| 2011 | Algorithms for MDC-Based Multi-locus Phylogeny Inference. | Yun Yu, Tandy J. Warnow, Luay Nakhleh |
| 2011 | Nonparametric Combinatorial Sequence Models. | Fabian L. Wauthier, Michael I. Jordan, Nebojsa Jojic |
| 2011 | An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. | Jrme Waldisphl, Yann Ponty |
| 2011 | Untitled record | Fabio Vandin, Eli Upfal, Benjamin J. Raphael |
| 2011 | Protein Loop Closure Using Orientational Restraints from NMR Data. | Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald |
| 2011 | Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection. | Ryan Tarpine, Fumei Lam, Sorin Istrail |
| 2011 | Increasing Power of Groupwise Association Test with Likelihood Ratio Test. | Jae Hoon Sul, Buhm Han, Eleazar Eskin |
| 2011 | Optimally Orienting Physical Networks. | Dana Silverbush, Michael Elberfeld, Roded Sharan |
| 2011 | Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. | Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jrme Waldisphl |
| 2011 | Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. | Emre Sefer, Carl Kingsford |
| 2011 | Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. | Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Bcker |
| 2011 | Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm. | Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce Randall Donald |
| 2011 | A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). | Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller |
| 2011 | Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. | Yosef Prat, Menachem Fromer, Michal Linial, Nathan Linial |
| 2011 | Experiment Specific Expression Patterns. | Tobias Petri, Robert Kffner, Ralf Zimmer |
| 2011 | T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome - (Extended Abstract). | Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin |
| 2011 | Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets. | Hanchuan Peng, Fuhui Long |
| 2011 | Optimization of Combinatorial Mutagenesis. | Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg |
| 2011 | A Three-Dimensional Model of the Yeast Genome. | William Stafford Noble, Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau |
| 2011 | Blocked Pattern Matching Problem and Its Applications in Proteomics. | Julio Ng, Amihood Amir, Pavel A. Pevzner |
| 2011 | AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization. | Daniel Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie |
| 2011 | Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk. | Joe Nadeau |
| 2011 | Multiplex De Novo Sequencing of Peptide Antibiotics. | Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner |
| 2011 | An Optimization-Based Sampling Scheme for Phylogenetic Trees. | Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz |
| 2011 | Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. | Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner |