| 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 | Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. | Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy |
| 2011 | Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals. | Xin Li, Jing Li |
| 2011 | IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly - (Extended Abstract). | Wei Li, Jianxing Feng, Tao Jiang |
| 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 | 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 | Pedigree Reconstruction Using Identity by Descent. | Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin |
| 2011 | PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract). | Jaebum Kim, Jian Ma |
| 2011 | Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions. | Shuai Jiang, Max A. Alekseyev |
| 2011 | Variable Selection through Correlation Sifting. | Jim C. Huang, Nebojsa Jojic |
| 2011 | Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. | Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew W. McPherson, Evan E. Eichler, Sleyman Cenk Sahinalp |
| 2011 | A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels. | Glenn Hickey, Mathieu Blanchette |
| 2011 | Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways. | Allison P. Heath, George N. Bennett, Lydia E. Kavraki |
| 2011 | Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. | Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir |
| 2011 | Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. | Song Gao, Niranjan Nagarajan, Wing-Kin Sung |
| 2011 | Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks. | Sinan Erten, Grkan Bebek, Mehmet Koyutrk |
| 2011 | Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome. | Jason Ernst, Manolis Kellis |
| 2011 | Hapsembler: An Assembler for Highly Polymorphic Genomes. | Nilgun Donmez, Michael Brudno |
| 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 | Metabolic Network Analysis Demystified. | Leonid Chindelevitch, Aviv Regev, Bonnie Berger |
| 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 | Bacterial Community Reconstruction Using Compressed Sensing. | Amnon Amir, Or Zuk |
| 2010 | A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. | Jianyang Zeng, Pei Zhou, Bruce Randall Donald |
| 2010 | On Exploring Genome Rearrangement Phylogenetic Patterns. | Andrew Wei Xu |
| 2010 | A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using | Yu-Wei Wu, Yuzhen Ye |