang, Vigdis Nygaard, Birgitte Smith-Sørensen, Eivind Hovig, Ola Myklebost v. 18 i. 8 p. 1139 - 1140
- Domain Fishing: a first step in protein comparative modellingby: B. Contreras-Moreira, P. A. Bates v. 18 i. 8 p. 1141 - 1142
- DiffTool: building, visualizing and querying protein clustersby: Farid Chetouani, Philippe Glaser, Frank Kunst v. 18 i. 8 p. 1143 - 1144
- The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentationby: Yuh-Jyh Hu v. 18 i. 8 p. 1145 - 1146
- XEMBL: distributing EMBL data in XML formatby: Lichun Wang, Jean-Jack M. Riethoven, Alan J. Robinson v. 18 i. 8 p. 1147 - 1148
- The EBI SRS server-new featuresby: Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold v. 18 i. 8 p. 1149 - 1150
- Genome structures embossed by oligonucleotide-stickinessby: Koichi Nishigaki, Ayumu Saito v. 18 i. 9 p. 1153 - 1161
- Pooled library tissue tags for EST-based gene discoveryby: Allen J. Gavin, Todd E. Scheetz, Chad A. Roberts, Brian O'Leary, Terry A. Braun, Val C. Sheffield, Marcelo Bento Soares, John P. Robinson, Thomas L. Casavant v. 18 i. 9 p. 1162 - 1166
- Identification of regulatory elements using a feature selection methodby: Sündüz Keles, Mark van der Laan, Michael B. Eisen v. 18 i. 9 p. 1167 - 1175
- Geometry of gene expression dynamicsby: S. A. Rifkin, J. Kim v. 18 i. 9 p. 1176 - 1183
- Determination of minimum sample size and discriminatory expression patterns in microarray databy: Daehee Hwang, William A. Schmitt, George Stephanopoulos, Gregory Stephanopoulos v. 18 i. 9 p. 1184 - 1193
- Bayesian infinite mixture model based clustering of gene expression profilesby: Mario Medvedovic, Siva Sivaganesan v. 18 i. 9 p. 1194 - 1206
- Ratio statistics of gene expression levels and applications to microarray data analysisby: Yidong Chen, Vishnu Kamat, Edward R. Dougherty, Michael L. Bittner, Paul S. Meltzer, Jeffrey M. Trent v. 18 i. 9 p. 1207 - 1215
- Multi-class cancer classification via partial least squares with gene expression profilesby: Danh V. Nguyen, David M. Rocke v. 18 i. 9 p. 1216 - 1226
- Optimal enhancement of immune responseby: Robert F. Stengel, Raffaele M. Ghigliazza, Nilesh V. Kulkarni v. 18 i. 9 p. 1227 - 1235
- The correlation error and finite-size correction in an ungapped sequence alignmentby: Yonil Park, John L. Spouge v. 18 i. 9 p. 1236 - 1242
- The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMsby: Sam Griffiths-Jones, Alex Bateman v. 18 i. 9 p. 1243 - 1249
- ESyPred3D: Prediction of proteins 3D structuresby: Christophe G. Lambert, Nadia Léonard, Xavier De Bolle, Eric Depiereux v. 18 i. 9 p. 1250 - 1256
- A dissimilarity matrix between protein atom classes based on Gaussian mixturesby: Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson v. 18 i. 9 p. 1257 - 1263
- VIZARD: analysis of Affymetrix Arabidopsis GeneChi® databy: Nick Moseyko, Lewis J. Feldman v. 18 i. 9 p. 1264 - 1265
- SEGE: A database on 'intron less/single exonic' genes from eukaryotesby: Meena K. Sakharkar, Pandjassarame Kangueane, Dmitri A. Petrov, Ashok S. Kolaskar, S. Subbiah v. 18 i. 9 p. 1266 - 1267
- UniBLAST: a system to filter, cluster, and display BLAST results and assign unique gene annotationby: Yan Zhou, Guyang Matthew Huang, Liping Wei v. 18 i. 9 p. 1268 - 1268
- Parallelized multiple alignmentby: Jens Kleinjung, Nigel Douglas, Jaap Heringa v. 18 i. 9 p. 1270 - 1271
- OrthoGUI: graphical presentation of Orthostrapper resultsby: Volker Hollich, Christian E. V. Storm, Erik L. L. Sonnhammer v. 18 i. 9 p. 1272 - 1273
- A kinase sequence database: sequence alignments and family assignmentby: Oleksandr V. Buzko, Kevan M. Shokat v. 18 i. 9 p. 1274 - 1275
- PeCoP: automatic determination of persistently conserved positions in protein familiesby: Iddo Friedberg, Hanah Margalit v. 18 i. 9 p. 1276 - 1277
- Applications of Tree-Maps to hierarchical biological databy: Patrick McConnell, Kimberly F. Johnson, Simon M. Lin v. 18 i. 9 p. 1278 - 1279
- An ontology driven architecture for derived representations of macromolecular structureby: Douglas S. Greer, John D. Westbrook, Philip E. Bourne v. 18 i. 9 p. 1280 - 1281
- Erratumv. 18 i. 9 p. 1282 - 1282
- Condition specific transcription factor binding site characterization in Saccharomyces cerevisiaeby: Rhonda Harrison, Charles DeLisi v. 18 i. 10 p. 289 - 1296
- An intelligent biological information management systemby: Mathew J. Palakal, Snehasis Mukhopadhyay, Javed Mostafa, Rajeev R. Raje, Mathias N'Cho, Santosh Mishra v. 18 i. 10 p. 1283 - 1288
- Optimal algorithms for local vertex quartet cleaningby: Gianluca Della Vedova, Todd Wareham v. 18 i. 10 p. 1297 - 1304
- Short inversions and conserved gene clusterby: David Sankoff v. 18 i. 10 p. 1305 - 1305
- Comparative ab initio prediction of gene structures using pair HMMsby: Irmtraud M. Meyer, Richard Durbin v. 18 i. 10 p. 1309 - 1318
- ayesian automatic relevance determination algorithms for classifying gene expression databy: Ilya Shmulevich, Edward R. Dougherty, Wei Zhang v. 18 i. 10 p. 1332 - 1339
- Selecting signature oligonucleotides to identify organisms using DNA arraysby: Lars Kaderali, Alexander Schliep v. 18 i. 10 p. 1340 - 1349
- Threading Using Neural nEtwork (TUNE): the measure of protein sequence-structure compatibilityby: Kuang Lin, Alex C. W. May, William R. Taylor v. 18 i. 10 p. 1350 - 1357
- Data mining of sequences and 3D structures of allergenic proteinsby: Ovidiu Ivanciuc, Catherine H. Schein, Werner Braun v. 18 i. 10 p. 1358 - 1364
- Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedureby: B. J. McConkey, Vladimir Sobolev, Marvin Edelman v. 18 i. 10 p. 1365 - 1373
- Finding motifs in the twilight zoneby: Uri Keich, Pavel A. Pevzner v. 18 i. 10 p. 1374 - 1381
- U Subtle motifs: defining the limits of motif finding algorithmsby: Uri Keich, Pavel A. Pevzner v. 18 i. 10 p. 1382 - 1390
- Fold-recognition detects an error in the Protein Data Bankby: Janusz M. Bujnicki, Leszek Rychlewski, Daniel Fischer v. 18 i. 10 p. 1391 - 1395
- GENOTRACE: cDNA-based local GENOme assembly from TRACE archivesby: Eugene Berezikov, Ronald H. A. Plasterk, Edwin Cuppen v. 18 i. 10 p. 1396 - 1397
- Genquire: genome annotation browser/editorby: Mark D. Wilkinson, D. Block, W. L. Crosby v. 18 i. 10 p. 1398 - 1399
- Genexp-a genetic network simulation environmentby: Tra Thi Vu, Jiri Vohradsky v. 18 i. 10 p. 1400 - 1401
- CINEMA-MX: a modular multiple alignment editorby: Phillip W. Lord, J. N. Selley, Terri K. Attwood v. 18 i. 10 p. 1402 - 1403
- GENIE: estimating demographic history from molecular phylogeniesby: O. G. Pybus, Andrew Rambaut v. 18 i. 10 p. 1404 - 1405
- Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns by: Jinyan Li, Limsoon Wong v. 18 i. 10 p. 1406 - 1407
- An open letter to the scientific journalsby: Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald Taylor, Alvis Brazma, John Quackenbush v. 18 i. 11 p. 1409 - 1409
- ARROGANT: an application to manipulate large gene collectionsby: Amit V. Kulkarni, Noelle Sevilir Williams, Yun Lian, Jonathan D. Wren, David Mittelman, Alexander Pertsemlidis, Harold R. Garner v. 18 i. 11 p. 1410 - 1417
- Identification of mixups among DNA sequencing platesby: Nikola Stojanovic, Jean L. Chang, Jessica Lehoczky, Michael C. Zody, Ken Dewar v. 18 i. 11 p. 1418 - 1426
- MethPrimer: designing primers for methylation PCRsby: Long-Cheng Li, Rajvir Dahiya v. 18 i. 11 p. 1427 - 1431
- PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysisby: Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, Ying Xu v. 18 i. 11 p. 1432 - 1437
- Comparison of microarray designs for class comparison and class discoveryby: Kevin Dobbin, Richard Simon v. 18 i. 11 p. 1438 - 1445
- Gene expression data analysis with a dynamically extended self-organized map that exploits class informationby: Seferina Mavroudi, Stergios Papadimitriou, Anastasios Bezerianos v. 18 i. 11 p. 1446 - 1453
- Nonparametric methods for identifying differentially expressed genes in microarray databy: Olga G. Troyanskaya, Mitchell E. Garber, Patrick O. Brown, David Botstein, Russ B. Altman v. 18 i. 11 p. 1454 - 1461
- Methods for assessing reproducibility of clustering patterns observed in analyses of microarray databy: Lisa M. McShane, Michael D. Radmacher, Boris Freidlin, Ren Yu, Ming-Chung Li, Richard Simon v. 18 i. 11 p. 1462 - 1469
- Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arraysby: William J. Lemon, Jeffrey J. T. Palatini, Ralf Krahe, Fred A. Wright v. 18 i. 11 p. 1470 - 1476
- Statistical analysis of a small set of time-ordered gene expression data using linear splinesby: Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano v. 18 i. 11 p. 1477 - 1485
- A duplication growth model of gene expression networksby: Ashish Bhan, David J. Galas, T. Gregory Dewey v. 18 i. 11 p. 1486 - 1493
- A simulated annealing algorithm for finding consensus sequencesby: Jonathan M. Keith, Peter Adams, Darryn E. Bryant, Dirk P. Kroese, Keith R. Mitchelson, Duncan A. E. Cochran, Gita H. Lala v. 18 i. 11 p. 1494 - 1499
- Empirical determination of effective gap penalties for sequence comparisonby: J. T. Reese, William R. Pearson v. 18 i. 11 p. 1500 - 1507
- An evaluation of ß-turn prediction methodsby: Harpreet Kaur, G. P. S. Raghava v. 18 i. 11 p. 1508 - 1514
- Finding relevant references to genes and proteins in Medline using a Bayesian approachby: Julie E. Leonard, Jeffrey B. Colombe, Joshua L. Levy v. 18 i. 11 p. 1515 - 1522
- Euclidian space and grouping of biological objectsby: Vyacheslav N. Grishin, Nick V. Grishin v. 18 i. 11 p. 1523 - 1534
- A motif of a microbial starch-binding domain found in human genethoninby: Stefan Janecek v. 18 i. 11 p. 1534 - 1537
- AcePrimer: automation of PCR primer design based on gene structureby: Sheldon J. McKay, Steven J. M. Jones v. 18 i. 11 p. 1538 - 1539
- SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysisby: Carlo Colantuoni, George Henry, Scott Zeger, Jonathan Pevsner v. 18 i. 11 p. 1540 - 1541
- GeneCardsTM 2002: towards a complete, object-oriented, human gene compendiumby: Marilyn Safran, Irina Solomon, Orit Shmueli, Michal Lapidot, Shai Shen-Orr, Avital Adato, Uri Ben-Dor, Nir Esterman, Naomi Rosen, Inga Peter, Tsviya Olender, Vered Chalifa-Caspi, Doron Lancet v. 18 i. 11 p. 1542 - 1543
- Poxvirus Orthologous Clusters (POCs)by: Angelika Ehlers, John Osborne, Stephanie Slack, Rachel L. Roper, Chris Upton v. 18 i. 11 p. 1544 - 1545
- QuickTree: building huge Neighbour-Joining trees of protein sequencesby: Kevin L. Howe, Alex Bateman, Richard Durbin v. 18 i. 11 p. 1546 - 1547
- Ramachandran plot on the webby: S. S. Sheik, P. Sundararajan, A. S. Z. Hussain, Krishna Sekar v. 18 i. 11 p. 1548 - 1549
- Bioinformatics: Biology by other meansby: Alfonso Valencia v. 18 i. 12 p. 1551 - 1552
- Accomplishments and challenges in literature data mining for biologyby: Lynette Hirschman, Jong C. Park, Jun-ichi Tsujii, Limsoon Wong, Cathy H. Wu v. 18 i. 12 p. 1553 - 1561
- The presence of signal peptide significantly affects transmembrane topology predictionby: Demelo Madrazo Lao, Masafumi Arai, Masami Ikeda, Toshio Shimizu v. 18 i. 12 p. 1562 - 1566
- Computational antisense oligo prediction with a neural network modelby: Alistair M. Chalk, Erik L. L. Sonnhammer v. 18 i. 12 p. 1567 - 1575
- Comparing expression profiles of genes with similar promoter regionsby: Peter J. Park, Atul J. Butte, Isaac S. Kohane v. 18 i. 12 p. 1576 - 1584
- Robust estimators for expression analysisby: Earl Hubbell, Wei-Min Liu, Rui Mei v. 18 i. 12 p. 1585 - 1592
- Analysis of high density expression microarrays with signed-rank call algorithmsby: Wei-Min Liu, Rui Mei, Xiaojun Di, Thomas B. Ryder, Earl Hubbell, S. Dee, Teresa A. Webster, C. A. Harrington, M.-H. Ho, J. Baid, S. P. Smeekens v. 18 i. 12 p. 1593 - 1599
- Between-group analysis of microarray databy: Aedín C. Culhane, Guy Perrière, Elizabeth C. Considine, Thomas G. Cotter, Desmond G. Higgins v. 18 i. 12 p. 1600 - 1608
- Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experimentsby: Michael A. Black, R. W. Doerge v. 18 i. 12 p. 1609 - 1616
- A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancerby: Ann-Marie Martoglio, James W. Miskin, Stephen K. Smith, David J. C. MacKay v. 18 i. 12 p. 1617 - 1624
- Partial least squares proportional hazard regression for application to DNA microarray survival databy: Danh V. Nguyen, David M. Rocke v. 18 i. 12 p. 1625 - 1632
- Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise modelby: R. Sásik, E. Calvo, Jacques Corbeil v. 18 i. 12 p. 1633 - 1640
- Modeling the percolation of annotation errors in a database of protein sequencesby: Walter R. Gilks, Benjamin Audit, Daniela De Angelis, Sophia Tsoka, Christos A. Ouzounis v. 18 i. 12 p. 1641 - 1649
- Local structure-based sequence profile database for local and global protein structure predictionsby: An-Suei Yang, Lu-yong Wang v. 18 i. 12 p. 1650 - 1657
- Structure-dependent sequence alignment for remotely related proteinsby: An-Suei Yang v. 18 i. 12 p. 1658 - 1665
- PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resourcesby: Adrian J. Shepherd, Nigel J. Martin, Roger G. Johnson, Paul Kellam, Christine A. Orengo v. 18 i. 12 p. 1666 - 1672
- A hierarchical approach to aligning collinear regions of genomesby: Mikhail A. Roytberg, Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Alexey S. Kondrashov v. 18 i. 12 p. 1673 - 1680
- SNPper: retrieval and analysis of human SNPsby: Alberto Riva, Isaac S. Kohane v. 18 i. 12 p. 1681 - 1685
- Oligodb-interactive design of oligo DNA for transcription profiling of human genesby: Ralf Mrowka, Johannes Schuchhardt, Christoph Gille v. 18 i. 12 p. 1686 - 1687
