| 2004 | Supervised Learning-Aided Optimization of Expert-Driven Functional Protein Sequence Annotation. | Lev Soinov, Alexander Kanapin, Misha Kapushesky |
| 2004 | Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations. | Alexandra Shulman-Peleg, Shira Mintz, Ruth Nussinov, Haim J. Wolfson |
| 2004 | Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting. | Daichi Shigemizu, Osamu Maruyama |
| 2004 | Fast Hare: A Fast Heuristic for Single Individual SNP Haplotype Reconstruction. | Alessandro Panconesi, Mauro Sozio |
| 2004 | Gapped Local Similarity Search with Provable Guarantees. | Manikandan Narayanan, Richard M. Karp |
| 2004 | Suboptimal Local Alignments Across Multiple Scoring Schemes. | Morris Michael, Christoph Dieterich, Jens Stoye |
| 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 | Joint Analysis of DNA Copy Numbers and Gene Expression Levels. | Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini |
| 2004 | Translation Initiation Sites Prediction with Mixture Gaussian Models. | Guoliang Li, Tze-Yun Leong, Louxin Zhang |
| 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 | Finding Missing Patterns. | Shunsuke Inenaga, Teemu Kivioja, Veli Mkinen |
| 2004 | Phylogenetic Super-networks from Partial Trees. | Daniel H. Huson, Tobias Dezulian, Tobias H. Klpper, Mike A. Steel |
| 2004 | Approximation Algorithms for the Selection of Robust Tag SNPs. | Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao |
| 2004 | Linear Reduction for Haplotype Inference. | Jingwu He, Alexander Zelikovsky |
| 2004 | A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals. | Tzvika Hartman, Roded Sharan |
| 2004 | A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns. | Jens Gramm |
| 2004 | Sorting by Reversals with Common Intervals. | Martin Figeac, Jean-Stphane Varr |
| 2004 | Sequence Database Compression for Peptide Identification from Tandem Mass Spectra. | Nathan Edwards, Ross Lippert |
| 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 | Algorithms for Finding Maximal-Scoring Segment Sets (Extended Abstract). | Mikls Csrs |
| 2004 | Adding Hidden Nodes to Gene Networks (Extended Abstract). | Benny Chor, Tamir Tuller |
| 2004 | Local Search Heuristic for Rigid Protein Docking. | Vicky Choi, Pankaj K. Agarwal, Herbert Edelsbrunner, Johannes Rudolph |
| 2004 | New Algorithms for Multiple DNA Sequence Alignment. | Daniel G. Brown, Alexander K. Hudek |
| 2004 | A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis. | Daniel G. Brown, Ian M. Harrower |