| 2008 | Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. | Cuong Than, Guohua Jin, Luay Nakhleh |
| 2008 | Hurdles Hardly Have to Be Heeded. | Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret |
| 2008 | Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. | Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou |
| 2008 | Accounting for Non-genetic Factors Improves the Power of eQTL Studies. | Oliver Stegle, Anitha Kannan, Richard Durbin, John M. Winn |
| 2008 | Computational Biology: Its Challenges Past, Present, and Future. | Temple F. Smith |
| 2008 | Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia. | Denis Smirnov, Vivian G. Cheung |
| 2008 | A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. | Yanxin Shi, Itamar Simon, Tom M. Mitchell, Ziv Bar-Joseph |
| 2008 | Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny. | David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude W. dePamphilis, James H. Leebens-Mack, Victor A. Albert |
| 2008 | On the Inference of Ancestries in Admixed Populations. | Sriram Sankararaman, Gad Kimmel, Eran Halperin, Michael I. Jordan |
| 2008 | Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs. | Michael Sammeth, Gabriel Valiente, Roderic Guig |
| 2008 | Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates. | Paul Ryvkin, Jin Jun, Edward Hemphill, Craig E. Nelson |
| 2008 | Sorting Cancer Karyotypes by Elementary Operations. | Michal Ozery-Flato, Ron Shamir |
| 2008 | An Integrative Network Approach to Map the Transcriptome to the Phenome. | Michael R. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael S. Waterman, Xianghong Jasmine Zhou |
| 2008 | Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. | Paul Medvedev, Michael Brudno |
| 2008 | More Efficient Algorithms for Closest String and Substring Problems. | Bin Ma, Xiaoming Sun |
| 2008 | Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. | Rune B. Lyngs, Yun S. Song, Jotun Hein |
| 2008 | At the Origin of Life: How Did Folded Proteins Evolve? | Andrei N. Lupas |
| 2008 | Automatic Recognition of Cells (ARC) for 3D Images of C. elegans. | Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K. Kim, Gene Myers |
| 2008 | Transcriptional Regulation and Cancer Genomics. | Edison T. Liu |
| 2008 | BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. | Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Selen Uguroglu, Eric P. Xing |
| 2008 | A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. | Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu |
| 2008 | A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. | Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang |
| 2008 | Systems Metabolic Engineering. | Sang Yup Lee |
| 2008 | Protein Function Prediction Based on Patterns in Biological Networks. | Mustafa Kirac, Gultekin zsoyoglu |
| 2008 | Fast and Accurate Alignment of Multiple Protein Networks. | Maxim Kalaev, Vineet Bafna, Roded Sharan |