- PCR designer for restriction analysis of various types of sequence mutationby: Xiayi Ke, Andrew Collins, Shu Ye v. 18 i. 12 p. 1688 - 1689
- Design of endonuclease restriction sites into primers for PCR cloningby: Jianghui Hou v. 18 i. 12 p. 1690 - 1691
- RED: the analysis, management and dissemination of expressed sequence tagsby: R. Everitt, S. E. Minnema, M. A. Wride, C. S. Koster, J. E. Hance, F. C. Mansergh, D. E. Rancourt v. 18 i. 12 p. 1692 - 1693
- GENECOUNTING: haplotype analysis with missing genotypesby: Jing Hua Zhao, Sebastien Lissarrague, Laurent Essioux, Pak Chung Sham v. 18 i. 12 p. 1694 - 1695
- DNACompress: fast and effective DNA sequence compressionby: Xin Chen, Ming Li, Bin Ma, John Tromp v. 18 i. 12 p. 1696 - 1698
- ADME-AP: a database of ADME associated proteinsby: L. Z. Sun, Z. L. Ji, X. Chen, J. F. Wang, Y. Z. Chen v. 18 i. 12 p. 1699 - 1700
- PoPMuSiC, rationally designing point mutations in protein structuresby: J. M. Kwasigroch, D. Gilis, Y. Dehouck, M. Rooman v. 18 i. 12 p. 1701 - 1702
- OWEN: aligning long collinear regions of genomesby: Aleksey Y. Ogurtsov, Mikhail A. Roytberg, Svetlana A. Shabalina, Alexey S. Kondrashov v. 18 i. 12 p. 1703 - 1704
- The GeneAround GO viewerby: Junko Tanoue, Masatoshi Yoshikawa, Shunsuke Uemura v. 18 i. 12 p. 1705 - 1706
- Bioinformatics - Challenges in 2001by: Chris Sander v. 17 i. 1 p. 1 - 2
- Registration of the expression patterns of Drosophila segmentation genes by two independent methodsby: Ekaterina Myasnikova, Anastassia Samsonova, Konstantin Kozlov, Maria Samsonova, John Reinitz v. 17 i. 1 p. 3 - 12
- Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errorsby: Andrey A. Mironov, Pavel S. Novichkov, Mikhail S. Gelfand v. 17 i. 1 p. 13 - 15
- PAQ: Partition Analysis of Quasispeciesby: Prasith Baccam, Robert J. Thompson, Olivier Fedrigo, Susan Carpenter, James L. Cornette v. 17 i. 1 p. 16 - 22
- Variations on probabilistic suffix trees: statistical modeling and prediction of protein familiesby: Gill Bejerano, Golan Yona v. 17 i. 1 p. 23 - 43
- Functional and structural genomics using PEDANTby: Dmitrij Frishman, Kaj Albermann, Jean Hani, Klaus Heumann, Agnes Metanomski, Alfred Zollner, Hans-Werner Mewes v. 17 i. 1 p. 44 - 57
- Alignment of 3D structures of macromolecular assembliesby: Salvatore Lanzavecchia, Francesca Cantele, Pier Luigi Bellon v. 17 i. 1 p. 58 - 62
- What are the baselines for protein fold recognition?by: Liam J. McGuffin, Kevin Bryson, David T. Jones v. 17 i. 1 p. 63 - 72
- A Web interface generator for molecular biology programs in Unixby: Catherine Letondal v. 17 i. 1 p. 73 - 82
- ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resourcesby: Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral v. 17 i. 1 p. 83 - 94
- Transcription-associated protein families are primarily taxon-specificby: Richard M. R. Coulson, Anton J. Enright, Christos A. Ouzounis v. 17 i. 1 p. 95 - 97
- PrimeArray: genome-scale primer design for DNA-microarray constructionby: Günter Raddatz, Michaela Dehio, Thomas F. Meyer, Christoph Dehio v. 17 i. 1 p. 98 - 99
- The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysisby: William C. Ray, Charles J. Daniels v. 17 i. 1 p. 100 - 104
- EASY-an Expert Analysis SYstem for interpreting database search outputsby: J. N. Selley, J. Swift, Terri K. Attwood v. 17 i. 1 p. 105 - 106
- The Predictive Toxicology Challenge 2000-2001by: Christoph Helma, Ross D. King, Stefan Kramer, Ashwin Srinivasan v. 17 i. 1 p. 107 - 108
- On the Importance of Standardisation in Life Sciencesby: Alvis Brazma v. 17 i. 1 p. 113 - 114
- XML, bioinformatics and data integrationby: Frédéric Achard, Guy Vaysseix, Emmanuel Barillot v. 17 i. 1 p. 115 - 125
- A hierarchical unsupervised growing neural network for clustering gene expression patternsby: Javier Herrero, Alfonso Valencia, Joaquín Dopazo v. 17 i. 1 p. 126 - 136
- The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variationby: Bruce A. Shapiro, Jin Chu Wu, David Bengali, Mark J. Potts v. 17 i. 1 p. 137 - 148
- An information-based sequence distance and its application to whole mitochondrial genome phylogenyby: Ming Li, Jonathan H. Badger, Xin Chen, Sam Kwong, Paul E. Kearney, Haoyong Zhang v. 17 i. 1 p. 149 - 154
- Automated extraction of information on protein-protein interactions from the biological literatureby: Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi v. 17 i. 1 p. 155 - 161
- GeneOrder: comparing the order of genes in small genomesby: Raja Mazumder, Ashok S. Kolaskar, Donald Seto v. 17 i. 1 p. 162 - 166
- ORI-GENE: gene classification based on the evolutionary treeby: Hideaki Mizuno, Yoshimasa Tanaka, Kenta Nakai, Akinori Sarai v. 17 i. 1 p. 167 - 173
- The art of pedigree drawing: algorithmic aspectsby: Frédéric Tores, Emmanuel Barillot v. 17 i. 1 p. 174 - 179
- A classification of tasks in bioinformaticsby: Robert Stevens, Carole A. Goble, Patricia G. Baker, Andy Brass v. 17 i. 1 p. 180 - 188
- Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomesby: Hiromi Nishida v. 17 i. 1 p. 189 - 191
- Virtual PCRby: Matej Lexa, J. Horak, B. Brzobohaty v. 17 i. 1 p. 192 - 193
- Using clusters of computers for large QU-GENE simulation experimentsby: Kevin P. Micallef, Mark Cooper, Dean W. Podlich v. 17 i. 1 p. 194 - 195
- MOSAIC: segmenting multiple aligned DNA sequencesby: Cécile André, Pierre Vincens, Jean-François Boisvieux, Serge A. Hazout v. 17 i. 1 p. 196 - 197
- COMBOSA3D: combining sequence alignments with three-dimensional structuresby: P. M. Stothard v. 17 i. 1 p. 198 - 199
- 3Dee: a database of protein structural domainsby: Asim S. Siddiqui, Uwe Dengler, Geoffrey J. Barton v. 17 i. 1 p. 200 - 201
- RCNPRED: prediction of the residue co-ordination numbers in proteinsby: Piero Fariselli, Rita Casadio v. 17 i. 1 p. 202 - 204
- Physical mapping with automatic capture of hybridization databy: David Hall, Suchendra M. Bhandarkar, Jonathan Arnold, Tongzhang Jiang v. 17 i. 3 p. 205 - 213
- Efficient primer design algorithmsby: Thomas Kämpke, Markus Kieninger, Michael Mecklenburg v. 17 i. 3 p. 214 - 225
- Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequencesby: Siu-wai Leung, Chris Mellish, Dave Robertson v. 17 i. 3 p. 226 - 236
- Flexibility of the genetic code with respect to DNA structureby: Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen v. 17 i. 3 p. 237 - 248
- MetaFam: a unified classification of protein families. I. Overview and statisticsby: Kevin A. T. Silverstein, Elizabeth Shoop, James E. Johnson, Ernest F. Retzel v. 17 i. 3 p. 249 - 261
- MetaFam: a unified classification of protein families. II. Schema and query capabilitiesby: Elizabeth Shoop, Kevin A. T. Silverstein, James E. Johnson, Ernest F. Retzel v. 17 i. 3 p. 262 - 271
- Picasso: generating a covering set of protein family profilesby: Andreas Heger, Liisa Holm v. 17 i. 3 p. 272 - 279
- Genview and Gencode: a pair of programs to test theories of genetic code evolutionby: T. Andrew Ronneberg, Stephen J. Freeland, Laura F. Landweber v. 17 i. 3 p. 280 - 281
- Clustering of highly homologous sequences to reduce the size of large protein databasesby: Weizhong Li, Lukasz Jaroszewski, Adam Godzik v. 17 i. 3 p. 282 - 283
- ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactionsby: Kurt S. Thorn, Andrew A. Bogan v. 17 i. 3 p. 284 - 285
- Dynamic simulation of the human red blood cell metabolic networkby: Neema Jamshidi, Jeremy S. Edwards, Tom Fahland, George M. Church, Bernhard O. Palsson v. 17 i. 3 p. 286 - 287
- MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systemsby: Pedro Mendes, Douglas B. Kell v. 17 i. 3 p. 288 - 289
- Time to defend what we have wonby: David J. States v. 17 i. 4 p. 299 - 299
- A relational schema for both array-based and SAGE gene expression experimentsby: Christian J. Stoeckert Jr., Angel Pizarro, Elisabetta Manduchi, M. Gibson, Brian P. Brunk, Jonathan Crabtree, Jonathan Schug, Shai Shen-Orr, G. Christian Overton v. 17 i. 4 p. 300 - 308
- Validating clustering for gene expression databy: Ka Yee Yeung, David R. Haynor, Walter L. Ruzzo v. 17 i. 4 p. 309 - 318
- Use of keyword hierarchies to interpret gene expression patternsby: Daniel R. Masys, John B. Welsh, J. Lynn Fink, Michael Gribskov, Igor Klacansky, Jacques Corbeil v. 17 i. 4 p. 319 - 326
- A new approach to sequence comparison: normalized sequence alignmentby: Abdullah N. Arslan, Ömer Egecioglu, Pavel A. Pevzner v. 17 i. 4 p. 327 - 337
- Limits of homology detection by pairwise sequence comparisonby: Rainer Spang, Martin Vingron v. 17 i. 4 p. 338 - 342
- NIFAS: visual analysis of domain evolution in proteinsby: Christian E. V. Storm, Erik L. L. Sonnhammer v. 17 i. 4 p. 343 - 348
- Multi-class protein fold recognition using support vector machines and neural networksby: Chris H. Q. Ding, Inna Dubchak v. 17 i. 4 p. 349 - 358
- Mining literature for protein-protein interactionsby: Edward M. Marcotte, Ioannis Xenarios, David Eisenberg v. 17 i. 4 p. 359 - 363
- Strategies for the development of a peptide computerby: Hubert Hug, Rainer Schuler v. 17 i. 4 p. 364 - 368
- J-Express: exploring gene expression data using Javaby: B. Dysvik, Inge Jonassen v. 17 i. 4 p. 369 - 370
- DeFries-Fulker multiple regression analysis of sibship QTL data: a SAS®macroby: J. L. Lessem, Stacey S. Cherny v. 17 i. 4 p. 371 - 372
- Mocca: semi-automatic method for domain huntingby: Cédric Notredame v. 17 i. 4 p. 373 - 374
- PALI: a database of alignments and phylogeny of homologous protein structuresby: S. Sujatha, S. Balaji, Narayanaswamy Srinivasan v. 17 i. 4 p. 375 - 376
- STRAP: editor for STRuctural Alignments of Proteinsby: Christoph Gille, Cornelius Frömmel v. 17 i. 4 p. 377 - 378
- ProDDO: a database of disordered proteins from the Protein Data Bank (PDB)by: Kim Lan Sim, Tomoyuki Uchida, Satoru Miyano v. 17 i. 4 p. 379 - 380
- MutaProt: a web interface for structural analysis of point mutationsby: Eran Eyal, Rafael Najmanovich, Vladimir Sobolev, Marvin Edelman v. 17 i. 4 p. 381 - 382
- ATV: display and manipulation of annotated phylogeneticby: Christian M. Zmasek, Sean R. Eddy v. 17 i. 4 p. 383 - 384
- PhyloBLAST: facilitating phylogenetic analysis of BLAST resultsby: Fiona S. L. Brinkman, Ivan Wan, Robert E. W. Hancock, Ann M. Rose, Steven J. Jones v. 17 i. 4 p. 385 - 387
- Bioinformatics needs to adopt statistical thinking - Editorialby: Martin Vingron v. 17 i. 5 p. 389 - 390
- Comparison of genomic DNA sequences: solved and unsolved problemsby: Webb Miller v. 17 i. 5 p. 391 - 397
- Construction of DNA restriction maps based on a simplified experimentby: Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, M. Jaroszewski, Wojciech T. Markiewicz v. 17 i. 5 p. 398 - 404
- Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clustersby: Alexander V. Lukashin, Rainer Fuchs v. 17 i. 5 p. 405 - 414
- Retrieval and on-the-fly alignment of sequence fragments from the HIV databaseby: Brian Gaschen, Carla Kuiken, Bette Korber, Brian Foley v. 17 i. 5 p. 415 - 418
- Efficient large-scale sequence comparison by locality-sensitive hashingby: Jeremy Buhler v. 17 i. 5 p. 419 - 428
- Analysis of genomic sequences by Chaos Game Representationby: Jonas S. Almeida, João A. Carriço, António Maretzek, Peter A. Noble, Madilyn Fletcher v. 17 i. 5 p. 429 - 437
- Unsupervised classification of noisy chromosomesby: Tony Y. T. Chan v. 17 i. 5 p. 438 - 444
- The utility of different representations of protein sequence for predicting functional classby: Ross D. King, Andreas Karwath, Amanda Clare, Luc Dehaspe v. 17 i. 5 p. 445 - 454
- Predicting protein-protein interactions from primary structureby: Joel R. Bock, David A. Gough v. 17 i. 5 p. 455 - 460
- A graph layout algorithm for drawing metabolic pathwaysby: Moritz Y. Becker, Isabel Rojas v. 17 i. 5 p. 461 - 467
- BioMolQuest: integrated database-based retrieval of protein structural and functional informationby: Yury V. Bukhman, Jeffrey Skolnick v. 17 i. 5 p. 468 - 478
- MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gapsby: Gráinne McGuire, Michael C. Denham, David J. Balding v. 17 i. 5 p. 479 - 480
- Cladogramer: incorporating haplotype frequency into cladogram analysisby: Louxin Zhang, Chew-Kiat Heng, Tin Wee Tan v. 17 i. 5 p. 481 - 482
- A-Cell: graphical user interface for the construction of biochemical reaction modelsby: Kazuhisa Ichikawa v. 17 i. 5 p. 483 - 484
- ExScript: An `EX'-Centric Approach to the Description of Transcript Diversityby: Win Hide v. 17 i. 6 p. 485 - 486
- Uniform integration of genome mapping data using intersection graphsby: Eric Harley, Anthony J. Bonner, Nathan Goodman v. 17 i. 6 p. 487 - 494
- Aligning gene expression time series with time warping algorithmsby: John Aach, George M. Church v. 17 i. 6 p. 495 - 508
- A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changesby: Pierre Baldi, Anthony D. Long v. 17 i. 6 p. 509 - 519
- Missing value estimation methods for DNA microarraysby: Olga G. Troyanskaya, Michael Cantor, Gavin Sherlock, Pat Brown, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman v. 17 i. 6 p. 520 - 525
- Database verification studies of SWISS-PROT and GenBankby: Peter D. Karp, Suzanne M. Paley, Jingchun Zhu v. 17 i. 6 p. 526 - 532
- Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et alby: Rolf Apweiler, Paul Kersey, Vivien Junker, Amos Bairoch v. 17 i. 6 p. 533 - 534
- TreeGeneBrowser: phylogenetic data mining of gene sequences from public databasesby: Ingrid B. Jakobsen, Jennifer A. Saleeba, Michael Poidinger, Timothy G. Littlejohn v. 17 i. 6 p. 535 - 540
- SCORE: predicting the core of protein modelsby: Charlotte M. Deane, Quentin Kaas, Tom L. Blundell v. 17 i. 6 p. 541 - 550
- Prediction of quaternary structure from primary structureby: Robert Garian v. 17 i. 6 p. 551 - 556
- Compositional symmetries in complete genomesby: Dong Qi, A. Jamie Cuticchia v. 17 i. 6 p. 557 - 559
- Identification of novel families of membrane proteins from the model plant Arabidopsis thalianaby: John M. Ward v. 17 i. 6 p. 560 - 563
- MAPS: a microarray project system for gene expression experiment information and data validationby: Pierre R. Bushel, Hisham Hamadeh, Lee Bennett, Stella Sieber, Karla Martin, Emile F. Nuwaysir, Kate Johnson, Kelli Reynolds, Richard S. Paules, Cynthia A. Afshari v. 17 i. 6 p. 564 - 565
- SVDMAN-singular value decomposition analysis of microarray databy: Michael E. Wall, Patricia A. Dyck, Thomas S. Brettin v. 17 i. 6 p. 566 - 568
- AMADA: analysis of microarray databy: Xuhua Xia, Zheng Xie v. 17 i. 6 p. 569 - 570
- The HIB database of annotated UniGene clustersby: Birgitta Geier, Gabi Kastenmüller, Matthias Fellenberg, Hans-Werner Mewes, Burkhard Morgenstern v. 17 i. 6 p. 571 - 572
- SOAP, cleaning multiple alignments from unstable blocksby: Ari Löytynoja, Michel C. Milinkovitch v. 17 i. 6 p. 573 - 574
- STOCHSIM: modelling of stochastic biomolecular processesby: Nicolas Le Novère, Thomas Simon Shimizu v. 17 i. 6 p. 575 - 576
- SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics servicesby: Malay Kumar Basu v. 17 i. 6 p. 577 - 578
- Reading the book of lifeby: David B. Searls v. 17 i. 7 p. 579 - 580
- LDB2000: sequence-based integrated maps of the human genomeby: Xiayi Ke, William Tapper, Andrew Collins v. 17 i. 7 p. 581 - 586
- Extending traditional query-based integration approaches for functional characterization of post-genomic databy: Barbara A. Eckman, Anthony Kosky, Leonardo A. Laroco Jr. v. 17 i. 7 p. 587 - 601
- Identifying the 3'-terminal exon in human DNAby: Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang v. 17 i. 7 p. 602 - 607
- Identifying target sites for cooperatively binding factorsby: Debraj Guha Thakurta, Gary D. Stormo v. 17 i. 7 p. 608 - 621
- Conformational model for binding site recognition by the E.coli MetJ transcription factorby: Rongxiang Liu, Thomas W. Blackwell, David J. States v. 17 i. 7 p. 622 - 633
- Automated image analysis for array hybridization experimentsby: Matthias Steinfath, Wasco Wruck, Henrik Seidel, Hans Lehrach, Uwe Radelof, John O'Brien v. 17 i. 7 p. 634 - 641
- Semi-automated update and cleanup of structural RNA alignment databasesby: Jan Gorodkin, Christian Zwieb, Bjarne Knudsen v. 17 i. 7 p. 642 - 645
- Evaluation of methods for the prediction of membrane spanning regionsby: Steffen Möller, Michael D. R. Croning, Rolf Apweiler v. 17 i. 7 p. 646 - 653
- An integrated system for high throughput TaqManTM based SNP genotypingby: Jochen Hampe, Andreas Wollstein, Timothy Lu, Hans-Jürgen Frevel, Marcus Will, Carl Manaster, Stefan Schreiber v. 17 i. 7 p. 654 - 655
- MEDUSA: large scale automatic selection and visual assessment of PCR primer pairsby: Raf M. Podowski, Erik L. L. Sonnhammer v. 17 i. 7 p. 656 - 657
- Visualization of expression clusters using Sammon's non-linear mappingby: Rob M. Ewing, J. Michael Cherry v. 17 i. 7 p. 658 - 659
- ADAPTSITE: detecting natural selection at single amino acid sitesby: Yoshiyuki Suzuki, Takashi Gojobori, Masatoshi Nei v. 17 i. 7 p. 660 - 661
- PAL: an object-oriented programming library for molecular evolution and phylogeneticsby: Alexei Drummond, Korbinian Strimmer v. 17 i. 7 p. 662 - 663
- T-REX: reconstructing and visualizing phylogenetic trees and reticulation networksby: Vladimir Makarenkov v. 17 i. 7 p. 664 - 668
- A Java applet for visualizing protein-protein interactionby: Ralf Mrowka v. 17 i. 7 p. 669 - 671
- Generation of a database containing discordant intron positions in eukaryotic genes (MIDB)by: Meena K. Sakharkar, Tin Wee Tan, Sandro J. de Souza v. 17 i. 8 p. 671 - 675
- Representation of amino acids as five-bit or three-bit patterns for filtering protein databasesby: Avril Coghlan, Dónall A. Mac Dónaill, Nigel H. Buttimore v. 17 i. 8 p. 676 - 685
- Amino acid similarity matrices based on force fieldsby: Zsuzsanna Dosztányi, Andrew E. Torda v. 17 i. 8 p. 686 - 699
- AL2CO: calculation of positional conservation in a protein sequence alignmentby: Jimin Pei, Nick V. Grishin v. 17 i. 8 p. 700 - 712
- Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test setby: Kevin Karplus, Birong Hu v. 17 i. 8 p. 713 - 720
- Support vector machine approach for protein subcellular localization predictionby: Sujun Hua, Zhirong Sun v. 17 i. 8 p. 721 - 728
- The Bioinformatics Template Library-generic components for biocomputingby: W. R. Pitt, M. A. Williams, M. Steven, B. Sweeney, Alan J. Bleasby, David S. Moss v. 17 i. 8 p. 729 - 737
- Genotype transposer: automated genotype manipulation for linkage disequilibrium analysisby: David G. Cox, Federico Canzian v. 17 i. 8 p. 738 - 739
- Polylink: to support two-point linkage analysis in autotetraploidsby: Yang He, Xiangming Xu, Kenneth R. Tobutt, Martin S. Ridout v. 17 i. 8 p. 740 - 741
- GRR: graphical representation of relationship errorsby: Gonçalo R. Abecasis, Stacey S. Cherny, W. O. C. Cookson, Lon R. Cardon v. 17 i. 8 p. 742 - 743
- Multi-query sequence BLAST output examination with MuSeqBoxby: Liqun Xing, Volker Brendel v. 17 i. 8 p. 744 - 745
- DBAli: a database of protein structure alignmentsby: Marc A. Martí-Renom, Valentin A. Ilyin, Andrej Sali v. 17 i. 8 p. 746 - 747
- HOMSTRAD: adding sequence information to structure-based alignments of homologous protein familiesby: Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, J. Shi, Hiroki Shirai, Tom L. Blundell v. 17 i. 8 p. 748 - 749
- Structure prediction meta serverby: Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski v. 17 i. 8 p. 750 - 751
- Easier threading through web-based comparisons and cross-validationsby: Dominique Douguet, Gilles Labesse v. 17 i. 8 p. 752 - 753
- MRBAYES: Bayesian inference of phylogenetic treesby: John P. Huelsenbeck, Fredrik Ronquist v. 17 i. 8 p. 754 - 755
- SIR: a simple indexing and retrieval system for biological flat file databasesby: Chenna Ramu v. 17 i. 8 p. 756 - 758
- Training for bioinformatics and computational biologyby: William R. Pearson v. 17 i. 9 p. 761 - 762
- Principal component analysis for clustering gene expression databy: Ka Yee Yeung, Walter L. Ruzzo v. 17 i. 9 p. 763 - 774
- A non-parametric approach to translating gene region heterogeneity associated with phenotype into location heterogeneityby: Jeanne Kowalski v. 17 i. 9 p. 775 - 790
- Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomesby: Katsuhisa Horimoto, Satoshi Fukuchi, Kentaro Mori v. 17 i. 9 p. 791 - 802
- Evolutionary HMMs: a Bayesian approach to multiple alignmentby: Ian Holmes, William J. Bruno v. 17 i. 9 p. 803 - 820
- A simple algorithm to infer gene duplication and speciation events on a gene treeby: Christian M. Zmasek, Sean R. Eddy v. 17 i. 9 p. 821 - 828
- Knowledge representation of signal transduction pathwaysby: Ken-ichiro Fukuda, Toshihisa Takagi v. 17 i. 9 p. 829 - 837
- PIRA PCR designer for restriction analysis of single nucleotide polymorphismsby: Xiayi Ke, Andrew Collins, Shu Ye v. 17 i. 9 p. 838 - 839
- Detecting the impact of sequencing errors on SAGE databy: Jacques Colinge, Georg Feger v. 17 i. 9 p. 840 - 842
- GeneMachine: gene prediction and sequence annotationby: Izabela Makalowska, Joseph F. Ryan, Andreas D. Baxevanis v. 17 i. 9 p. 843 - 844
- CHROMA: consensus-based colouring of multiple alignments for publicationby: Leo Goodstadt, Chris P. Ponting v. 17 i. 9 p. 845 - 846
- InterProScan - an integration platform for the signature-recognition methods in InterProby: Evgeni M. Zdobnov, Rolf Apweiler v. 17 i. 9 p. 847 - 848
- The HMMTOP transmembrane topology prediction serverby: Gábor E. Tusnády, István Simon v. 17 i. 9 p. 849 - 850
- VISTRAJ: exploring protein conformational spaceby: John J. Salama, Howard J. Feldman, Christopher W. V. Hogue v. 17 i. 9 p. 851 - 852
- BioLayout-an automatic graph layout algorithm for similarity visualizationby: Anton J. Enright, Christos A. Ouzounis v. 17 i. 9 p. 853 - 854
- BioWAP, mobile Internet service for bioinformaticsby: Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen v. 17 i. 9 p. 855 - 856
- Critical Assessment of Microarray Data Analysis: the 2001 challengeby: Kimberly F. Johnson, Simon M. Lin v. 17 i. 9 p. 857 - 858
- The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA)by: Mark Borodovsky, Eugene Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor Zhulin v. 17 i. 10 p. 859 - 861
- Dealing with errors in interactive sequencing by hybridizationby: Vinhthuy T. Phan, Steven Skiena v. 17 i. 10 p. 862 - 870
- Enrichment of regulatory signals in conserved non-coding genomic sequenceby: Samuel Levy, Sridhar Hannenhalli, Christopher Workman v. 17 i. 10 p. 871 - 877
- Detection of cis -element clusters in higher eukaryotic DNAby: Martin C. Frith, Ulla Hansen, Zhiping Weng v. 17 i. 10 p. 878 - 889
- Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a `weak' context of the start codonby: Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi v. 17 i. 10 p. 890 - 900
- An analysis of gene-finding programs for Neurospora crassaby: Eileen Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan Arnold v. 17 i. 10 p. 901 - 912
- DIANA-EST: a statistical analysisby: Artemis G. Hatzigeorgiou, Petko Fiziev, Martin Reczko v. 17 i. 10 p. 913 - 919
- Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROTby: Ernst Kretschmann, Wolfgang Fleischmann, Rolf Apweiler v. 17 i. 10 p. 920 - 926
- Markovian domain fingerprinting: statistical segmentation of protein sequencesby: Gill Bejerano, Yevgeny Seldin, Hanah Margalit, Naftali Tishby v. 17 i. 10 p. 927 - 934
- Clustering protein sequences-structure prediction by transitive homologyby: Eva Bolten, Alexander Schliep, Sebastian Schneckener, Dietmar Schomburg, Rainer Schrader v. 17 i. 10 p. 935 - 941
- Predicting class II MHC/peptide multi-level binding with an iterative stepwise discriminant analysis meta-algorithmby: R. R. Mallios v. 17 i. 10 p. 942 - 948
- Determining the minimum number of types necessary to represent the sizes of protein atomsby: Jerry Tsai, Neil Voss, Mark Gerstein v. 17 i. 10 p. 949 - 956
- Prediction of disulfide connectivity in proteinsby: Piero Fariselli, Rita Casadio v. 17 i. 10 p. 957 - 964
- Sequence and structural aspects of functional diversification in class I-mannosidase evolutionby: I. King Jordan, G. Reid Bishop, Daniel S. Gonzalez v. 17 i. 10 p. 965 - 976
- Model-based clustering and data transformations for gene expression databy: Ka Yee Yeung, Chris Fraley, A. Murua, Adrian E. Raftery, Walter L. Ruzzo v. 17 i. 10 p. 977 - 987
- Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genomeby: Andrey Rzhetsky, Shawn M. Gomez v. 17 i. 10 p. 988 - 996
- The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000by: Nikolay A. Kolchanov, Charlie Hodgman v. 17 i. 11 p. 997 - 997
- Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysisby: Victor G. Levitsky, Olga A. Podkolodnaya, Nikolay A. Kolchanov, Nikolay L. Podkolodny v. 17 i. 11 p. 998 - 1010
- Gene recognition in eukaryotic DNA by comparison of genomic sequencesby: Pavel S. Novichkov, Mikhail S. Gelfand, Andrey A. Mironov v. 17 i. 11 p. 1011 - 1018
- Combining frequency and positional information to predict transcription factor binding sitesby: Szymon M. Kielbasa, Jan O. Korbel, Dieter Beule, Johannes Schuchhardt, Hanspeter Herzel v. 17 i. 11 p. 1019 - 1026
- Thermodynamic database for protein-nucleic acid interactions (ProNIT)by: Ponraj Prabakaran, Jianghong An, M. Michael Gromiha, Samuel Selvaraj, Hatsuho Uedaira, Hidetoshi Kono, Akinori Sarai v. 17 i. 11 p. 1027 - 1034
- Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutionsby: Dmitry A. Afonnikov, D. Yu. Oshchepkov, Nikolay A. Kolchanov v. 17 i. 11 p. 1035 - 1046
- MDB: a database system utilizing automatic construction of modules and STAR-derived universal languageby: Eugenia Migliavacca, Alexei A. Adzhubei, Manuel C. Peitsch v. 17 i. 11 p. 1047 - 1052
- The TRANSPATH signal transduction database: a knowledge base on signal transduction networksby: Frank Schacherer, Claudia Choi, Ulrike Götze, Mathias Krull, Susanne Pistor, Edgar Wingender v. 17 i. 11 p. 1053 - 1057
- Concepts to automate the theoretical design of effective antisense oligonucleotidesby: Rosel Kretschmer-Kazemi Far, Wolfgang Nedbal, Georg Sczakiel v. 17 i. 11 p. 1058 - 1061
- Nucleosome formation potential of exons, introns, and Alu repeatsby: Victor G. Levitsky, Olga A. Podkolodnaya, Nikolay A. Kolchanov, Nikolay L. Podkolodny v. 17 i. 11 p. 1062 - 1064
- Segmentation of long genomic sequences into domains with homogeneous composition with BASIO softwareby: Vasily Ramensky, Vsevolod Makeev, Mikhail A. Roytberg, Vladimir Tumanyan v. 17 i. 11 p. 1065 - 1066
- Selection of optimal DNA oligos for gene expression arraysby: Fugen Li, Gary D. Stormo v. 17 i. 11 p. 1067 - 1076
- Database-driven Multi Locus Sequence Typing (MLST) of bacterial pathogensby: Man-Suen Chan, Martin C. J. Maiden, Brian G. Spratt v. 17 i. 11 p. 1077 - 1083
- Automatic analysis of agarose gel imagesby: P. S. Umesh Adiga, A. Bhomra, M. G. Turri, A. Nicod, S. R. Datta, Peter Jeavons, Richard Mott, Jonathan Flint v. 17 i. 11 p. 1084 - 1089
- Towards Computer Aided Design (CAD) of Useful Microorganismsby: Masaru Tomita v. 17 i. 12 p. 1091 - 1092
- DNA sequence quality trimming and vector removalby: Hui-Hsien Chou, Michael H. Holmes v. 17 i. 12 p. 1093 - 1104
- Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic featuresby: William C. Ray, Robert S. Munson Jr., Charles J. Daniels v. 17 i. 12 p. 1105 - 1112
