| 2004 | A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals. Tzvika Hartman, Roded Sharan |
| 2004 | A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statistic. Uri Keich, Niranjan Nagarajan |
| 2004 | A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences Through Alignment. Jesper Jansson, See-Kiong Ng, Wing-Kin Sung, Hugo Willy |
| 2004 | A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis. Daniel G. Brown, Ian M. Harrower |
| 2004 | A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns. Jens Gramm |
| 2004 | ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences. Stanislav Angelov, Sanjeev Khanna, Li Li, Fernando Pereira |
| 2004 | Adding Hidden Nodes to Gene Networks (Extended Abstract). Benny Chor, Tamir Tuller |
| 2004 | Algorithms for Finding Maximal-Scoring Segment Sets (Extended Abstract). Miklós Csürös |
| 2004 | Algorithms in Bioinformatics, 4th International Workshop, WABI 2004, Bergen, Norway, September 17-21, 2004, Proceedings Inge Jonassen, Junhyong Kim |
| 2004 | Approximation Algorithms for the Selection of Robust Tag SNPs. Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao |
| 2004 | Chaining Algorithms for Alignment of Draft Sequence. Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou |
| 2004 | Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction. Alessandro Panconesi, Mauro Sozio |
| 2004 | Finding Missing Patterns. Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen |
| 2004 | Finding Optimal Pairs of Patterns. Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2004 | Gapped Local Similarity Search with Provable Guarantees. Manikandan Narayanan, Richard M. Karp |
| 2004 | Genome Identification and Classification by Short Oligo Arrays. Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, Li-San Wang |
| 2004 | Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding. Sing-Hoi Sze, Songjian Lu, Jianer Chen |
| 2004 | Joint Analysis of DNA Copy Numbers and Gene Expression Levels. Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini |
| 2004 | Linear Reduction for Haplotype Inference. Jingwu He, Alexander Zelikovsky |
| 2004 | Local Search Heuristic for Rigid Protein Docking. Vicky Choi, Pankaj K. Agarwal, Herbert Edelsbrunner, Johannes Rudolph |
| 2004 | Monotone Scoring of Patterns with Mismatches: (Extended Abstract). Alberto Apostolico, Cinzia Pizzi |
| 2004 | Multiple Vector Seeds for Protein Alignment. Daniel G. Brown |
| 2004 | New Algorithms for Multiple DNA Sequence Alignment. Daniel G. Brown, Alexander K. Hudek |
| 2004 | Novel Tree Edit Operations for RNA Secondary Structure Comparison. Julien Allali, Marie-France Sagot |
| 2004 | Online Consensus and Agreement of Phylogenetic Trees. Tanya Y. Berger-Wolf |
| 2004 | Phylogenetic Super-networks from Partial Trees. Daniel H. Huson, Tobias Dezulian, Tobias H. Klöpper, Mike A. Steel |
| 2004 | Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations. Alexandra Shulman-Peleg, Shira Mintz, Ruth Nussinov, Haim J. Wolfson |
| 2004 | Reconstructing Ancestral Gene Orders Using Conserved Intervals. Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cédric Chauve |
| 2004 | Relation of Residues in the Variable Region of 16S rDNA Sequences and Their Relevance to Genus-Specificity. Maciej Liskiewicz, Hemant J. Purohit, Dhananjay V. Raje |
| 2004 | Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data. Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M. E. Moret |
| 2004 | Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting. Daichi Shigemizu, Osamu Maruyama |
| 2004 | Sequence Database Compression for Peptide Identification from Tandem Mass Spectra. Nathan Edwards, Ross Lippert |
| 2004 | Solving the Protein Threading Problem by Lagrangian Relaxation. Stefan Balev |
| 2004 | Sorting by Reversals with Common Intervals. Martin Figeac, Jean-Stéphane Varré |
| 2004 | Suboptimal Local Alignments Across Multiple Scoring Schemes. Morris Michael, Christoph Dieterich, Jens Stoye |
| 2004 | Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation. Lev Soinov, Alexander Kanapin, Misha Kapushesky |
| 2004 | The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approach. Behshad Behzadi, Jean-Marc Steyaert |
| 2004 | The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. Brona Brejová, Daniel G. Brown, Tomás Vinar |
| 2004 | Topological Rearrangements and Local Search Method for Tandem Duplication Trees. Denis Bertrand, Olivier Gascuel |
| 2004 | Translation Initiation Sites Prediction with Mixture Gaussian Models. Guoliang Li, Tze-Yun Leong, Louxin Zhang |