Algorithms in Bioinformatics
2004
- Novel Tree Edit Operations for RNA Secondary Structure Comparisonby: Julien Allali, Marie-France Sagot
- New Algorithms for Multiple DNA Sequence Alignmentby: Daniel G. Brown, Alexander K. Hudek
- ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequencesby: Stanislav Angelov, Sanjeev Khanna, Li Li, Fernando Pereira
- Online Consensus and Agreement of Phylogenetic Treesby: Tanya Y. Berger-Wolf
- Relation of Residues in the Variable Region of 16S rDNA Sequences and Their Relevance to Genus-Specificityby: Maciej Liskiewicz, Hemant J. Purohit, Dhananjay V. Raje
- Algorithms for Finding Maximal-Scoring Segment Sets (Extended Abstract)by: Miklós Csürös
- Genome Identification and Classification by Short Oligo Arraysby: Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, Li-San Wang
- Suboptimal Local Alignments Across Multiple Scoring Schemesby: Morris Michael, Christoph Dieterich, Jens Stoye
- A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences Through Alignmentby: Jesper Jansson, See-Kiong Ng, Wing-Kin Sung, Hugo Willy
- Local Search Heuristic for Rigid Protein Dockingby: Vicky Choi, Pankaj K. Agarwal, Herbert Edelsbrunner, Johannes Rudolph
- A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patternsby: Jens Gramm
- Phylogenetic Super-networks from Partial Treesby: Daniel H. Huson, Tobias Dezulian, Tobias Klöpper, Mike A. Steel
- The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approachby: Behshad Behzadi, Jean-Marc Steyaert
- Translation Initiation Sites Prediction with Mixture Gaussian Modelsby: Guoliang Li, Tze-Yun Leong, Louxin Zhang
- Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstructionby: Alessandro Panconesi, Mauro Sozio
- Solving the Protein Threading Problem by Lagrangian Relaxationby: Stefan Balev
- Joint Analysis of DNA Copy Numbers and Gene Expression Levelsby: Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini
- Sequence Database Compression for Peptide Identification from Tandem Mass Spectraby: Nathan Edwards, Ross Lippert
- Integrating Sample-Driven and Pattern-Driven Approaches in Motif Findingby: Sing-Hoi Sze, Songjian Lu, Jianer Chen
- Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizationsby: Alexandra Shulman-Peleg, Shira Mintz, Ruth Nussinov, Haim J. Wolfson
- Finding Missing Patternsby: Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen
- Finding Optimal Pairs of Patternsby: Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
- Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Databy: Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M. E. Moret
- Reconstructing Ancestral Gene Orders Using Conserved Intervalsby: Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cedric Chauve
- A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversalsby: Tzvika Hartman, Roded Sharan
- The Most Probable Labeling Problem in HMMs and Its Application to Bioinformaticsby: Brona Brejová, Daniel G. Brown, Tomás Vinar
- Multiple Vector Seeds for Protein Alignmentby: Daniel G. Brown
- A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysisby: Daniel G. Brown, Ian M. Harrower
- Topological Rearrangements and Local Search Method for Tandem Duplication Treesby: Denis Bertrand, Olivier Gascuel
- Adding Hidden Nodes to Gene Networks (Extended Abstract)by: Benny Chor, Tamir Tuller
- Approximation Algorithms for the Selection of Robust Tag SNPsby: Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao
- Linear Reduction for Haplotype Inferenceby: Jingwu He, Alexander Zelikovsky
- Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprintingby: Daichi Shigemizu, Osamu Maruyama
- Gapped Local Similarity Search with Provable Guaranteesby: Manikandan Narayanan, Richard M. Karp
- Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotationby: Lev Soinov, Alexander Kanapin, Misha Kapushesky
- A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statisticby: Uri Keich, Niranjan Nagarajan
- Chaining Algorithms for Alignment of Draft Sequenceby: Mukund Sundararajan, Michael Brudno, Kerrin Small, Arend Sidow, Serafim Batzoglou
- Monotone Scoring of Patterns with Mismatches: (Extended Abstract)by: Alberto Apostolico, Cinzia Pizzi
- Sorting by Reversals with Common Intervalsby: Martin Figeac, Jean-Stéphane Varré
- Speedup LP Approach to Protein Threading via Graph Reductionby: Jinbo Xu
- New Efficient Algorithm for Detection of Horizontal Gene Transfer Eventsby: Alix Boc, Vladimir Makarenkov
- Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Powerby: Jan A. Spriet
- A Local Chaining Algorithm and Its Applications in Comparative Genomicsby: Mohamed Ibrahim Abouelhoda, Enno Ohlebusch
- Designing Optimally Multiplexed SNP Genotyping Assaysby: Yonatan Aumann, Efrat Manisterski, Zohar Yakhini
- Ancestral Maximum Likelihood of Evolutionary Trees Is Hardby: Louigi Addario-Berry, Benny Chor, Michael T. Hallett, Jens Lagergren, Alessandro Panconesi, Todd Wareham
- Better Hill-Climbing Searches for Parsimonyby: Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy Warnow
- Consensus Networks: A Method for Visualising Incompatibilities in Collections of Treesby: Barbara Holland, Vincent Moulton
- Composition Alignmentby: Gary Benson
- Computing Refined Buneman Trees in Cubic Timeby: Gerth Stølting Brodal, Rolf Fagerberg, Anna Östlin, Christian N. S. Pedersen, S. Srinivasa Rao
- Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependencyby: Brona Brejová, Daniel G. Brown, Tomás Vinar
- Identifying Blocks and Sub-populations in Noisy SNP Databy: Gad Kimmel, Roded Sharan, Ron Shamir
- Bounds for Resquencing by Hybridizationby: Dekel Tsur
- Dynamic Programming Algorithms for Two Statistical Problems in Computational Biologyby: Sven Rahmann
- Efficient Generation of Uniform Samples from Phylogenetic Treesby: Paul E. Kearney, J. Ian Munro, Derek Phillips
- Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ ntby: Sebastian Böcker
- New Algorithm for the Simplified Partial Digest Problemby: Jacek Blazewicz, M. Jaroszewski
- A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methodsby: Boris Hollas, Rainer Schuler
- A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequenceby: Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi
- Minimum Recombiant Haplotype Configuration on Tree Pedigreesby: Koichiro Doi, Jing Li, Tao Jiang
- A Linear-Time Majority Tree Algorithmby: Nina Amenta, Frederick Clarke, Katherine St. John
- Distance Corrections on Recombinant Sequencesby: David Bryant, Daniel H. Huson, Tobias Klöpper, Kay Nieselt-Struwe
- Noisy Data Make the Partial Digest Problem NP-hardby: Mark Cieliebak, Stephan Eidenbenz, Paolo Penna
- A Combinatorial Approach to Automatic Discovery of Cluster-Patternsby: Revital Eres, Gad M. Landau, Laxmi Parida
- A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoringby: Jacques Colinge, Alexandre Masselot, Jérôme Magnin
- Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocksby: Yun S. Song, Jotun Hein
- Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifityby: Brona Brejová, Daniel G. Brown, Tomás Vinar
- Common Intervals of Two Sequencesby: Gilles Didier
- Efficient Energy Computation for Monte Carlo Simulation of Proteinsby: Itay Lotan, Fabian Schwarzer, Jean-Claude Latombe
- Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Modelby: Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Jotun Hein
- Selecting Degenerate Multiplex PCR Primersby: Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang
- Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Treeby: Bjarne Knudsen
- A Large Version of the Small Parsimony Problemby: Jakob Fredslund, Jotun Hein, Tejs Scharling
- Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignmentby: Jahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda
- Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functionsby: Alban Mancheron, Irena Rusu
- Match Chaining Algorithms for cDNA Mappingby: Tetsuo Shibuya, Igor Kurochkin
- Segment Match Refinement and Applicationsby: Aaron L. Halpern, Daniel H. Huson, Knut Reinert
- Efficient Methods for Inferring Tandem Duplication Historyby: Louxin Zhang, Bin Ma, Lusheng Wang
- The Algorithmic of Gene Teamsby: Anne Bergeron, Sylvie Corteel, Mathieu Raffinot
- Invited Lecture - Molecule as Computation: Towards an Abstraction of Biomolecular Systemsby: Ehud Y. Shapiro
- Sequence-Length Requirements for Phylogenetic Methodsby: Bernard M. E. Moret, Usman Roshan, Tandy Warnow
- A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Findingby: Mihaela Pertea, Steven Salzberg
- Functional Consequences in Metabolic Pathways from Phylogenetic Profilesby: Yonatan Bilu, Michal Linial
- Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformaticsby: Michael Goldwasser, Ming-Yang Kao, Hsueh-I Lu
- Modified Mincut Supertreesby: Roderic D. M. Page
- Exploring the Set of All Minimal Sequences of Reversals - An Application to Test the Replication-Directed Reversal Hypothesisby: Yasmine Ajana, Jean-François Lefebvre, Elisabeth R. M. Tillier, Nadia El-Mabrouk
- Approximating the Expected Number of Inversions Given the Number of Breakpointsby: Niklas Eriksen
- Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Databy: Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu
- Simultaneous Relevant Feature Identification and Classification in High-Dimensional Spacesby: L. R. Grate, Chiranjib Bhattacharyya, Michael I. Jordan, I. Saira Mian
- Genome Rearrangement Phylogeny Using Weighborby: Li-San Wang
- Methods for Inferring Block-Wise Ancestral History from Haploid Sequencesby: Russell Schwartz, Andrew G. Clark, Sorin Istrail
- Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principleby: Richard Desper, Olivier Gascuel
- Rapid Large-Scale Oligonucleotide Selection for Microarraysby: Sven Rahmann
- Improved Approximation Algorithms for NMR Spectral Peak Assignmentby: Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Ying Xu
- Estimating the Deviation from a Molecular Clockby: Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy Warnow
- Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptomeby: Doron Lipson, Peter Webb, Zohar Yakhini