- A higher-order background model improves the detection of promoter regulatory elements by Gibbs samplingby: Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau v. 17 i. 12 p. 1113 - 1122
- A probabilistic method for identifying start codons in bacterial genomesby: Baris E. Suzek, Maria D. Ermolaeva, Mark Schreiber, Steven Salzberg v. 17 i. 12 p. 1123 - 1130
- Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN methodby: Leping Li, Clarice R. Weinberg, Thomas A. Darden, Lee G. Pedersen v. 17 i. 12 p. 1131 - 1142
- Statistical estimation of cluster boundaries in gene expression profile databy: Katsuhisa Horimoto, Hiroyuki Toh v. 17 i. 12 p. 1143 - 1151
- Differential expression of genes coding for ribosomal proteins in different human tissuesby: S. Bortoluzzi, F. d'Alessi, Chiara Romualdi, G. A. Danieli v. 17 i. 12 p. 1152 - 1157
- Estimation of P-values for global alignments of protein sequencesby: Caleb Webber, Geoffrey J. Barton v. 17 i. 12 p. 1158 - 1167
- Minimum conflict: a divide-and-conquer approach to phylogeny estimationby: Georg Fuellen, Johann-Wolfgang Wägele, Robert Giegerich v. 17 i. 12 p. 1168 - 1178
- Taxonomy workbenchby: Michael Wildpaner, Georg Schneider, Alexander Schleiffer, Frank Eisenhaber v. 17 i. 12 p. 1179 - 1182
- How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy stepsby: Andreas Wagner v. 17 i. 12 p. 1183 - 1197
- Visualizing plant metabolomic correlation networks using clique-metabolite matricesby: Frank Kose, Wolfram Weckwerth, Thomas Linke, Oliver Fiehn v. 17 i. 12 p. 1198 - 1208
- SPiD: a subtilis protein interaction databaseby: Mark Hoebeke, Hélène Chiapello, Philippe Noirot, Philippe Bessières v. 17 i. 12 p. 1209 - 1212
- A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cellsby: Michael V. Boland, Robert F. Murphy v. 17 i. 12 p. 1213 - 1223
- Evolution of amino acid biosynthesis and enzymes with broad substrate specificityby: Hiromi Nishida v. 17 i. 12 p. 1224 - 1225
- MELTING, computing the melting temperature of nucleic acid duplexby: Nicolas Le Novère v. 17 i. 12 p. 1226 - 1227
- Progenetix.net: an online repository for molecular cytogenetic aberration databy: Michael Baudis, Michael L. Cleary v. 17 i. 12 p. 1228 - 1229
- Sequence type analysis and recombinational tests (START)by: K. A. Jolley, E. J. Feil, M.-S. Chan, Martin C. J. Maiden v. 17 i. 12 p. 1230 - 1231
- Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genesby: Theresa Zhang, Michael Q. Zhang v. 17 i. 12 p. 1232 - 1233
- mmsearch: a motif arrangement language and search programby: Thomas Junier, Marco Pagni, Philipp Bucher v. 17 i. 12 p. 1234 - 1235
- ProPred: prediction of HLA-DR binding sitesby: Harpreet Singh, G. P. S. Raghava v. 17 i. 12 p. 1236 - 1237
- TMCompare: transmembrane region sequence and structureby: Roberto C. Togawa, J. F. Antoniw, J. G. L. Mullins v. 17 i. 12 p. 1238 - 1239
- ToolShop: prerelease inspections for protein structure prediction serversby: Leszek Rychlewski v. 17 i. 12 p. 1240 - 1241
- EVA: continuous automatic evaluation of protein structure prediction serversby: Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost v. 17 i. 12 p. 1242 - 1243
- MEGA2: molecular evolutionary genetics analysis softwareby: Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei v. 17 i. 12 p. 1244 - 1245
- CONSEL: for assessing the confidence of phylogenetic tree selectionby: Hidetoshi Shimodaira, Masami Hasegawa v. 17 i. 12 p. 1246 - 1247
- The early days of bioinformatics publishingby: Richard J. Roberts v. 16 i. 1 p. 2 - 4
- Earliest pages of bioinformaticsby: Edward N. Trifonov v. 16 i. 1 p. 5 - 9
- A historical perspective on gene/protein functional assignmentby: T. Charles Hodgman v. 16 i. 1 p. 10 - 15
- DNA binding sites: representation and discoveryby: Gary D. Stormo v. 16 i. 1 p. 16 - 23
- On the trail of protein sequencesby: Russell F. Doolittle v. 16 i. 1 p. 24 - 33
- History of the enzyme nomenclature systemby: Keith Tipton, Sinéad Boyce v. 16 i. 1 p. 34 - 40
- The early introduction of dynamic programming into computational biologyby: David Sankoff v. 16 i. 1 p. 41 - 47
- Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!by: Amos Bairoch v. 16 i. 1 p. 48 - 64
- A brief history of genome research and bioinformatics in Franceby: Antoine Danchin v. 16 i. 1 p. 65 - 75
- Bioinformatics Education-A UK perspectiveby: Andy Brass v. 16 i. 2 p. 77 - 78
- The complexities of genome analysis, the Retroid agent perspectiveby: Marcella A. McClure v. 16 i. 2 p. 79 - 95
- Self-organization and competition in the immune response to cancer invasion: a phase-orientated computational model of oncogenesisby: Sorinel Adrian Oprisan, Aurel Ardelean, Petre T. Frangopol v. 16 i. 2 p. 96 - 100
- Darwin v. 2.0: an interpreted computer language for the biosciencesby: Gaston H. Gonnet, Michael T. Hallett, Chantal Korostensky, Laurent Bernardin v. 16 i. 2 p. 101 - 103
- Sequence search algorithm assessment and testing toolkit (SAT)by: Jong Park, Liisa Holm, Cyrus Chothia v. 16 i. 2 p. 104 - 110
- ProtEST: protein multiple sequence alignments from expressed sequence tagsby: James A. Cuff, Ewan Birney, Michele E. Clamp, Geoffrey J. Barton v. 16 i. 2 p. 111 - 116
- Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISLby: Sarah A. Teichmann, Cyrus Chothia, George M. Church, Jong Park v. 16 i. 2 p. 117 - 124
- SAWTED: Structure Assignment With Text Description-Enhanced detection of remote homologues with automated SWISS-PROT annotation comparisonsby: Robert M. MacCallum, Lawrence A. Kelley, Michael J. E. Sternberg v. 16 i. 2 p. 125 - 129
- TOPAL 2.0: improved detection of mosaic sequences within multiple alignmentsby: Gráinne McGuire, Frank Wright v. 16 i. 2 p. 130 - 134
- TeXshade: shading and labeling of multiple sequence alignments using LaTeX2eby: Eric Beitz v. 16 i. 2 p. 135 - 139
- Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary treesby: Paul Walton Purdom Jr., Phillip G. Bradford, Koichiro Tamura, Sudhir Kumar v. 16 i. 2 p. 140 - 151
- Modeling splice sites with Bayes networksby: Deyou Cai, Arthur L. Delcher, Ben Kao, Simon Kasif v. 16 i. 2 p. 152 - 158
- STAR/mmCIF: An ontology for macromolecular structureby: John D. Westbrook, Philip E. Bourne v. 16 i. 2 p. 159 - 168
- PNAD-CSS: a workbench for constructing a protein name abbreviation dictionaryby: Mikio Yoshida, Ken-ichiro Fukuda, Toshihisa Takagi v. 16 i. 2 p. 169 - 175
- The Human Transcript Database: a catalogue of full length cDNA insertsby: John Bouck, Michael P. McLeod, Kim Worley, Richard A. Gibbs v. 16 i. 2 p. 176 - 177
- Dotlet: diagonal plots in a Web browserby: Thomas Junier, Marco Pagni v. 16 i. 2 p. 178 - 179
- SISEQ: manipulation of multiple sequence and large database files for common platformsby: Naoki Sato v. 16 i. 2 p. 180 - 181
- GOLD-Graphical Overview of Linkage Disequilibriumby: Gonç R. Abecasis, W. O. C. Cookson v. 16 i. 2 p. 182 - 183
- TAMBIS: Transparent Access to Multiple Bioinformatics Information Sourcesby: Robert Stevens, Patricia G. Baker, Sean Bechhofer, Gary Ng, Alex Jacoby, Norman W. Paton, Carole A. Goble, Andy Brass v. 16 i. 2 p. 184 - 186
- Two or three myths about bioinformaticsby: Christos A. Ouzounis v. 16 i. 3 p. 187 - 189
- Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gapsby: Osamu Gotoh v. 16 i. 3 p. 190 - 202
- Optimal spliced alignment of homologous cDNA to a genomic DNA templateby: Jonathan Usuka, Wei Zhu, Volker Brendel v. 16 i. 3 p. 203 - 211
- Net Nearest Neighbor Analysis (NNNA) summarizes non-compensated dinucleotides within gene sequencesby: Dorothy M. Lang v. 16 i. 3 p. 212 - 221
- Combinatorial motif analysis and hypothesis generation on a genomic scaleby: Yuh-Jyh Hu, Suzanne B. Sandmeyer, Calvin McLaughlin, Dennis F. Kibler v. 16 i. 3 p. 222 - 232
- Fast probabilistic analysis of sequence function using scoring matricesby: Thomas D. Wu, Craig G. Nevill-Manning, Douglas L. Brutlag v. 16 i. 3 p. 233 - 244
- Adaptive encoding neural networks for the recognition of human signal peptide cleavage sitesby: B. Jagla, Johannes Schuchhardt v. 16 i. 3 p. 245 - 250
- Predicting the oxidation state of cysteines by multiple sequence alignmentby: András Fiser, István Simon v. 16 i. 3 p. 251 - 256
- An ontology for biological function based on molecular interactionsby: Peter D. Karp v. 16 i. 3 p. 269 - 285
- Sequence-structure specificity of a knowledge based energy function at the secondary structure levelby: Dong Xu, Michael A. Unseren, Ying Xu, Edward C. Uberbacher v. 16 i. 3 p. 269 - 285
- MPSA: integrated system for multiple protein sequence analysis with client/server capabilitiesby: Christophe Blanchet, Christophe Combet, Christophe Geourjon, Gilbert Deléage v. 16 i. 3 p. 286 - 287
- Storing biological sequence databases in relational formby: Guochun Xie, Reynold DeMarco, Richard Blevins, Yuhong Wang v. 16 i. 3 p. 288 - 289
- PIR: a new resource for bioinformaticsby: Peter B. McGarvey, Hongzhan Huang, Winona C. Barker, Bruce C. Orcutt, John S. Garavelli, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Chunlin Xiao, Cathy H. Wu v. 16 i. 3 p. 290 - 291
- HELM: searching for helix motifs within protein sequencesby: Angelo M. Facchiano v. 16 i. 3 p. 292 - 293
- EDIBLE: experimental design and information calculations in phylogeneticsby: T. Massingham, N. Goldman v. 16 i. 3 p. 294 - 295
- RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic treeby: Marc Robinson-Rechavi, Dorothée Huchon v. 16 i. 3 p. 296 - 297
- PRoMT: inferring demographic history from DNA sequencesby: Stephen Wooding v. 16 i. 3 p. 298 - 299
- GABAagent: a system for integrating data on GABA receptorsby: Abdelkrim Rachedi, Michael Rebhan, Hong Xue v. 16 i. 4 p. 301 - 312
- JESAM: CORBA software components to create and publish EST alignments and clustersby: J. D. Parsons, Patricia Rodriguez-Tomé v. 16 i. 4 p. 313 - 325
- Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotationby: Lars Juhl Jensen, Steen Knudsen v. 16 i. 4 p. 326 - 333
- The language of RNA: a formal grammar that includes pseudoknotsby: Elena Rivas, Sean R. Eddy v. 16 i. 4 p. 334 - 340
- SPLASH: structural pattern localization analysis by sequential histogramsby: Andrea Califano v. 16 i. 4 p. 341 - 357
- PROF_ PAT 1.3: Updated database of patterns used to detect local similaritiesby: Alexander G. Bachinsky, Anatoly S. Frolov, Andrey N. Naumochkin, Lily Ph. Nizolenko, Andrey A. Yarigin v. 16 i. 4 p. 358 - 366
- On the convergence of a clustering algorithm for protein-coding regions in microbial genomesby: Pierre Baldi v. 16 i. 4 p. 367 - 371
- Database of Structural Motifs in Proteinsby: Kunchur Guruprasad, Maheshuni S. Prasad, Gundu R. Kumar v. 16 i. 4 p. 372 - 375
- Wavelet change-point prediction of transmembrane proteinsby: Pietro Lió, Marina Vannucci v. 16 i. 4 p. 376 - 382
- TrExML: a maximum-likelihood approach for extensive tree-space explorationby: Marty J. Wolf, Simon Easteal, Margaret Kahn, Brendan D. McKay, Lars S. Jermiin v. 16 i. 4 p. 383 - 394
- Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogeniesby: Andrew Rambaut v. 16 i. 4 p. 395 - 399
- Detecting hypermutations in viral sequences with an emphasis on G A hypermutationby: Patrick P. Rose, Bette T. Korber v. 16 i. 4 p. 400 - 401
- A browser for expression databy: Matthew R. Pocock, Tim J. P. Hubbard v. 16 i. 4 p. 402 - 403
- The PSIPRED protein structure prediction serverby: Liam J. McGuffin, Kevin Bryson, David T. Jones v. 16 i. 4 p. 404 - 405
- Taxonomic markup language: applying XML to systematic databy: R. Gilmour v. 16 i. 4 p. 406 - 407
- Mathematica packages for simulation of experimental geneticsby: Kenneth F. Manly v. 16 i. 4 p. 408 - 410
- From data to knowledgeby: François Rechenmann v. 16 i. 5 p. 411 - 411
- Assessing the accuracy of prediction algorithms for classification: an overviewby: Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen v. 16 i. 5 p. 412 - 424
- Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignmentby: Peter M. Hooper, Haiyan Zhang, David S. Wishart v. 16 i. 5 p. 425 - 438
- PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significanceby: Graziano Pesole, Sabino Liuni, Mark D'Souza v. 16 i. 5 p. 439 - 450
- GeneRAGE: a robust algorithm for sequence clustering and domain detectionby: Anton J. Enright, Christos A. Ouzounis v. 16 i. 5 p. 451 - 457
- RSDB: representative protein sequence databases have high information contentby: Jong Park, Liisa Holm, Andreas Heger, Cyrus Chothia v. 16 i. 5 p. 458 - 464
- BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathwaysby: Gary D. Bader, Christopher W. V. Hogue v. 16 i. 5 p. 465 - 477
- A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiaeby: Chang Zhu, Kevin Karplus, Leslie Grate, Philip Coffino v. 16 i. 5 p. 478 - 481
- GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analysesby: Gustavo Glusman, Doron Lancet v. 16 i. 5 p. 482 - 483
- Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomesby: David Hiscock, Chris Upton v. 16 i. 5 p. 484 - 485
- RadCon: phylogenetic tree comparison and consensusby: Joseph L. Thorley, Roderic D. M. Page v. 16 i. 5 p. 486 - 487
- Concerning the accuracy of MAST E-valuesby: Timothy L. Bailey, Michael Gribskov v. 16 i. 5 p. 488 - 489
- Analyse This...Or: Intelligent Help for The Rest of Usby: Rainer Fuchs v. 16 i. 6 p. 491 - 493
- A case study in genome-level fragment assemblyby: Ting Chen, Steven Skiena v. 16 i. 6 p. 494 - 500
- Phylogenetically enhanced statistical tools for RNA structure predictionby: Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo v. 16 i. 6 p. 501 - 512
- Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structureby: David F. Burke, Charlotte M. Deane, Tom L. Blundell v. 16 i. 6 p. 513 - 519
