| 2012 | Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis. | Sebastien Roch, Sagi Snir |
| 2012 | Finding Maximum Colorful Subtrees in Practice. | Imran Rauf, Florian Rasche, Franois Nicolas, Sebastian Bcker |
| 2012 | Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. | Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev |
| 2012 | Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures. | Dmitri D. Pervouchine, Ekaterina Khrameeva, Marina Pichugina, Olexii Nikolaienko, Mikhail S. Gelfand, Petr Rubtsov, Andrey A. Mironov |
| 2012 | Structure-Guided Deimmunization of Therapeutic Proteins. | Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg |
| 2012 | Network-Based Prediction and Analysis of HIV Dependency Factors. | T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze |
| 2012 | Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. | Andrew W. McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin C. Collins, Sleyman Cenk Sahinalp |
| 2012 | The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation. | Marc A. Mart-Renom |
| 2012 | Synthetic Sequence Design for Signal Location Search. | Yaw-Ling Lin, Charles B. Ward, Steven Skiena |
| 2012 | TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq. | Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma |
| 2012 | Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. | Marcus Kinsella, Vineet Bafna |
| 2012 | A Robust Method for Transcript Quantification with RNA-seq Data. | Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, Jinze Liu |
| 2012 | LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins. | Daniel Holtby, Shuai Cheng Li, Ming Li |
| 2012 | Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. | Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk |
| 2012 | Ballast: A Ball-Based Algorithm for Structural Motifs. | Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg |
| 2012 | Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data. | Dan He, Buhm Han, Eleazar Eskin |
| 2012 | lobSTR: A Short Tandem Repeat Profiler for Personal Genomes. | Melissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich |
| 2012 | Quantifying the Dynamics of Coupled Networks of Switches and Oscillators. | Matthew R. Francis, Elana J. Fertig |
| 2012 | Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. | Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu |
| 2012 | Charge Group Partitioning in Biomolecular Simulation. | Stefan Canzar, Mohammed El-Kebir, Ren Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau |
| 2012 | Increased Methylation Variation in Epigenetic Domains across Cancer Types. | Hctor Corrada Bravo |
| 2012 | Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models. | Sivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou |
| 2012 | Protein Structure by Semidefinite Facial Reduction. | Babak Alipanahi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson, Ming Li |
| 2011 | A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. | Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald |
| 2011 | Rich Parameterization Improves RNA Structure Prediction. | Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson |