| 2014 | On the Representation of de Bruijn Graphs. | Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev |
| 2014 | Changepoint Analysis for Efficient Variant Calling. | Adam E. Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael I. Jordan, David A. Patterson, Bin Yu, Yun S. Song |
| 2014 | HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. | Emily Berger, Deniz Yrkoglu, Jian Peng, Bonnie Berger |
| 2014 | Tractatus: An Exact and Subquadratic Algorithm for Inferring Identical-by-Descent Multi-shared Haplotype Tracts. | Derek Aguiar, Eric M. Morrow, Sorin Istrail |
| 2013 | Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data. | ZhiZhuo Zhang, Guoliang Li, Kim-Chuan Toh, Wing-Kin Sung |
| 2013 | Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. | Dong Xu, Hua Li, Yang Zhang |
| 2013 | An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. | Yufeng Wu |
| 2013 | SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. | Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Mhl, Rolf Backofen |
| 2013 | Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance. | Mingxun Wang, Nuno Bandeira |
| 2013 | Genome-Wide Survival Analysis of Somatic Mutations in Cancer. | Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal |
| 2013 | Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure. | Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou, Bruce Randall Donald |
| 2013 | Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data - (Extended Abstract). | Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang |
| 2013 | MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods. | Michael Stevens, Jeffrey B. Cheng, Mingchao Xie, Joseph F. Costello, Ting Wang |
| 2013 | Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. | Evan Senter, Saad Sheikh, Ivn Dot, Yann Ponty, Peter Clote |
| 2013 | Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. | Raheleh Salari, Syed Shayon Saleh, Dorna Kashef Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou |
| 2013 | Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks. | Mohammad Javad Sadeh, Giusi Moffa, Rainer Spang |
| 2013 | Learning Natural Selection from the Site Frequency Spectrum. | Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna |
| 2013 | An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test. | Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici |
| 2013 | A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. | Vladimir Reinharz, Yann Ponty, Jrme Waldisphl |
| 2013 | High Resolution Modeling of Chromatin Interactions. | Christopher Reeder, David Gifford |
| 2013 | NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources. | Kriti Puniyani, Eric P. Xing |
| 2013 | Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. | Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael |
| 2013 | Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. | Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton I. Korobeynikov, Alla L. Lapidus, Andrey D. Prjibelsky, Alex Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey S. McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner |
| 2013 | Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors. | Alina Munteanu, Raluca Gordn |
| 2013 | Identification of Ultramodified Proteins Using Top-Down Spectra. | Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic, Pavel A. Pevzner |