- Quick selection of representative protein chain sets based on customizable requirementsby: Tamotsu Noguchi, Kentaro Onizuka, Makoto Ando, Hideo Matsuda, Yutaka Akiyama v. 16 i. 6 p. 520 - 526
- Comparing systemic properties of ensembles of biological networks by graphical and statistical methodsby: Rui Alves, Michael A. Savageau v. 16 i. 6 p. 527 - 533
- Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathwaysby: Rui Alves, Michael A. Savageau v. 16 i. 6 p. 534 - 547
- Conceptual modelling of genomic informationby: Norman W. Paton, Shakeel A. Khan, Andrew Hayes, Fouzia Moussouni, Andy Brass, Karen Eilbeck, Carole A. Goble, Simon J. Hubbard, Stephen G. Oliver v. 16 i. 6 p. 548 - 557
- IMpRH Server: an RH mapping server available on the Webby: Denis Milan, Rachel Hawken, Cédric Cabau, Sophie Leroux, Carine Genet, Yvette Lahbib, Gwenola Tosser, Annie Robic, Francois Hatey, Lee Alexander, Craig Beattie, Larry Schook, Martine Yerle, Joël Gellin v. 16 i. 6 p. 558 - 559
- Oriloc: prediction of replication boundaries in unannotated bacterial chromosomesby: A. C. Frank, J. R. Lobry v. 16 i. 6 p. 560 - 561
- RDP: detection of recombination amongst aligned sequencesby: Darren Martin, Ed Rybicki v. 16 i. 6 p. 562 - 563
- Disperse: a simple and efficient approach to parallel database searchingby: Raphaël Clifford, Aaron J. Mackey v. 16 i. 6 p. 564 - 565
- DaliLite workbench for protein structure comparisonby: Liisa Holm, Jong Park v. 16 i. 6 p. 566 - 567
- MIPSIM: similarity analysis of molecular interaction potentialsby: Miquel de Càceres, Jordi Villà, Juan J. Lozano, Ferran Sanz v. 16 i. 6 p. 568 - 569
- The Economic Value of Bioinformationby: Aleksandar Milosavljevic v. 16 i. 7 p. 571 - 572
- Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequencesby: Mark J. Gibbs, John S. Armstrong, Adrian J. Gibbs v. 16 i. 7 p. 573 - 582
- Secondary structure alone is generally not statistically significant for the detection of noncoding RNAsby: Elena Rivas, Sean R. Eddy v. 16 i. 7 p. 583 - 605
- Clustalnet: the joining of Clustal and CORBAby: Fabien Campagne v. 16 i. 7 p. 606 - 612
- Domain size distributions can predict domain boundariesby: S. J. Wheelan, Aron Marchler-Bauer, Stephen H. Bryant v. 16 i. 7 p. 613 - 618
- Using traveling salesman problem algorithms for evolutionary tree constructionby: Chantal Korostensky, Gaston H. Gonnet v. 16 i. 7 p. 619 - 627
- Object-oriented parsing of biological databases with Pythonby: Chenna Ramu, Christine Gemünd, Toby J. Gibson v. 16 i. 7 p. 628 - 638
- Digital reviews in molecular biology: approaches to structured digital publicationby: David L. Steffen, Alan E. Levine, S. Yarus, R. A. Baasiri, D. A. Wheeler v. 16 i. 7 p. 639 - 649
- eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE)by: Elliott H. Margulies, Jeffrey W. Innis v. 16 i. 7 p. 650 - 651
- DNAssist: the integrated editing and analysis of molecular biology sequences in Windowsby: Hugh-G. Patterton, Steven Graves v. 16 i. 7 p. 652 - 653
- A cross-comparison of a large dataset of genesby: G. Cannarozzi, Michael T. Hallett, J. Norberg, X. Zhou v. 16 i. 7 p. 654 - 655
- NAIL-Network Analysis Interface for Linking HMMER resultsby: Luis Sánchez-Pulido, Yan P. Yuan, Miguel A. Andrade, Peer Bork v. 16 i. 7 p. 656 - 657
- SChiSM: creating interactive web page annotations of molecular structure models using Chimeby: Stephen A. Cammer v. 16 i. 7 p. 658 - 659
- Visualizing large hierarchical clusters in hyperbolic spaceby: Jonathan Bingham, Sucha Sudarsanam v. 16 i. 7 p. 660 - 661
- Bioinformatics-the necessity of the quest for 'first principles' in lifeby: Akiyoshi Wada v. 16 i. 8 p. 663 - 664
- A systematic approach to dynamic programming in bioinformaticsby: Robert Giegerich v. 16 i. 8 p. 665 - 677
- ComboScreen facilitates the multiplex hybridization-based screening of high-density clone arraysby: D. Curtis Jamison, James W. Thomas, Eric D. Green v. 16 i. 8 p. 678 - 684
- Generation of patterns from gene expression data by assigning confidence to differentially expressed genesby: Elisabetta Manduchi, Gregory R. Grant, Steven E. McKenzie, G. Christian Overton, Saul Surrey, Christian J. Stoeckert Jr. v. 16 i. 8 p. 685 - 698
- Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessorsby: Torbjørn Rognes, Erling Seeberg v. 16 i. 8 p. 699 - 706
- Genetic network inference: from co-expression clustering to reverse engineeringby: Patrik D'haeseleer, Shoudan Liang, Roland Somogyi v. 16 i. 8 p. 707 - 726
- Inferring qualitative relations in genetic networks and metabolic pathwaysby: Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara v. 16 i. 8 p. 727 - 734
- In silico identification of transcripts and SNPs from a region of 4p linked with bipolar affective disorderby: C. A. M. Semple, S. W. Morris, D. J. Porteous, K. L. Evans v. 16 i. 8 p. 735 - 738
- TRES: comparative promoter sequence analysisby: Mukund V. Katti, Meena K. Sakharkar, Prabhakar K. Ranjekar, Vidya S. Gupta v. 16 i. 8 p. 739 - 740
- A comparison of signal sequence prediction methods using a test set of signal peptidesby: Kerstin M. L. Menne, Henning Hermjakob, Rolf Apweiler v. 16 i. 8 p. 741 - 742
- gff2ps: visualizing genomic annotationsby: Josep F. Abril, Roderic Guigó v. 16 i. 8 p. 743 - 744
- BBID: the biological biochemical image databaseby: Kevin G. Becker, Shawnte L. White, Jerri Muller, James Engel v. 16 i. 8 p. 745 - 746
- PASS: prediction of activity spectra for biologically active substancesby: Alexey Lagunin, Alla Stepanchikova, Dmitrii Filimonov, Vladimir Poroikov v. 16 i. 8 p. 747 - 748
- ISMB-2000: Bioinformatics enters a new millenniumby: Philip E. Bourne, Michael Gribskov v. 16 i. 9 p. 749 - 749
- Ballast: Blast post-processing based on locally conserved segmentsby: Frédéric Plewniak, Julie D. Thompson, Olivier Poch v. 16 i. 9 p. 750 - 759
- PHAT: a transmembrane-specific substitution matrixby: Pauline C. Ng, Jorja G. Henikoff, Steven Henikoff v. 16 i. 9 p. 760 - 766
- Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural propertiesby: Junhyong Kim, Etsuko N. Moriyama, Coral G. Warr, Peter J. Clyne, John R. Carlson v. 16 i. 9 p. 767 - 775
- MaxSub: an automated measure for the assessment of protein structure prediction qualityby: Naomi Siew, Arne Elofsson, Leszek Rychlewski, Daniel Fischer v. 16 i. 9 p. 776 - 785
- Extending the method of mathematically controlled comparison to include numerical comparisonsby: Rui Alves, Michael A. Savageau v. 16 i. 9 p. 786 - 798
- Engineering support vector machine kernels that recognize translation initiation sitesby: Alexander Zien, Gunnar Rätsch, Sebastian Mika, Bernhard Schölkopf, Thomas Lengauer, Klaus-Robert Müller v. 16 i. 9 p. 799 - 807
- An iterative method for faster sum-of-pairs multiple sequence alignmentby: Knut Reinert, Jens Stoye, Torsten Will v. 16 i. 9 p. 808 - 814
- BALL-rapid software prototyping in computational molecular biologyby: Oliver Kohlbacher, Hans-Peter Lenhof v. 16 i. 9 p. 815 - 824
- Pathway analysis in metabolic databases via differential metabolic display (DMD)by: Robert Küffner, Ralf Zimmer, Thomas Lengauer v. 16 i. 9 p. 825 - 836
- Detection of a surface-exposed PEST like sequence in the metabotropic glutamate receptor mGluR1by: M. M. Soloviev v. 16 i. 9 p. 837 - 838
- Profiles from structure based sequence alignment of porins can identify ß stranded integral membrane proteinsby: T. V. Gnanasekaran, Suraj Peri, A. Arockiasamy, S. Krishnaswamy v. 16 i. 9 p. 839 - 842
- ODNBase-a web database for antisense oligonucleotide effectiveness studiesby: Michael C. Giddings, Olga V. Matveeva, John F. Atkins, Raymond F. Gesteland v. 16 i. 9 p. 843 - 844
- TRITON: in silico construction of protein mutants and prediction of their activitiesby: Martin Prokop, Jirí Damborský, Jaroslav Koca v. 16 i. 9 p. 845 - 846
- LIAN 3.0: detecting linkage disequilibrium in multilocus databy: Bernhard Haubold, Richard R. Hudson v. 16 i. 9 p. 847 - 849
- Bioinformatics in Australiaby: Timothy G. Littlejohn v. 16 i. 10 p. 849 - 850
- Bioinorganic motifs: towards functional classification of metalloproteinsby: Kirill Degtyarenko v. 16 i. 10 p. 851 - 864
- Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengthsby: Pierre Baldi, Pierre-François Baisnée v. 16 i. 10 p. 865 - 889
- Information theoretical probe selection for hybridisation experimentsby: Ralf Herwig, Armin O. Schmitt, Matthias Steinfath, John O'Brien, Henrik Seidel, Sebastian Meier-Ewert, Hans Lehrach, Uwe Radelof v. 16 i. 10 p. 890 - 898
- USAGE: a web-based approach towards the analysis of SAGE databy: Antoine H. C. van Kampen, B. D. C. van Schaik, E. Pauws, E. M. C. Michiels, J. M. Ruijter, H. N. Caron, R. Versteeg, S. H. Heisterkamp, Jack A. M. Leunissen, F. Baas, M. van der Mee v. 16 i. 10 p. 899 - 905
- Support vector machine classification and validation of cancer tissue samples using microarray expression databy: Terrence S. Furey, Nello Cristianini, Nigel Duffy, David W. Bednarski, Michèl Schummer, David Haussler v. 16 i. 10 p. 906 - 914
- CAST: an iterative algorithm for the complexity analysis of sequence tractsby: Vassilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy, Stavros J. Hamodrakas, Chris Sander, Christos A. Ouzounis v. 16 i. 10 p. 915 - 922
- The reduction of large molecular profiles to informative components using a Genetic Algorithmby: F. M. Stefanini, A. Camussi v. 16 i. 10 p. 923 - 931
- Finding pathogenicity islands and gene transfer events in genome databy: Pietro Lió, Marina Vannucci v. 16 i. 10 p. 932 - 940
- Matching amino acid and nucleotide sequences of mouse rheumatoid factor CDRH3-FRH4 segments to other mouse antibodies with known specificitiesby: George Johnson, Tai Te Wu v. 16 i. 10 p. 941 - 943
- Artemis: sequence visualization and annotationby: Kim Rutherford, Julian Parkhill, James Crook, Terry Horsnell, Peter Rice, Marie-Adèle Rajandream, Bart Barrell v. 16 i. 10 p. 944 - 945
- MAD: a suite of tools for microarray data management and processingby: Birong Liao, Walker Hale, Charles B. Epstein, Ronald A. Butow, Harold R. Garner v. 16 i. 10 p. 946 - 947
- A space-efficient algorithm for aligning large genomic sequencesby: Burkhard Morgenstern v. 16 i. 10 p. 948 - 949
- MASIA: recognition of common patterns and properties in multiple aligned protein sequencesby: H. Zhu, Catherine H. Schein, Werner Braun v. 16 i. 10 p. 950 - 951
- POWER_SAGE: comparing statistical tests for SAGE experimentsby: Michael Z. Man, Xuning Wang, Yixin Wang v. 16 i. 11 p. 953 - 959
- Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequencesby: Tetsuo Nishikawa, Toshio Ota, Takao Isogai v. 16 i. 11 p. 960 - 967
- Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidisby: Ana Tereza R. Vasconcelos, Marco A. Grivet Mattoso Maia, Darcy F. de Almeida v. 16 i. 11 p. 968 - 977
- Estimating the significance of sequence order in protein secondary structure and predictionby: Jong Park, Sabine Dietmann, Andreas Heger, Liisa Holm v. 16 i. 11 p. 978 - 987
- Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databasesby: Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy v. 16 i. 11 p. 988 - 1002
- Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensionsby: Derek A. Ruths, Edward S. Chen, Leland Ellis v. 16 i. 11 p. 1003 - 1009
- Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertaintyby: Simon Blomberg v. 16 i. 11 p. 1010 - 1013
- Processing and quality control of DNA array hybridization databy: T. Beißbarth, Kurt Fellenberg, Benedikt Brors, R. Arribas-Prat, J. M. Boer, Nicole C. Hauser, M. Scheideler, Jörg D. Hoheisel, G. Schütz, Annemarie Poustka, Martin Vingron v. 16 i. 11 p. 1014 - 1022
- Biochemical systems analysis of genome-wide expression databy: Eberhard O. Voit, Tomas Radivoyevitch v. 16 i. 11 p. 1023 - 1037
- DRAGON: Database Referencing of Array Genes Onlineby: Christopher M. L. S. Bouton, Jonathan Pevsner v. 16 i. 11 p. 1038 - 1039
- MaskerAid : a performance enhancement to RepeatMaskerby: Joseph A. Bedell, Ian Korf, Warren Gish v. 16 i. 11 p. 1040 - 1041
- Circles: automating the comparative analysis of RNA secondary structureby: Roderic D. M. Page v. 16 i. 11 p. 1042 - 1043
- model.it : building three dimensional DNA models from sequence databy: Kristian Vlahovicek, Sándor Pongor v. 16 i. 11 p. 1044 - 1045
- VISTA : visualizing global DNA sequence alignments of arbitrary lengthby: Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak v. 16 i. 11 p. 1046 - 1047
- VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBLby: Paul Kersey, Henning Hermjakob, Rolf Apweiler v. 16 i. 11 p. 1048 - 1049
- TEXtopo: shaded membrane protein topology plots in LATEX2by: Eric Beitz v. 16 i. 11 p. 1050 - 1051
- MPBLAST : improved BLAST performance with multiplexed queriesby: Ian Korf, Warren Gish v. 16 i. 11 p. 1052 - 1053
- BLAST Search Updater: a notification system for new database matchesby: Matthew Boone, Chris Upton v. 16 i. 11 p. 1054 - 1055
- PhyloDraw: a phylogenetic tree drawing systemby: Jeong-Hyeon Choi, Ho-Youl Jung, Hye-Sun Kim, Hwan-Gue Cho v. 16 i. 11 p. 1056 - 1058
- The need for a human gene indexby: C. Victor Jongeneel v. 16 i. 12 p. 1059 - 1061
- Neural network schemes for detecting rare events in human genomic DNAby: Wooyoung Choe, Okan K. Ersoy, Minou Bina v. 16 i. 12 p. 1062 - 1072
- Frequency-domain analysis of biomolecular sequencesby: Dimitris Anastassiou v. 16 i. 12 p. 1073 - 1081
- Optimizing reduced-space sequence analysisby: Raymond Wheeler, Richard Hughey v. 16 i. 12 p. 1082 - 1090
- Protein domain decomposition using a graph-theoretic approachby: Ying Xu, Dong Xu, Harold N. Gabow v. 16 i. 12 p. 1091 - 1104
- Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homologyby: Weizhong Li, Frederic Pio, Krzysztof Pawlowski, Adam Godzik v. 16 i. 12 p. 1105 - 1110
- Analysis of conservation and substitutions of secondary structure elements within protein superfamiliesby: Kenji Mizuguchi, Tom L. Blundell v. 16 i. 12 p. 1111 - 1119
- A knowledge model for analysis and simulation of regulatory networksby: Andrey Rzhetsky, Tomohiro Koike, Sergey Kalachikov, Shawn M. Gomez, Michael Krauthammer, Sabina H. Kaplan, Pauline Kra, James J. Russo, Carol Friedman v. 16 i. 12 p. 1120 - 1128
- Semiotes: a semantics for sharingby: Toni Kazic v. 16 i. 12 p. 1129 - 1144
- InterPro-an integrated documentation resource for protein families, domains and functional sitesby: Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov v. 16 i. 12 p. 1145 - 1150
- IE-Kb: intron exon knowledge baseby: Meena K. Sakharkar, Pandjassarame Kangueane, Tong W. Woon, Tin Wee Tan, Prasanna R. Kolatkar, Manyuan Long, Sandro J. de Souza v. 16 i. 12 p. 1151 - 1152
- ASAP: analysis of peptide compositionby: Xavier Serra-Hartmann, Xavier Rebordosa, Jaume Piñol, Enrique Querol, Marc A. Martí-Renom v. 16 i. 12 p. 1153 - 1154
- A simple probabilistic scoring method for protein domain identificationby: Jámps Murvai, Kristian Vlahovicek, Sándor Pongor v. 16 i. 12 p. 1155 - 1156
- PANAL: an integrated resource for Protein sequence ANALysisby: Kevin A. T. Silverstein, Alan Kilian, John L. Freeman, James E. Johnson, Ihab A. Awad, Ernest F. Retzel v. 16 i. 12 p. 1157 - 1158
- A collection of well characterised integral membrane proteinsby: Steffen Möller, Evgenia V. Kriventseva, Rolf Apweiler v. 16 i. 12 p. 1159 - 1160
- Imagene: an integrated computer environment for sequence annotation and analysisby: Claudine Médigue, François Rechenmann, Antoine Danchin, Alain Viari v. 15 i. 1 p. 2 - 15
- Stem Trace: an interactive visual tool for comparative RNA structure analysisby: Wojciech Kasprzak, Bruce A. Shapiro v. 15 i. 1 p. 16 - 31
- RNA movies: visualizing RNA secondary structure spacesby: Dirk Evers, Robert Giegerich v. 15 i. 1 p. 32 - 37
- Bayesian inference on biopolymer modelsby: Jun S. Liu, Charles E. Lawrence v. 15 i. 1 p. 38 - 52
- Using imperfect secondary structure predictions to improve molecular structure computationsby: Cheng Che Chen, Jaswinder Pal Singh, Russ B. Altman v. 15 i. 1 p. 53 - 65
- A fast, stochastic threading algorithm for proteinsby: Oakley H. Crawford v. 15 i. 1 p. 66 - 71
- E-CELL: software environment for whole-cell simulationby: Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Thomas Simon Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, K. Saito, S. Tanida, Katsuyuki Yugi, J. C. Venter, C. A. Hutchison III v. 15 i. 1 p. 72 - 84
- Genetic Simulation Libraryby: John S. Conery, Michael Lynch v. 15 i. 1 p. 85 - 86
- BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programsby: Julie D. Thompson, Frédéric Plewniak, Olivier Poch v. 15 i. 1 p. 87 - 88
- Application of distance geometry to 3D visualization of sequence relationshipsby: M. Forster, A. Heath, M. Afzal v. 15 i. 1 p. 89 - 90
- A computer-driven approach to PCR-based differential screening, alternative to differential displayby: G. G. Consalez, A. Cabibbo, A. Corradi, C. Alli, M. Sardella, R. Sitia, R. Fesce v. 15 i. 2 p. 93 - 105
- Establishing a method of vector contamination identification in database sequencesby: G. A. Seluja, Andrew D. Farmer, Mia McLeod, Carol Harger, P. A. Schad v. 15 i. 2 p. 106 - 110
- A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databasesby: C. Miller, J. Gurd, Andy Brass v. 15 i. 2 p. 111 - 121
- Combining many multiple alignments in one improved alignmentby: K. Bucka-Lassen, O. Caprani, J. Hein v. 15 i. 2 p. 122 - 130
- FORESST: fold recognition from secondary structure predictions of proteinsby: Valentina Di Francesco, Peter J. Munson, Jean Garnier v. 15 i. 2 p. 131 - 140
- The hydrophobic cores of proteins predicted by wavelet analysisby: H. Hirakawa, S. Muta, S. Kuhara v. 15 i. 2 p. 141 - 148
- HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic treesby: Y. Zhong, Y. Luo, Sakti Pramanik, J. H. Beaman v. 15 i. 2 p. 149 - 156
- A proposal for a standard CORBA interface for genome mapsby: Emmanuel Barillot, Ulf Leser, Philip Lijnzaad, Christophe Cussat-Blanc, Kim Jungfer, F. Guyon, Guy Vaysseix, Carsten Helgesen, Patricia Rodriguez-Tomé v. 15 i. 2 p. 157 - 169
- An extensive list of genes that produce alternative transcripts in the mouseby: M. E. Mangan, K. S. Frazer v. 15 i. 2 p. 170 - 171
- TargetFinder: searching annotated sequence databases for target genes of transcription factorsby: Giovanni Lavorgna, Alessandro Guffanti, G. Borsani, A. Ballabio, E. Boncinelli v. 15 i. 2 p. 172 - 173
- DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysisby: Julio Rozas, Ricardo Rozas v. 15 i. 2 p. 174 - 175
- PredAcc: prediction of solvent accessibilityby: M. H. Mucchielli-Giorgi, Serge A. Hazout, Pierre Tufféry v. 15 i. 2 p. 176 - 177
- Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarityby: Andreas Klingenhoff, Kornelie Frech, Kerstin Quandt, Thomas Werner v. 15 i. 3 p. 180 - 186
- 10-11 bp periodicities in complete genomes reflect protein structure and DNA foldingby: Hanspeter Herzel, Olaf Weiss, Edward N. Trifonov v. 15 i. 3 p. 187 - 193
- Transformation distances: a family of dissimilarity measures based on movements of segmentsby: Jean-Stéphane Varré, Jean-Paul Delahaye, Eric Rivals v. 15 i. 3 p. 194 - 202
- An exact solution for the segment-to-segment multiple sequence alignment problemby: Hans-Peter Lenhof, Burkhard Morgenstern, Knut Reinert v. 15 i. 3 p. 203 - 210
- DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignmentby: Burkhard Morgenstern v. 15 i. 3 p. 211 - 218
- EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotationby: Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler v. 15 i. 3 p. 219 - 227
- A novel method for automatic functional annotation of proteinsby: Wolfgang Fleischmann, Steffen Möller, Alain Gateau, Rolf Apweiler v. 15 i. 3 p. 228 - 233
- Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabetsby: Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer v. 15 i. 3 p. 234 - 242
- Docking of hydrophobic ligands with interaction-based matching algorithmsby: Matthias Rarey, Bernd Kramer, Thomas Lengauer v. 15 i. 3 p. 243 - 250
- METATOOL: for studying metabolic networksby: Thomas Pfeiffer, Ignacio Sánchez-Valdenebro, Juan Carlos Nuño, Francisco Montero, Stefan Schuster v. 15 i. 3 p. 251 - 257
- Removing redundancy in SWISS-PROT and TrEMBLby: Claire O'Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler v. 15 i. 3 p. 258 - 259
- KIND-a non-redundant protein databaseby: Yvonne Kallberg, Bengt Persson v. 15 i. 3 p. 260 - 261
- WWW access to the SYSTERS protein sequence cluster setby: Antje Krause, P. Nicodeme, Erich Bornberg-Bauer, Marc Rehmsmeier, Martin Vingron v. 15 i. 3 p. 262 - 263
- DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequencesby: R. F. Lascaris, W. H. Mager, J. Planta v. 15 i. 4 p. 267 - 277
- Revealing hidden interval graph structure in STS-content databy: Eric Harley, Anthony J. Bonner, Nathan Goodman v. 15 i. 4 p. 278 - 285
- A vector-based method for drawing RNA secondary structureby: K. Han, D. Kim, H. J. Kim v. 15 i. 4 p. 286 - 297
- Calign: aligning sequences with restricted affine gap penaltiesby: Kun-Mao Chao v. 15 i. 4 p. 298 - 304
- ESPript: analysis of multiple sequence alignments in PostScriptby: Patrice Gouet, Emmanuel Courcelle, D. I. Stuart, F. Metoz v. 15 i. 4 p. 305 - 308
- DINAMO: interactive protein alignment and model buildingby: J. Bentz, A. Baucom, M. Hansen, L. Gregoret v. 15 i. 4 p. 309 - 316
- Motif-based searching in TOPS protein topology databasesby: David Gilbert, David R. Westhead, N. Nagano, Janet M. Thornton v. 15 i. 4 p. 317 - 326
- Automated analysis of interatomic contacts in proteinsby: Vladimir Sobolev, A. Sorokine, J. Prilusky, E. E. Abola, Marvin Edelman v. 15 i. 4 p. 327 - 332
- Wrapping SRS with CORBA: from textual data to distributed objectsby: Thierry Coupaye v. 15 i. 4 p. 333 - 338
- The Biopolymer Markup Languageby: D. Fenyo v. 15 i. 4 p. 339 - 340
- MIAH: automatic alignment of eukaryotic SSU rRNAsby: P. Thebault, P. Monestie, A. McGrath, Desmond G. Higgins v. 15 i. 4 p. 341 - 342
- The domain-server: direct prediction of protein domain-homologies from BLAST searchby: Jámps Murvai, Kristian Vlahovicek, Endre Barta, S. Parthasarathy, Hedvig Hegyi, Friedhelm Pfeiffer, Sándor Pongor v. 15 i. 4 p. 343 - 344
- CoPE: a collaborative pedigree drawing environmentby: L. Brun-Samarcq, Sophie Gallina, A. Philippi, F. Demenais, Guy Vaysseix, Emmanuel Barillot v. 15 i. 4 p. 345 - 346
- ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assaysby: Steven Bushnell, J. Budde, T. Catino, J. Cole, A. Derti, R. Kelso, M. L. Collins, G. Molino, P. Sheridan, J. Monahan, M. Urdea v. 15 i. 5 p. 348 - 355
- Promoter2.0: for the recognition of PolII promoter sequencesby: Steen Knudsen v. 15 i. 5 p. 356 - 361
- Interpolated markov chains for eukaryotic promoter recognitionby: Uwe Ohler, Stefan Harbeck, Heinrich Niemann, Elmar Nöth, Martin G. Reese v. 15 i. 5 p. 362 - 369
- Statistical mechanical simulation of polymeric DNA melting with MELTSIMby: Richard D. Blake, J. W. Bizzaro, Jonathan D. Blake, G. R. Day, S. G. Delcourt, J. Knowles, K. A. Marx, J. SantaLucia Jr. v. 15 i. 5 p. 370 - 375
- CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequencesby: A. Chou, J. Burke v. 15 i. 5 p. 376 - 381
- PIR-ALN: a database of protein sequence alignmentsby: Geetha Y. Srinivasarao, Lai-Su L. Yeh, Christopher R. Marzec, Bruce C. Orcutt, Winona C. Barker v. 15 i. 5 p. 382 - 390
- Automated genome sequence analysis and annotationby: Miguel A. Andrade, N. P. Brown, Christophe Leroy, S. Hoersch, Antoine de Daruvar, C. Reich, A. Franchini, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis, Chris Sander v. 15 i. 5 p. 391 - 412
- Improved performance in protein secondary structure prediction by inhomogeneous score combinationby: Yann Guermeur, Christophe Geourjon, Patrick Gallinari, Gilbert Deléage v. 15 i. 5 p. 413 - 421
- WebBLAST 2.0: an integrated solution for organizing and analyzing sequence databy: Prakash S. Ferlanti, Joseph F. Ryan, Izabela Makalowska, Andreas D. Baxevanis v. 15 i. 5 p. 422 - 423
- JaDis: computing distances between nucleic acid sequencesby: I. Goncalves, M. Robinson, Guy Perrière, Dominique Mouchiroud v. 15 i. 5 p. 424 - 425
- REPuter: fast computation of maximal repeats in complete genomesby: Stefan Kurtz, Chris Schleiermacher v. 15 i. 5 p. 426 - 427
- Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta- algorithmby: R. R. Mallios v. 15 i. 6 p. 432 - 439
- Fast evaluation of internal loops in RNA secondary structure predictionby: Rune B. Lyngsø, Michael Zuker, Christian N. S. Pedersen v. 15 i. 6 p. 440 - 445
- RNA secondary structure prediction using stochastic context-free grammars and evolutionary historyby: Bjarne Knudsen, Jotun Hein v. 15 i. 6 p. 446 - 454
- Local sequence alignments with monotonic gap penaltiesby: Richard Mott v. 15 i. 6 p. 455 - 462
- Family pairwise search with embedded motif modelsby: William Noble Grundy, Timothy L. Bailey v. 15 i. 6 p. 463 - 470
- Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilationsby: Steven Henikoff, Jorja G. Henikoff, Shmuel Pietrokovski v. 15 i. 6 p. 471 - 479
- A comparison of sequence and structure protein domain families as a basis for structural genomicsby: Arne Elofsson, Erik L. L. Sonnhammer v. 15 i. 6 p. 480 - 500
- Clustering of non-polar contacts in proteinsby: Finn Drabløs v. 15 i. 6 p. 501 - 509
- An ontology for bioinformatics applicationsby: Patricia G. Baker, Carole A. Goble, Sean Bechhofer, Norman W. Paton, Robert Stevens, Andy Brass v. 15 i. 6 p. 510 - 520
- Protein analyst - a distributed object environment for protein sequence and structure analysisby: Mansoor A. S. Saqi, D. L. Wild, M. J. Hartshorn v. 15 i. 6 p. 521 - 522
- BLAST PRINTS - alternative perspectives on sequence similarityby: W. Wright, P. Scordis, Terri K. Attwood v. 15 i. 6 p. 523 - 524
- SECOST: sequence-conformation-structure database for amino acid residues in proteinsby: Oleg Shats, I. I. Vaisman, A. Shats, Simon Sherman v. 15 i. 6 p. 525 - 526
- Evaluation of human-readable annotation in biomolecular sequence databases with biological rule librariesby: Frank Eisenhaber, Peer Bork v. 15 i. 7 p. 528 - 535
- Complete genomes in WWW Entrez: data representation and analysisby: Tatiana A. Tatusova, Ilene Karsch-Mizrachi, James Ostell v. 15 i. 7 p. 536 - 543
- Development of the receptor database (RDB): application to the endocrine disruptor problemby: K. Nakata, T. Takai, Tsuguchika Kaminuma v. 15 i. 7 p. 544 - 552
- Regression trees for analysis of mutational spectra in nucleotide sequencesby: V. B. Berikov, Igor B. Rogozin v. 15 i. 7 p. 553 - 562
- Identifying DNA and protein patterns with statistically significant alignments of multiple sequencesby: G. Z. Hertz, Gary D. Stormo v. 15 i. 7 p. 563 - 577
- Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotesby: Y. Osada, Rintaro Saito, Masaru Tomita v. 15 i. 7 p. 578 - 581
- Nucleosomal DNA property databaseby: Victor G. Levitsky, Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay A. Kolchanov v. 15 i. 7 p. 582 - 592
- Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysisby: L. Mendoza, Denis Thieffry, E. R. Alvarez-Buylla v. 15 i. 7 p. 593 - 606
- SCPD: a promoter database of the yeast Saccharomyces cerevisiaeby: J. Zhu, Michael Q. Zhang v. 15 i. 7 p. 607 - 611
- GeneBuilder: interactive in silico prediction of gene structureby: Luciano Milanesi, D. D'Angelo, Igor B. Rogozin v. 15 i. 7 p. 612 - 621
- Estimating transcription factor bindability on DNAby: T. Tsunoda, Toshihisa Takagi v. 15 i. 7 p. 622 - 630
