| 2008 | High-Resolution Modeling of Cellular Signaling Networks. | Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger |
| 2008 | De Novo Sequencing of Nonribosomal Peptides. | Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger G. Linington, Pieter C. Dorrestein, Pavel A. Pevzner |
| 2008 | An Evolutionary Study of the Human Papillomavirus Genomes. | Dunarel Badescu, Abdoulaye Banir Diallo, Mathieu Blanchette, Vladimir Makarenkov |
| 2007 | Parts of the Problem of Polyploids in Rearrangement Phylogeny. | Chunfang Zheng, Qian Zhu, David Sankoff |
| 2007 | A Rigorous Analysis of the Pattern of Intron Conservation Supports the | Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka |
| 2007 | Recovering True Rearrangement Events on Phylogenetic Trees. | Hao Zhao, Guillaume Bourque |
| 2007 | Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding. | Noah Zaitlen, Manuel Reyes-Gomez, David Heckerman, Nebojsa Jojic |
| 2007 | Support Vector Training of Protein Alignment Models. | Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy |
| 2007 | Minimizing and Learning Energy Functions for Side-Chain Prediction. | Chen Yanover, Ora Schueler-Furman, Yair Weiss |
| 2007 | Reconstructing an Inversion History in the | Ai Xia, Maria V. Sharakhova, Igor V. Sharakhov |
| 2007 | Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms. | Yufeng Wu |
| 2007 | Variational Upper Bounds for Probabilistic Phylogenetic Models. | Ydo Wexler, Dan Geiger |
| 2007 | Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models. | Wenyi Wang, Benilton S. Carvalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry |
| 2007 | Tools for Simulating and Analyzing RNA Folding Kinetics. | Xinyu Tang, Shawna L. Thomas, Lydia Tapia, Nancy M. Amato |
| 2007 | An Efficient and Accurate Graph-Based Approach to Detect Population Substructure. | Srinath Sridhar, Satish Rao, Eran Halperin |
| 2007 | Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. | Rohit Singh, Jinbo Xu, Bonnie Berger |
| 2007 | GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data. | Yanxin Shi, Fan Guo, Wei Wu, Eric P. Xing |
| 2007 | A Feature-Based Approach to Modeling Protein-DNA Interactions. | Eilon Sharon, Eran Segal |
| 2007 | A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data. | Ole Schulz-Trieglaff, Rene Hussong, Clemens Grpl, Andreas Hildebrandt, Knut Reinert |
| 2007 | Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data. | Jol R. Pradines, Vlado Danck, Alan Ruttenberg, Victor Farutin |
| 2007 | Multivariate Segmentation in the Analysis of Transcription Tiling Array Data. | Antonio Piccolboni |
| 2007 | Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. | Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk |
| 2007 | Rearrangements in Genomes with Centromeres Part I: Translocations. | Michal Ozery-Flato, Ron Shamir |
| 2007 | Reconstructing the Phylogeny of Mobile Elements. | Sean O'Rourke, Noah Zaitlen, Nebojsa Jojic, Eleazar Eskin |
| 2007 | Protein Conformational Flexibility Analysis with Noisy Data. | Anshul Nigham, David Hsu |