- Generating Peptide Candidates from Amino-Acid Sequence Databases for Protein Identification via Mass Spectrometryby: Nathan Edwards, Ross Lippert
- Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Searchby: Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder
- Border Length Minimization in DNA Array Designby: Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky
- Finding Founder Sequences from a Set of Recombinantsby: Esko Ukkonen
- Comparative Methods for Gene Structure Prediction in Homologous Sequencesby: Christian N. S. Pedersen, Tejs Scharling
- Invited Lecture - Accelerating Smith-Waterman Searchesby: Gene Myers, Richard Durbin
- Pooled Genomic Indexing (PGI): Mathematical Analysis and Experiment Designby: Miklós Csürös, Aleksandar Milosavljevic
- A Hybrid Scoring Function for Protein Multiple Alignmentby: Emily Rocke
- On the Control of Hybridization Noise in DNA Sequencing-by-Hybridizationby: Hon Wai Leong, Franco P. Preparata, Wing-Kin Sung, Hugo Willy
- Efficient Unbound Docking of Rigid Moleculesby: Dina Duhovny, Ruth Nussinov, Haim J. Wolfson
- The Enhanced Suffix Array and Its Applications to Genome Analysisby: Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch
- Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentationby: Ezekiel F. Adebiyi, Michael Kaufmann
- Combinatorial Use of Short Probes for Differential Gene Expression Profilingby: Liling L. Warren, Ben Hui Liu
- FAUST: An Algorithm for Extracting Functionally Relevant Templates from Protein Structuresby: Mariusz Milik, Sandor Szalma, Krzysztof A. Olszewski
- NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networksby: David Bryant, Vincent Moulton
- A Method of Consolidating and Combining EST and mRNA Alignments to a Genome to Enumerate Supported Splice Variantsby: Raymond Wheeler
- Practical Algorithms and Fixed-Parameter Tractability for the Single Individual SNP Haplotyping Problemby: Romeo Rizzi, Vineet Bafna, Sorin Istrail, Giuseppe Lancia
- MultiProt - A Multiple Protein Structural Alignment Algorithmby: Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
- K-ary Clustering with Optimal Leaf Ordering for Gene Expression Databy: Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi Jaakkola, Nathan Srebro
- Finding Signal Peptides in Human Protein Sequences Using Recurrent Neural Networksby: Martin Reczko, Petko Fiziev, Eike Staub, Artemis G. Hatzigeorgiou
- Restricting SBH Ambiguity via Restriction Enzymesby: Steven Skiena, Sagi Snir
- A Chemical-Distance-Based Test for Positive Darwinian Selectionby: Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur
- Analytic Solutions for Three-Taxon MLMC Trees with Variable Rates Across Sitesby: Benny Chor, Michael D. Hendy, David Penny
- Placing Probes along the Genome Using Pairwise Distance Databy: Will Casey, Bud Mishra, Mike Wigler
- (1+epsilon)-Approximation of Sorting by Reversals and Transpositionsby: Niklas Eriksen
- Finding an Optimal Inversion Median: Experimental Resultsby: Adam C. Siepel, Bernard M. E. Moret
- Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomesby: Li-San Wang
- The Performance of Phylogenetic Methods on Trees of Bounded Diameterby: Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow
- Comparing a Hidden Markov Model and a Stochastic Context-Free Grammarby: Arun K. Jagota, Rune B. Lyngsø, Christian N. S. Pedersen
- Improving Profile-Profile Alignments via Log Average Scoringby: Niklas von Öhsen, Ralf Zimmer
- Side Chain-Positioning as an Integer Programming Problemby: Olivia Eriksson, Yishao Zhou, Arne Elofsson
- Assessing the Statistical Significance of Overrepresented Oligonucleotidesby: Alain Denise, Mireille Régnier, Mathias Vandenbogaert
- Determination of Binding Amino Acids Based on Random Peptide Array Screening Databy: Peter J. van der Veen, L. F. A. Wessels, J. W. Slootstra, R. H. Meloen, Marcel J. T. Reinders, J. Hellendoorn
- Algorithms for Finding Gene Clustersby: Steffen Heber, Jens Stoye
- False Positives in Genomic Map Assembly and Sequence Validationby: Thomas S. Anantharaman, Bud Mishra
- An Improved Model for Statistical Alignmentby: István Miklós, Zoltán Toroczkai
- Experiments in Computing Sequences of Reversalsby: Anne Bergeron, François Strasbourg
- Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Timeby: Ganeshkumar Ganapathysaravanabavan, Tandy Warnow
- Computing Linking Numbers of a Filtrationby: Herbert Edelsbrunner, Afra Zomorodian
- Pattern Matching and Pattern Discovery Algorithms for Protein Topologiesby: Juris Viksna, David Gilbert
- On the Practical Solution of the Reversal Median Problemby: Alberto Caprara
- Comparing Assemblies Using Fragments and Mate-Pairsby: Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton
- Boosting EM for Radiation Hybrid and Genetic Mappingby: Thomas Schiex, Patrick Chabrier, Martin Bouchez, Denis Milan
- A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sitesby: Yoseph Barash, Gill Bejerano, Nir Friedman
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