- Oligonucleotide frequency matrices addressed to recognizing functional DNA sitesby: Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Olga A. Podkolodnaya, D. G. Vorobyev, Nikolay A. Kolchanov, G. Christian Overton v. 15 i. 7 p. 631 - 643
- Investigating extended regulatory regions of genomic DNA sequencesby: Vladimir N. Babenko, P. S. Kosarev, Oleg V. Vishnevsky, Victor G. Levitsky, V. V. Basin, Anatoly S. Frolov v. 15 i. 7 p. 644 - 653
- Conformational and physicochemical DNA features specific for transcription factor binding sitesby: Julia V. Ponomarenko, Mikhail P. Ponomarenko, Anatoly S. Frolov, D. G. Vorobyev, G. Christian Overton, Nikolay A. Kolchanov v. 15 i. 7 p. 654 - 668
- Integrated databases and computer systems for studying eukaryotic gene expressionby: Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Anatoly S. Frolov, Elena A. Ananko, F. A. Kolpakov, Elena V. Ignatieva, Olga A. Podkolodnaya, T. N. Goryachkovskaya, Irina L. Stepanenko, Tatyana I. Merkulova, V. V. Babenko, Y. V. Ponomarenko, Alexey V. Kochetov, Nikolay L. Podkolodny, Denis G. Vorobiev, Sergey V. Lavryushev, Dmitry A. Grigorovich, Y. V. Kondrakhin, Luciano Milanesi, Edgar Wingender, Victor V. Solovyev, G. Christian Overton v. 15 i. 7 p. 669 - 686
- Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteinsby: Mikhail P. Ponomarenko, Julia V. Ponomarenko, Anatoly S. Frolov, Nikolay L. Podkolodny, L. K. Savinkova, Nikolay A. Kolchanov, G. Christian Overton v. 15 i. 7 p. 687 - 703
- Prediction of eukaryotic mRNA translational propertiesby: Alexey V. Kochetov, Mikhail P. Ponomarenko, Anatoly S. Frolov, L. L. Kisselev, Nikolay A. Kolchanov v. 15 i. 7 p. 704 - 712
- Interactive data input into the GeneNet databaseby: F. A. Kolpakov, Elena A. Ananko v. 15 i. 7 p. 713 - 714
- Financing a future for public biological databy: L. B. Ellis, D. Kalumbi v. 15 i. 9 p. 717 - 722
- Neural network input representations that produce accurate consensus sequences from DNA fragment assembliesby: Carolyn F. Allex, Jude W. Shavlik, Frederick R. Blattner v. 15 i. 9 p. 723 - 728
- Shotgun: getting more from sequence similarity searchesby: S. C. Pegg, Patricia C. Babbitt v. 15 i. 9 p. 729 - 740
- Associative database of protein sequencesby: Jens Hanke, G. Lehmann, Peer Bork, Jens G. Reich v. 15 i. 9 p. 741 - 748
- Mathematical simulation and analysis of cellular metabolism and regulationby: I. I. Goryanin, T. Charles Hodgman, Evgeni Selkov v. 15 i. 9 p. 749 - 758
- Finding families for genomic ORFansby: Daniel Fischer, David Eisenberg v. 15 i. 9 p. 759 - 762
- K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervalsby: Josep M. Comeron v. 15 i. 9 p. 763 - 764
- TargetDB: a database of peptides targeting proteins to subcellular locationsby: T. Wei, Michael O'Connell v. 15 i. 9 p. 765 - 766
- SWEET - WWW-based rapid 3D construction of oligo- and polysaccharidesby: Andreas Bohne, Elke Lang, Claus-Wilhelm von der Lieth v. 15 i. 9 p. 767 - 768
- MatrixPlot: visualizing sequence constraintsby: Jan Gorodkin, H. H. Staerfeldt, Ole Lund, Søren Brunak v. 15 i. 9 p. 769 - 770
- Swissknife - 'lazy parsing' of SWISS-PROT entriesby: Henning Hermjakob, Wolfgang Fleischmann, Rolf Apweiler v. 15 i. 9 p. 771 - 772
- Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wideby: N. C. Kyrpides v. 15 i. 9 p. 773 - 774
- Editorial. The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99)by: Thomas Lengauer v. 15 i. 10 p. 775 - 775
- Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomesby: Andreas Wagner v. 15 i. 10 p. 776 - 784
- A new method to predict the consensus secondary structure of a set of unaligned RNA sequencesby: Dominique Bouthinon, Henry Soldano v. 15 i. 10 p. 785 - 798
- FingerPRINTScan: intelligent searching of the PRINTS motif databaseby: P. Scordis, Darren R. Flower, Terri K. Attwood v. 15 i. 10 p. 799 - 806
- An analysis of the Protein Data Bank in search of temporal and global trendsby: Helge Weissig, Philip E. Bourne v. 15 i. 10 p. 807 - 831
- Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP)by: Robert Preissner, Andrean Goede, Cornelius Frömmel v. 15 i. 10 p. 832 - 836
- bioWidgets: data interaction components for genomicsby: S. Fischer, Jonathan Crabtree, Brian P. Brunk, M. Gibson, G. Christian Overton v. 15 i. 10 p. 837 - 846
- ORBIT: an integrated environment for user-customized bioinformatics toolsby: Matthew I. Bellgard, Hong Liang Hiew, Adam Hunter, Michael Wiebrands v. 15 i. 10 p. 847 - 851
- MUTbase: maintenance and analysis of distributed mutation databasesby: Pentti Riikonen, Mauno Vihinen v. 15 i. 10 p. 852 - 859
- Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequenceby: G. H. Thomas v. 15 i. 10 p. 860 - 861
- MULTICLUSTAL: a systematic method for surveying Clustal W alignment parametersby: Jeffrey Yuan, A. Amend, J. Borkowski, R. DelMarco, W. Bailey, Yuan Liu, Guohun Xie, Richard Blevins v. 15 i. 10 p. 862 - 863
- Erratum. Finding families for genomic ORFansby: Daniel Fischer, David Eisenberg v. 15 i. 10 p. 864 - 864
- The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA)by: Chris Burge, Andrej Sali, Mark Borodovsky v. 15 i. 11 p. 865 - 866
- FramePlus: aligning DNA to protein sequencesby: Eran Halperin, Simchon Faigler, Raveh Gill-More v. 15 i. 11 p. 867 - 873
- Finding prokaryotic genes by the `frame-by-frame' algorithm: targeting gene starts and overlapping genesby: Anton M. Shmatkov, Arik A. Melikyan, Felix L. Chernousko, Mark Borodovsky v. 15 i. 11 p. 874 - 886
- Evaluation of gene prediction software using a genomic data set: application to <$O_SSF>Arabidopsis thaliana<$C_SSF>sequencesby: Nathalie Pavy, Stephane Rombauts, Patrice Déhais, Catherine Mathé, Ramana V. Davuluri, Philippe Leroy, Pierre Rouzé v. 15 i. 11 p. 887 - 899
- An automated comparative analysis of 17 complete microbial genomesby: Arvind K. Bansal v. 15 i. 11 p. 900 - 908
- Genome rearrangement with gene familiesby: David Sankoff v. 15 i. 11 p. 909 - 917
- Structural basis for triplet repeat disorders: a computational analysisby: Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen v. 15 i. 11 p. 918 - 929
- A simple algorithm for detecting circular permutations in proteinsby: S. Uliel, A. Fliess, Amihood Amir, Ron Unger v. 15 i. 11 p. 930 - 936
- Exploiting the past and the future in protein secondary structure predictionby: Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri v. 15 i. 11 p. 937 - 946
- Local multiple sequence alignment using dead-end eliminationby: Alexander V. Lukashin, Joseph J. Rosa v. 15 i. 11 p. 947 - 953
- Bioinformatics and the Y2K Problemv. 15 i. 12 p. 955 - 956
- Polymer chromosome models and Monte Carlo simulations of radiation breaking DNAby: A. L. Ponomarev, R. K. Sachs v. 15 i. 12 p. 957 - 964
- IMAGEne I: clustering and ranking of I.M.A.G.E. cDNA clones corresponding to known genesby: M. Cariaso, P. Folta, M. Wagner, Tom Kuczmarski, G. Lennon v. 15 i. 12 p. 965 - 973
- SEGMENT: identifying compositional domains in DNA sequencesby: José L. Oliver, Ramón Román-Roldán, Javier Pérez, Pedro Bernaola-Galván v. 15 i. 12 p. 974 - 979
- Segmentation of yeast DNA using hidden Markov modelsby: Leonid Peshkin, Mikhail S. Gelfand v. 15 i. 12 p. 980 - 986
- Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov modelsby: Tetsushi Yada, Mitsuteru Nakao, Yasushi Totoki, Kenta Nakai v. 15 i. 12 p. 987 - 993
- On the complexity measures of genetic sequencesby: Vladimir D. Gusev, Lubov A. Nemytikova, Nadia A. Chuzhanova v. 15 i. 12 p. 994 - 999
- IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matricesby: Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul v. 15 i. 12 p. 1000 - 1011
- Post-processing long pairwise alignmentsby: Zheng Zhang, Piotr Berman, Thomas Wiehe, Webb Miller v. 15 i. 12 p. 1012 - 1019
- Browsing protein families via the `Rich Family Description' formatby: Florence Corpet, Jérôme Gouzy, Daniel Kahn v. 15 i. 12 p. 1020 - 1027
- PHYSEAN: PHYsical SEquence ANalysis for the identification of protein domains on the basis of physical and chemical properties of amino acidsby: Istvan Ladunga v. 15 i. 12 p. 1028 - 1038
- Decision tree-based formation of consensus protein secondary structure predictionby: Joachim Selbig, Heinz-Theodor Mevissen, Thomas Lengauer v. 15 i. 12 p. 1039 - 1046
- Ontology for immunogenetics: the IMGT-ONTOLOGYby: Véronique Giudicelli, Marie-Paule Lefranc v. 15 i. 12 p. 1047 - 1054
- A plant calmodulin-binding motor is part kinesin and part myosinby: V. S. Reddy, A. S. N. Reddy v. 15 i. 12 p. 1055 - 1057
- Shufflet: shuffling sequences while conserving the k-let countsby: Eivind Coward v. 15 i. 12 p. 1058 - 1059
- ModBase: A database of comparative protein structure modelsby: Roberto Sánchez v. 15 i. 12 p. 1060 - 1061
- A platform for integrating threading results with protein family analysesby: Florencio Pazos, Burkhard Rost, Alfonso Valencia v. 15 i. 12 p. 1062 - 1063
- Sausage: protein threading with flexible force fieldsby: Thomas Huber, Anthony J. Russell, Daniel Ayers, Andrew E. Torda v. 15 i. 12 p. 1064 - 1065
- Representation of functional information in the SWISS-PROT Data Bankby: V. L. Junker, Rolf Apweiler, Amos Bairoch v. 15 i. 12 p. 1066 - 1067
- WebPHYLIP: a web interface to PHYLIPby: Allison Lim, Louxin Zhang v. 15 i. 12 p. 1068 - 1069
- The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data miningby: Barbara A. Eckman, Jeffery S. Aaronson, J. A. Borkowski, W. J. Bailey, K. O. Elliston, A. R. Williamson, R. A. Blevins v. 14 i. 1 p. 2 - 13
- Algorithms and software for support of gene identification experimentsby: Sing-Hoi Sze, Mikhail A. Roytberg, Mikhail S. Gelfand, Andrey A. Mironov, Tatiana V. Astakhova, Pavel A. Pevzner v. 14 i. 1 p. 14 - 19
- GenXref. VI: Automatic generation of links between two heterogeneous databasesby: Frédéric Achard, Philippe Dessen v. 14 i. 1 p. 20 - 24
- Bayesian adaptive sequence alignment algorithmsby: Jun Zhu, Jun S. Liu, Charles E. Lawrence v. 14 i. 1 p. 25 - 39
- Comparative accuracy of methods for protein sequence similarity searchby: Pankaj Agarwal, David J. States v. 14 i. 1 p. 40 - 47
- Combining evidence using p-values: application to sequence homology searchesby: Timothy L. Bailey, Michael Gribskov v. 14 i. 1 p. 48 - 54
- Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2): 229]by: Isidore Rigoutsos, Aris Floratos v. 14 i. 1 p. 55 - 67
- SplitsTree: analyzing and visualizing evolutionary databy: Daniel H. Huson v. 14 i. 1 p. 68 - 73
- Xlandscape: the graphical display of word frequencies in sequencesby: Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo v. 14 i. 1 p. 74 - 80
- Design and implementation of a qualitative simulation model of lambda phage infectionby: Karsten R. Heidtke, Steffen Schulze-Kremer v. 14 i. 1 p. 81 - 91
- Trace alignment and some of its applicationsby: Richard Mott v. 14 i. 1 p. 92 - 97
- Spectrum: spectral analysis of phylogenetic databy: Michael A. Charleston v. 14 i. 1 p. 98 - 99
- Mapper: an intelligent restriction mapping toolby: J. A. Inglehart, P. C. Nelson, Y. Zou v. 14 i. 2 p. 101 - 111
- Design and implementation of a CORBA-based genome mapping system prototypeby: Jian Hu, Chris Mungall, David Nicholson, Alan L. Archibald v. 14 i. 2 p. 112 - 120
- Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural networkby: Vladimir Brusic, George B. Rudy, G. Honeyman, Jürgen Hammer, L. Harrison v. 14 i. 2 p. 121 - 130
- Analysis of DNA curvature using artificial neural networksby: Rupali V. Parbhane, Sanjeev S. Tambe, Bhaskar D. Kulkarni v. 14 i. 2 p. 131 - 138
- Feature selection for genetic sequence classificationby: Nadia A. Chuzhanova, Antonia J. Jones, Steve Margetts v. 14 i. 2 p. 139 - 143
- DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteinsby: Jong Park, Sarah A. Teichmann v. 14 i. 2 p. 144 - 150
- A major component approach to presenting consensus sequencesby: D. K. Smith, H. Xue v. 14 i. 2 p. 151 - 156
- Rose: generating sequence familiesby: Jens Stoye, Dirk Evers, Folker Meyer v. 14 i. 2 p. 157 - 163
- Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignmentby: Jérôme Gracy, P. Argos v. 14 i. 2 p. 164 - 173
- Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similaritiesby: Jérôme Gracy, P. Argos v. 14 i. 2 p. 174 - 187
- 3DinSight: an integrated relational database and search tool for the structure, function and properties of biomoleculesby: J. An, T. Nakama, Y. Kubota, Akinori Sarai v. 14 i. 2 p. 188 - 195
- Estimation and filtering of potential protein-protein docking positionsby: Friedrich Ackermann, Grit Herrmann, Stefan Posch, Gerhard Sagerer v. 14 i. 2 p. 196 - 205
- Incremental threading optimization (TITO) to help alignment and modelling of remote homologuesby: Gilles Labesse, J. P. Mornon v. 14 i. 2 p. 206 - 211
- Fast computation of 3D radon transform via a direct Fourier methodby: Salvatore Lanzavecchia, Pier Luigi Bellon v. 14 i. 2 p. 212 - 216
- Automated management of gene discovery projectsby: S. Taylor, T. Charles Hodgman, C. B. Littler, Roger A. Sayle, R. W. Gill, M. D. Oxer, C. H. O'Donnell, Andrew Lyall v. 14 i. 2 p. 217 - 218
- TOPAL: recombination detection in DNA and protein sequencesby: Gráinne McGuire, Frank Wright v. 14 i. 2 p. 219 - 220
- STRIRED: graphical analysis of string repeatsby: Giovanni Iazzetti, M. L. Chiusano, Raffaele Calogero v. 14 i. 2 p. 221 - 222
- GeneFIND web server for protein family identification and information retrievalby: C. H. Wu, S. Shivakumar, C. V. Shivakumar, S. C. Chen v. 14 i. 2 p. 223 - 224
- MEICPS: substitution mutations to engineer intracellular protein stabilityby: B. V. B. Reddy, P. Ramesh, S. Tiwari v. 14 i. 2 p. 225 - 226
- An EXCEL template for calculation of enzyme kinetic parameters by non-linear regressionby: A. Hernandez, M. T. Ruiz v. 14 i. 2 p. 227 - 228
