| 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 | A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs. Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald |
| 2011 | A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. Glenn Hickey, Mathieu Blanchette |
| 2011 | A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of Transcription. Sooraj KuttyKrishnan, Jeffrey Sabina, Laura Langton, Mark Johnston, Michael R. Brent |
| 2011 | A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract). Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller |
| 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 | AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization. Daniel Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie |
| 2011 | Algorithms for MDC-Based Multi-locus Phylogeny Inference. Yun Yu, Tandy J. Warnow, Luay Nakhleh |
| 2011 | An Optimization-Based Sampling Scheme for Phylogenetic Trees. Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz |
| 2011 | An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. Jérôme Waldispühl, Yann Ponty |
| 2011 | Bacterial Community Reconstruction Using Compressed Sensing. Amnon Amir, Or Zuk |
| 2011 | Blocked Pattern Matching Problem and Its Applications in Proteomics. Julio Ng, Amihood Amir, Pavel A. Pevzner |
| 2011 | Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes - (Extended Abstract). Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch S. Huang |
| 2011 | Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker |
| 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 | Constrained De Novo Sequencing of Peptides with Application to Conotoxins. Swapnil Bhatia, Yong J. Kil, Beatrix Ueberheide, Brian T. Chait, Lemmuel Lara Tayo, Lourdes J. Cruz, Bingwen Lu, John R. Yates III, Marshall W. Bern |
| 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 | Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome. Jason Ernst, Manolis Kellis |
| 2011 | Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks. Sinan Erten, Gürkan Bebek, Mehmet Koyutürk |
| 2011 | Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl |
| 2011 | Experiment Specific Expression Patterns. Tobias Petri, Robert Küffner, Ralf Zimmer |
| 2011 | Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk. Joe Nadeau |
| 2011 | Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. Yosef Prat, Menachem Fromer, Michal Linial, Nathan Linial |
| 2011 | Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals. Xin Li, Jing Li |
| 2011 | Hapsembler: An Assembler for Highly Polymorphic Genomes. Nilgun Donmez, Michael Brudno |
| 2011 | Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways. Allison P. Heath, George N. Bennett, Lydia E. Kavraki |
| 2011 | Increasing Power of Groupwise Association Test with Likelihood Ratio Test. Jae Hoon Sul, Buhm Han, Eleazar Eskin |
| 2011 | Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut. Mark D. M. Leiserson, Diana Tatar, Lenore J. Cowen, Benjamin J. Hescott |
| 2011 | IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly - (Extended Abstract). Wei Li, Jianxing Feng, Tao Jiang |
| 2011 | Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy |
| 2011 | Metabolic Network Analysis Demystified. Leonid Chindelevitch, Aviv Regev, Bonnie Berger |
| 2011 | Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. Emre Sefer, Carl Kingsford |
| 2011 | Multiplex De Novo Sequencing of Peptide Antibiotics. Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudêncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner |
| 2011 | Nonparametric Combinatorial Sequence Models. Fabian L. Wauthier, Michael I. Jordan, Nebojsa Jojic |
| 2011 | Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. Song Gao, Niranjan Nagarajan, Wing-Kin Sung |
| 2011 | Optimally Orienting Physical Networks. Dana Silverbush, Michael Elberfeld, Roded Sharan |
| 2011 | Optimization of Combinatorial Mutagenesis. Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg |
| 2011 | PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract). Jaebum Kim, Jian Ma |
| 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 |
| 2011 | Pedigree Reconstruction Using Identity by Descent. Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin |
| 2011 | Protein Loop Closure Using Orientational Restraints from NMR Data. Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald |
| 2011 | Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings Vineet Bafna, Süleyman Cenk Sahinalp |
| 2011 | Rich Parameterization Improves RNA Structure Prediction. Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson |
| 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 | Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew W. McPherson, Evan E. Eichler, Süleyman Cenk Sahinalp |
| 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 | Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir |
| 2011 | Variable Selection through Correlation Sifting. Jim C. Huang, Nebojsa Jojic |
| 2011 | Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions. Shuai Jiang, Max A. Alekseyev |