| 2015 | CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer. | Mark D. M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael |
| 2015 | An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations. | Seunghak Lee, Aurlie C. Lozano, Prabhanjan Kambadur, Eric P. Xing |
| 2015 | Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models. | Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski |
| 2015 | BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. | Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald |
| 2015 | Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure. | Jong Wha J. Joo, Eun Yong Kang, Elin Org, Nicholas A. Furlotte, Brian Parks, Aldons J. Lusis, Eleazar Eskin |
| 2015 | Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. | Mark Hallen, Bruce Randall Donald |
| 2015 | Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. | Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng |
| 2015 | Locating a Tree in a Phylogenetic Network in Quadratic Time. | Philippe Gambette, Andreas D. M. Gunawan, Anthony Labarre, Stphane Vialette, Louxin Zhang |
| 2015 | KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids. | Rasmus Fonseca, Henry van den Bedem, Julie Bernauer |
| 2015 | Fragmentation Trees Reloaded. | Kai Dhrkop, Sebastian Bcker |
| 2015 | Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks. | Hyunghoon Cho, Bonnie Berger, Jian Peng |
| 2015 | CIDANE: Comprehensive Isoform Discovery and Abundance Estimation. | Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau |
| 2015 | Immunoglobulin Classification Using the Colored Antibody Graph. | Stefano Bonissone, Pavel A. Pevzner |
| 2015 | Learning Microbial Interaction Networks from Metagenomic Count Data. | Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl, Vladimir Jojic |
| 2015 | Read Clouds Uncover Variation in Complex Regions of the Human Genome. | Alex Bishara, Yuling Liu, Dorna Kashef Haghighi, Ziming Weng, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou |
| 2015 | HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data. | Emily Berger, Deniz Yrkoglu, Bonnie Berger |
| 2015 | CRISPR Detection from Short Reads Using Partial Overlap Graphs. | Ilan Ben-Bassat, Benny Chor |
| 2015 | DockStar: A Novel ILP Based Integrative Method for Structural Modelling of Multimolecular Protein Complexes (Extended Abstract). | Naama Amir, Dan Cohen, Haim J. Wolfson |
| 2015 | Efficient Alignment Free Sequence Comparison with Bounded Mismatches. | Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan |
| 2014 | Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion. | Marinka Zitnik, Blaz Zupan |
| 2014 | Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models. | Jianling Zhong, Todd Wasson, Alexander J. Hartemink |
| 2014 | Reconciliation with Non-binary Gene Trees Revisited. | Yu Zheng, Louxin Zhang |
| 2014 | Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. | Shay Zakov, Vineet Bafna |
| 2014 | Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. | Yun William Yu, Deniz Yrkoglu, Bonnie Berger |
| 2014 | A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation. | Wen-Yun Yang, Farhad Hormozdiari, Eleazar Eskin, Bogdan Pasaniuc |