- GeneGenerator - a flexible algorithm for gene prediction and its application to maize sequencesby: Jürgen Kleffe, Klaus Hermann, W. Vahrson, B. Wittig, Volker Brendel v. 14 i. 3 p. 232 - 243
- Transcription regulatory region analysis using signal detection and fuzzy clusteringby: L. Pickert, Ingmar Reuter, Frank Klawonn, Edgar Wingender v. 14 i. 3 p. 244 - 251
- A distributed environment for physical map constructionby: Andrei Grigoriev, Alexander Levin, Hans Lehrach v. 14 i. 3 p. 252 - 258
- A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamilyby: Alexander E. Kel, Andrey A. Ptitsyn, Vladimir N. Babenko, Sebastian Meier-Ewert, Hans Lehrach v. 14 i. 3 p. 259 - 270
- Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approachesby: Thomas Dandekar, Katrin Beyer, Peer Bork, Mary-Rose Kenealy, Kostas Pantopoulos, Mathias Hentze, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, Sonja Schreiber v. 14 i. 3 p. 271 - 278
- Statistics of large-scale sequence searchingby: Rainer Spang, Martin Vingron v. 14 i. 3 p. 279 - 284
- Towards detection of orthologues in sequence databasesby: Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork v. 14 i. 3 p. 285 - 289
- DIALIGN: finding local similarities by multiple sequence alignmentby: Burkhard Morgenstern, Kornelie Frech, Andreas W. M. Dress, Thomas Werner v. 14 i. 3 p. 290 - 294
- New scoring schemes for protein fold recognition based on Voronoi contactsby: Ralf Zimmer, Marko Wöhler, Ralf Thiele v. 14 i. 3 p. 295 - 308
- Mapmerge: merge genomic mapsby: Prakash M. Nadkarni v. 14 i. 4 p. 310 - 316
- Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequencesby: Tetsushi Yada, Yasushi Totoki, M. Ishikawa, K. Asai, Kenta Nakai v. 14 i. 4 p. 317 - 325
- DIAMOD: display and modeling of DNA bendingby: M. Dlakic, R. E. Harrington v. 14 i. 4 p. 326 - 331
- Optimization of ribosomal RNA profile alignmentsby: Emmet A. O'Brien, Cédric Notredame, Desmond G. Higgins v. 14 i. 4 p. 332 - 341
- The new Virgil database: a service of rich linksby: Frédéric Achard, Christophe Cussat-Blanc, Eric Viara, Emmanuel Barillot v. 14 i. 4 p. 342 - 348
- Searching DNA databases for similarities to DNA sequences: when is a match significant?by: I. Anderson, A. Brass v. 14 i. 4 p. 349 - 356
- Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictionsby: P. Briffeuil, G. Baudoux, C. Lambert, X. De Bolle, C. Vinals, Ernest Feytmans, E. Depiereux v. 14 i. 4 p. 357 - 366
- Frame: detection of genomic sequencing errorsby: N. P. Brown, Chris Sander, Peer Bork v. 14 i. 4 p. 367 - 371
- GCUA: general codon usage analysisby: James O. McInerney v. 14 i. 4 p. 372 - 373
- POLINA: detection and evaluation of single amino acid substitutions in protein superfamiliesby: S. Levin, B. H. Satir v. 14 i. 4 p. 374 - 375
- Self-organizing tree growing network for classifying amino acidsby: Huaichun Wang, Joaquín Dopazo, José María Carazo v. 14 i. 4 p. 376 - 377
- SOSUI: classification and secondary structure prediction system for membrane proteinsby: Takatsug Hirokawa, S. Boon-Chieng, Shigeki Mitaku v. 14 i. 4 p. 378 - 379
- MView: a web-compatible database search or multiple alignment viewerby: N. P. Brown, Christophe Leroy, Chris Sander v. 14 i. 4 p. 380 - 381
- Assessing protein coding region integrity in cDNA sequencing projectsby: Asaf A. Salamov, Tetsuo Nishikawa, Mark B. Swindells v. 14 i. 5 p. 384 - 390
- Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12by: Denis Thieffry, Heladia Salgado, Araceli M. Huerta, Julio Collado-Vides v. 14 i. 5 p. 391 - 400
- Reduced space hidden Markov model trainingby: C. Tarnas, Richard Hughey v. 14 i. 5 p. 401 - 406
- COFFEE: an objective function for multiple sequence alignmentsby: Cédric Notredame, Liisa Holm, Desmond G. Higgins v. 14 i. 5 p. 407 - 422
- Removing near-neighbour redundancy from large protein sequence collectionsby: Liisa Holm, Chris Sander v. 14 i. 5 p. 423 - 429
- A set-theoretic approach to database searching and clusteringby: Antje Krause, Martin Vingron v. 14 i. 5 p. 430 - 438
- Computational space reduction and parallelization of a new clustering approach for large groups of sequencesby: Oswaldo Trelles, Miguel A. Andrade, Alfonso Valencia, Emilio L. Zapata, José María Carazo v. 14 i. 5 p. 439 - 451
- W2H: WWW interface to the GCG sequence analysis packageby: Martin Senger, T. Flores, Karl-Heinz Glatting, Peter Ernst, Agnes Hotz-Wagenblatt, Sándor Suhai v. 14 i. 5 p. 452 - 457
- POPSIM: a general population simulation programby: Jochen Hampe, T. Wienker, Stefan Schreiber, P. Nurnberg v. 14 i. 5 p. 458 - 464
- CloneIt: finding cloning strategies, in-frame deletions and frameshiftsby: P. Lindenbaum v. 14 i. 5 p. 465 - 466
- SWAN: sliding window analysis of nucleotide sequence variabilityby: V. Proutski, E. Holmes v. 14 i. 5 p. 467 - 468
- The BioCatalogby: Patricia Rodriguez-Tomé v. 14 i. 5 p. 469 - 470
- Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented libraryby: Toshitsugu Okayama, T. Tamura, Takashi Gojobori, Yoshio Tateno, Kazuho Ikeo, Satoru Miyazaki, Kaoru Fukami-Kobayashi, Hideaki Sugawara v. 14 i. 6 p. 472 - 478
- The bio-objects project. Part I: the object data model core elementsby: S. Z. Maltchenko v. 14 i. 6 p. 479 - 485
- A metadata approach to query interoperation between molecular biology databasesby: Kei-Hoi Cheung, Prakash M. Nadkarni, Dong-Guk Shin v. 14 i. 6 p. 486 - 497
- Detecting periodic patterns in biological sequencesby: Eivind Coward, Finn Drabløs v. 14 i. 6 p. 498 - 507
- SSMAL: similarity searching with alignment graphsby: P. Nicodeme v. 14 i. 6 p. 508 - 515
- A geometric algorithm to find small but highly similar 3D substructures in proteinsby: Xavier Pennec, Nicholas Ayache v. 14 i. 6 p. 516 - 522
- Homology modeling, model and software evaluation: three related resourcesby: R. Rodriguez, G. Chinea, N. Lopez, T. Pons, Gert Vriend v. 14 i. 6 p. 523 - 528
- GeneNet: a gene network database and its automated visualizationby: F. A. Kolpakov, Elena A. Ananko, G. B. Kolesov, Nikolay A. Kolchanov v. 14 i. 6 p. 529 - 537
- Z extensions to the RHMAPPER packageby: Carol Soderlund, Timun Lau, Panos Deloukas v. 14 i. 6 p. 538 - 539
- TLCQA: quantitative study of thin-layer chromatographyby: F. T. Chau, T. P. Chan, J. Wang v. 14 i. 6 p. 540 - 541
- EUCLID: automatic classification of proteins in functional classes by their database annotationsby: Javier Tamames, Christos A. Ouzounis, Georg Casari, Chris Sander, Alfonso Valencia v. 14 i. 6 p. 542 - 543
- New phylogenetic venues opened by a novel implementation of the DNAml algorithmby: Oswaldo Trelles, C. Ceron, Huaichun Wang, Joaquín Dopazo, José María Carazo v. 14 i. 6 p. 544 - 545
- Graphical interface to the genetic network database GeNetby: V. N. Serov, Alexander V. Spirov, Maria Samsonova v. 14 i. 6 p. 546 - 547
- A curriculum for bioinformatics: the time is ripeby: Russ B. Altman v. 14 i. 7 p. 549 - 550
- Comprehensive, comprehensible, distributed and intelligent databases: current statusby: Dmitrij Frishman, Klaus Heumann, A. Lesk, Hans-Werner Mewes v. 14 i. 7 p. 551 - 561
- The LabBase system for data management in large scale biology research laboratoriesby: Nathan Goodman, Steve Rozen, Lincoln Stein, A. G. Smith v. 14 i. 7 p. 562 - 574
- A model system for studying the integration of molecular biology databasesby: J. Macauley, H. Wang, Nathan Goodman v. 14 i. 7 p. 575 - 582
- Issues in developing integrated genomic databases and application to the human X chromosomeby: Ulf Leser, Hans Lehrach, Hugues Roest Crollius v. 14 i. 7 p. 583 - 590
- LIGAND: chemical database for enzyme reactionsby: S. Goto, T. Nishioka, M. Kanehisa v. 14 i. 7 p. 591 - 599
- Automatic extraction of keywords from scientific text: application to the knowledge domain of protein familiesby: Miguel A. Andrade, Alfonso Valencia v. 14 i. 7 p. 600 - 607
- The effect of evenly spaced constant sites on the distribution of the random division of a molecular sequenceby: P. H. Sneath v. 14 i. 7 p. 608 - 616
- JOY: protein sequence-structure representation and analysisby: Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington v. 14 i. 7 p. 617 - 623
- An NMR assignment module implemented in the Gifa NMR processing programby: Therese E. Malliavin, Jean-Luc Pons, Marc-André Delsuc v. 14 i. 7 p. 624 - 631
- QU-GENE: a simulation platform for quantitative analysis of genetic modelsby: Dean W. Podlich, Mark Cooper v. 14 i. 7 p. 632 - 653
- GeneCards: a novel functional genomics compendium with automated data mining and query reformulation supportby: Michael Rebhan, Vered Chalifa-Caspi, J. Prilusky, Doron Lancet v. 14 i. 8 p. 656 - 664
- Gene recognition by combination of several gene-finding programsby: K. Murakami, T. Takagi v. 14 i. 8 p. 665 - 675
- Recognition of splice junctions on DNA sequences by BRAIN learning algorithmby: S. Rampone v. 14 i. 8 p. 676 - 684
- A new fourier transform approach for protein coding measure based on the format of the Z curveby: M. Yan, Z. S. Lin, C. T. Zhang v. 14 i. 8 p. 685 - 690
- An RNA folding method capable of identifying pseudoknots and base triplesby: Jack E. Tabaska, Robert B. Cary, Harold N. Gabow, Gary D. Stormo v. 14 i. 8 p. 691 - 699
- Prediction of RNA secondary structure based on helical regions distributionby: Li Wuju, W. JiaJin v. 14 i. 8 p. 700 - 706
- Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequenceby: Mark Gerstein v. 14 i. 8 p. 707 - 714
- A strategy for finding regions of similarity in complete genome sequencesby: Pierre Vincens, L. Buffat, Cécile André, Jean-Paul Chevrolat, Jean-François Boisvieux, Serge A. Hazout v. 14 i. 8 p. 715 - 725
- PASSML: combining evolutionary inference and protein secondary structure predictionby: Pietro Lió, N. Goldman, Jeffrey L. Thorne, David T. Jones v. 14 i. 8 p. 726 - 733
- Mapplet: a CORBA-based genome map viewerby: Kim Jungfer, Patricia Rodriguez-Tomé v. 14 i. 8 p. 734 - 738
- A visual environment for the manipulation and integration of JAVA beansby: J. Boyle v. 14 i. 8 p. 739 - 748
- A web server to locate periodicities in a sequenceby: C. M. Pasquier, Vassilis J. Promponas, N. J. Varvayannis, Stavros J. Hamodrakas v. 14 i. 8 p. 749 - 750
- PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequencesby: T. R. Burglin v. 14 i. 8 p. 751 - 752
- Profile hidden Markov modelsby: Sean R. Eddy v. 14 i. 9 p. 755 - 763
- Molecules to maps: tools for visualization and interaction in support of computational biologyby: Eileen Kraemer, Thomas E. Ferrin v. 14 i. 9 p. 764 - 771
- Weighting hidden Markov models for maximum discriminationby: Rachel Karchin, Richard Hughey v. 14 i. 9 p. 772 - 782
- Domain identification by clustering sequence alignmentsby: X. Guan, L. Du v. 14 i. 9 p. 783 - 788
- A method for comparing circular genomes from gene locations: application to mitochondrial genomesby: Katsuhisa Horimoto, M. Suyama, Hiroyuki Toh, Kentaro Mori, Jinya Otsuka v. 14 i. 9 p. 789 - 802
- Representing metabolic pathway information: an object-oriented approachby: L. B. Ellis, S. M. Speedie, R. McLeish v. 14 i. 9 p. 803 - 806
- Zomit: biological data visualization and browsingby: Stuart Pook, Guy Vaysseix, Emmanuel Barillot v. 14 i. 9 p. 807 - 814
- VIRTLAB: a virtual molecular biology laboratoryby: Giovanni Iazzetti, G. Santini, M. Rau, E. Bucci, Raffaele Calogero v. 14 i. 9 p. 815 - 816
- MODELTEST: testing the model of DNA substitutionby: David Posada, Keith A. Crandall v. 14 i. 9 p. 817 - 818
- GeneTree: comparing gene and species phylogenies using reconciled treesby: Roderic D. M. Page v. 14 i. 9 p. 819 - 820
- JavaShade: multiple sequence alignment box-and-shading on the World Wide Webby: M. R. Southern, A. P. Lewis v. 14 i. 9 p. 821 - 822
- SPEM: a parser for EMBL style flat file database entriesby: Matthew R. Pocock, Tim J. P. Hubbard, Ewan Birney v. 14 i. 9 p. 823 - 824
- WEBMAP: radiation hybrid mapping on the WWWby: W. Newell, P. Sanseau, J. Riley, A. Lyall v. 14 i. 9 p. 825 - 826
- An Internet linkage and mutation database for the complex phenotype asthmaby: Matthias Wjst, Thomas Immervoll v. 14 i. 9 p. 827 - 828
- Empirical estimation of the reliability of ribosomal RNA alignmentsby: Emmet A. O'Brien, Desmond G. Higgins v. 14 i. 10 p. 830 - 838
- SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignmentsby: Torbjørn Rognes, Erling Seeberg v. 14 i. 10 p. 839 - 845
- Hidden Markov models for detecting remote protein homologiesby: Kevin Karplus, C. Barrett, Richard Hughey v. 14 i. 10 p. 846 - 856
- A new criterion to classify globular proteins based on their secondary structure contentsby: C. T. Zhang, R. Zhang v. 14 i. 10 p. 857 - 865
- VHMPT: a graphical viewer and editor for helical membrane protein topologiesby: W. J. Lin, M. J. Hwang v. 14 i. 10 p. 866 - 868
- Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimationby: Pedro Mendes, Douglas B. Kell v. 14 i. 10 p. 869 - 883
- GeneDn: for high-level expression design of heterologous genes in a prokaryotic systemby: L. W. Ju, L. H. Xing, P. W. Hong, W. J. Jin v. 14 i. 10 p. 884 - 885
- HIV-1 genotypic resistance: automated sequence analysis and interpretationby: C. P. Goujon, V. M. Schneider, C. Jacomet, J. C. Nicolas v. 14 i. 10 p. 886 - 887
- BioABACUS: a database of abbreviations and acronyms in biotechnology and computer scienceby: M. Rimer, Michael O'Connell v. 14 i. 10 p. 888 - 889
- BEAUTY-X: enhanced BLAST searches for DNA queriesby: K. C. Worley, P. Culpepper, B. A. Wiese, R. F. Smith v. 14 i. 10 p. 890 - 891
- JPred: a consensus secondary structure prediction serverby: James A. Cuff, Michele E. Clamp, Asim S. Siddiqui, M. Finlay, Geoffrey J. Barton v. 14 i. 10 p. 892 - 893
