| 2016 | Locating a Tree in a Reticulation-Visible Network in Cubic Time. | Andreas D. M. Gunawan, Bhaskar DasGupta, Louxin Zhang |
| 2016 | Flexible Modelling of Genetic Effects on Function-Valued Traits. | Nicol Fusi, Jennifer Listgarten |
| 2016 | Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. | Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael |
| 2016 | Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data. | Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Sleyman Cenk Sahinalp |
| 2016 | AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. | Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka |
| 2016 | pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. | Simona Cristea, Jack Kuipers, Niko Beerenwinkel |
| 2016 | Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. | Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky |
| 2016 | Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. | Sean Simmons, S. Cenk Sahinalp, Bonnie Berger |
| 2015 | Computational Protein Design Using AND/OR Branch-and-Bound Search. | Yichao Zhou, Yuexin Wu, Jianyang Zeng |
| 2015 | Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. | Shuo Yang, Shai Carmi, Itsik Pe'er |
| 2015 | A Novel Probabilistic Methodology for eQTL Analysis of Signaling Networks. | Roni Wilentzik, Irit Gat-Viks |
| 2015 | On the Sample Complexity of Cancer Pathways Identification. | Fabio Vandin, Benjamin J. Raphael, Eli Upfal |
| 2015 | Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions (Extended Abstract). | Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy |
| 2015 | A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. | Mingfu Shao, Bernard M. E. Moret |
| 2015 | Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations. | Emre Sefer, Geet Duggal, Carl Kingsford |
| 2015 | Gap Filling as Exact Path Length Problem. | Leena Salmela, Kristoffer Sahlin, Veli Mkinen, Alexandru I. Tomescu |
| 2015 | Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele. | Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, Vineet Bafna |
| 2015 | Topological Signatures for Population Admixture. | Laxmi Parida, Filippo Utro, Deniz Yrkoglu, Anna Paola Carrieri, David Kuhn, Saugata Basu |
| 2015 | Ultra-Large Alignments Using Ensembles of Hidden Markov Models. | Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow |
| 2015 | Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. | Andrew W. McPherson, Andrew Roth, Cdric Chauve, Sleyman Cenk Sahinalp |
| 2015 | Functional Alignment of Metabolic Networks. | Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan |
| 2015 | Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. | Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu |
| 2015 | A Symmetric Length-Aware Enrichment Test. | David Manescu, Uri Keich |
| 2015 | ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching. | Igor Mandric, Alex Zelikovsky |
| 2015 | Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. | Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman |