Accepted papers

You can find links to full versions of papers that only have abstracts in the procedings here

19 Yifeng Li, Chih-Yu Chen and Wyeth Wasserman. Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters
30 Jong Wha Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks, Aldons Lusis and Eleazar Eskin. Efficient and accurate multiple-phenotype regression method for high dimensional data considering population structure
31 Sumudu Leelananda, Robert Jernigan and Andrzej Kloczkowski. Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models
36 Laxmi Parida, Deniz Yorukoglu, Filippo Utro, Anna Paola Carrieri, Saugata Basu and David Kuhn. Topological Signatures for Population Admixture
41 Mark Hallen and Bruce Donald. COMETS (Constrained Optimization of Multistate Energies by Tree Search): A provable and efficient algorithm to optimize binding affinity and specificity with respect to sequence
46 Alex Bishara, Yuling Liu, Dorna Kashef-Haghighi, Ziming Weng, Daniel Newburger, Robert West, Arend Sidow and Serafim Batzoglou. Synthetic Long Reads Uncover Variation in Complex Regions of the Human Genome
54 Yichao Zhou, Yuexin Wu and Jianyang Zeng. Computational Protein Design Using AND/OR Branch-and-Bound Search
55 Roni Wilentzik and Irit Gat-Viks. A statistical framework for revealing signaling pathways perturbed by DNA variants
57 Maja Temerinac-Ott, Armaghan W. Naik and Robert F. Murphy. Deciding when to stop: Efficient experimentation to learn to predict drug-target interactions
59 Seunghak Lee, Aurelie Lozano, Prabhanjan Kambadur and Eric Xing. An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations
63 Leena Salmela, Kristoffer Sahlin, Veli Mäkinen and Alexandru Tomescu. Gap Filling as Exact Path Length Problem
66 Mingfu Shao and Bernard Moret. A Fast and Exact Algorithm for the Exemplar Breakpoint Distance
73 Fabio Vandin, Ben Raphael and Eli Upfal. On the Sample Complexity of Cancer Pathways Identification
74 Kai Dührkop and Sebastian Böcker. Fragmentation trees reloaded
76 Naama Amir, Dan Cohen and Haim J. Wolfson. DockStar: A novel ILP based integrative method for structural modelling of multimolecular protein complexes
89 Rasmus Fonseca, Henry van den Bedem and Julie Bernauer. KGSrna: Efficient 3D kinematics-based sampling for nucleic acids
93 Ilan Ben-Bassat and Benny Chor. CRISPR detection from very short reads using partial overlap graph
95 Emily Berger, Deniz Yorukoglu and Bonnie Berger. HapTree-X: An integrative Bayesian framework for haplotype reconstruction from transcriptome and genome sequencing data
98 Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong and Jianyang Zeng. Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data
113 Arnon Mazza, Allon Wagner, Eytan Ruppin and Roded Sharan. Functional alignment of metabolic networks
114 Jonathan D Jou, Swati Jain, Ivelin Georgiev and Bruce R Donald. BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design
119 Nam-Phuong Nguyen, Siavash Mirarab, Keerthana Kumar and Tandy Warnow. Ultra-large alignments using ensembles of Hidden Markov Models
120 Shou Yang, Shai Carmi and Itsik Pe'Er. Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs
126 Stefano Bonissone and Pavel Pevzner. Immunoglobulin classification using the colored antibody graph
129 Srinivas Aluru, Alberto Apostolico and Sharma V. Thankachan. Efficient Alignment Free Sequence Comparison with Bounded Mismatches
137 Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu. Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning
138 Roy Ronen, Glenn Tesler, Noah A. Rosenberg and Vineet Bafna. Clade Fitness Proxy: Predicting Carriers of Ongoing Selective Sweeps Barring Knowledge of the Adaptive Allele
146 Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert and Gunnar W. Klau. CIDANE: Comprehensive isoform discovery and abundance estimation
150 Emre Sefer, Geet Duggal and Carl Kingsford. Deconvolution Of Ensemble Chromatin Interaction Data Reveals The Latent Mixing Structures In Cell Subpopulations
156 Mark Leiserson, Hsin-Ta Wu, Fabio Vandin and Benjamin Raphael. Comet: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer
160 Hyunghoon Cho, Bonnie Berger and Jian Peng. Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
161 Igor Mandric and Alex Zelikovsky. ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching
166 David Manescu and Uri Keich. A symmetric length-aware enrichment test
167 Surojit Biswas, Meredith McDonald, Jeffery Dangl and Vladimir Jojic. Learning microbial interaction networks from metagenomic count data
170 Andrew McPherson, Andrew Roth, Cedric Chauve and Cenk Sahinalp. Joint inference of genome structure and content in heterogeneous tumor samples
173 Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stephane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time