| 2005 | Topological Robustness of the Protein-Protein Interaction Networks. | Chien-Hung Huang, Jywe-Fei Fang, Jeffrey J. P. Tsai, Ka-Lok Ng |
| 2005 | Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes. | Michiel J. L. de Hoon, Dennis Vitkup |
| 2005 | The Incompatible Desiderata of Gene Cluster Properties. | Rose Hoberman, Dannie Durand |
| 2005 | HAPLOFREQ - Estimating Haplotype Frequencies E.ciently. | Eran Halperin, Elad Hazan |
| 2005 | A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. | Dan Gusfield, Vikas Bansal |
| 2005 | Using Multiple Alignments to Improve Gene Prediction. | Samuel S. Gross, Michael R. Brent |
| 2005 | The Factor Graph Network Model for Biological Systems. | Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir |
| 2005 | Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. | Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes |
| 2005 | Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. | Ari Frank, Stephen Tanner, Pavel A. Pevzner |
| 2005 | A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. | Dannie Durand, Bjarni V. Halldrsson, Benjamin Vernot |
| 2005 | A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. | Zhihong Ding, Vladimir Filkov, Dan Gusfield |
| 2005 | The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways. | David L. Dill, Merrill Knapp, Pamela Gage, Carolyn L. Talcott, Keith Laderoute, Patrick Lincoln |
| 2005 | OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements. | Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander C. J. Roth, Adrian Schneider, Gaston H. Gonnet |
| 2005 | Discovery and Annotation of Genetic Modules. | Charles DeLisi |
| 2005 | The String Barcoding Problem is NP-Hard. | Marcello Dalpasso, Giuseppe Lancia, Romeo Rizzi |
| 2005 | Likely Scenarios of Intron Evolution. | Mikls Csrs |
| 2005 | Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology. | James J. Collins |
| 2005 | Maximum Likelihood of Evolutionary Trees Is Hard. | Benny Chor, Tamir Tuller |
| 2005 | A Practical Approach to Significance Assessment in Alignment with Gaps. | Nicholas Chia, Ralf Bundschuh |
| 2005 | Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data. | Elissa J. Chesler, Michael A. Langston |
| 2005 | Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis. | Chih-Yu Chen, Von-Wun Soo, Chi-Li Kuo |
| 2005 | An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes. | Liran Carmel, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin |
| 2005 | Information Theoretic Approaches to Whole Genome Phylogenies. | David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor |
| 2005 | Maximizing Synteny Blocks to Identify Ancestral Homologs. | Guillaume Bourque, Yasmine Yacef, Nadia El-Mabrouk |
| 2005 | Genes Order and Phylogenetic Reconstruction: Application to | Guillaume Blin, Cdric Chauve, Guillaume Fertin |