Peter S. Kim, Stanford University
Rob Knight, University of California, San Diego
Leonid Kruglyak, University of California, Los Angeles
Phil Bradley, Fred Hutchinson Cancer Center
Teresa Przytycka, NIH
Karen Adelman, NIH
  1. Hao Wang, Joel McManus and Carl Kingsford. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast
  1. Shashank Singh, Sabrina Rashid, Saket Navlakha and Ziv Bar-Joseph. Distributed Gradient Descent in Bacterial Food Search
  1. Meghana Kshirsagar, Jaime Carbonell, Judith Klein-Seetharaman and Keerthiram Murugesan. Multitask matrix completion for learning protein interactions across diseases
  1. Yuqing Yang, Ning Chen and Ting Chen. mLDM: a Statistical Model for Sparse Microbial Association Discovery
  1. David Pellow, Darya Filippova and Carl Kingsford. Improving Bloom filter performance on sequence data using k-mer Bloom filters
  1. Yael Steuerman and Irit Gat-Viks. Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System
  1. Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen and Teresa Przytycka. AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments
  1. Kristoffer Sahlin, Mattias Frånberg and Lars Arvestad. Structural variation detection with read pair information — An improved null-hypothesis reduces bias
  1. Alexandru I. Tomescu and Paul Medvedev. Safe and complete contig assembly via omnitigs
  1. Ahmed Sobih, Alexandru I. Tomescu and Veli Mäkinen. MetaFlow: Metagenomic profiling based on whole-genome coverage analysis with min-cost flows
  1. Luis Antonio B. Kowada, Daniel Doerr, Simone Dantas and Jens Stoye. New Genome Similarity Measures based on Conserved Gene Adjacencies
  1. Sergey Nurk, Dmitry Meleshko and Pavel Pevzner. metaSPAdes: a new versatile de novo metagenomics assembler
  1. Sean Simmons, Cenk Sahinalp and Bonnie Berger. Enabling Privacy-Preserving GWAS in Heterogenous Human Populations
  1. Somaye Hashemifar, Qixing Huang and Jinbo Xu. Joint alignment of multiple protein-protein interaction networks via convex optimization
  1. Chandler Zuo, Kailei Chen and Sunduz Keles. A MAD-Bayes Algorithm for State-space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets
  1. Alexander Artyomenko, Nicholas Wu, Serghei Mangul, Eleazar Eskin, Ren Sun and Alex Zelikovsky. Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants
  1. Mark Hallen, Jonathan Jou and Bruce Donald. LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency
  1. Tommy Hansen and Fabio Vandin. Finding Mutated Subnetworks Associated with Survival Time in Cancer
  2. Joshua Welch, Ziqing Liu, Li Wang, Junjie Liu, Paul Lerou, Jeremy Purvis, Li Qian, Alexander Hartemink and Jan Prins. SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data
  1. Simona Constantinescu, Jack Kuipers and Niko Beerenwinkel. pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and their Dependencies in Tumor Progression
  1. Mingfu Shao and Bernard Moret. On Computing Pairwise Breakpoint Distances
  1. Emre Sefer and Ziv Bar-Joseph. Shall we dense? Comparing design strategies for time series expression experiments
  1. Nilgun Donmez, Salem Malikic, Alexander Wyatt, Colin Collins, Martin Gleave and Cenk Sahinalp. Clonality inference from single tumor samples using low coverage sequence data
  1. Chenchen Zou, Yuping Zhang and Zhengqing Ouyang. Multi-track modeling for genome-scale reconstruction of 3D chromatin structure from Hi-C data
  1. John Wiedenhoeft, Eric Brugel and Alexander Schliep. Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
  1. Yu Lin, Max W. Shen, Jeffrey Yuan and Pavel Pevzner. Assembly of Long Error-Prone Reads Using de Bruijn Graphs
  1. Nicolo Fusi and Jennifer Listgarten. Leveraging Non-Linear Genetic Effects on Functional Traits for GWAS
  1. Mohammed El-Kebir, Gryte Satas, Layla Oesper and Ben Raphael. Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing
  1. Xiuli Ma, Guangyu Zhou, Jingjing Wang, Jian Peng and Jiawei Han. Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining
  1. Yang Li, Shiguo Zhou, David Schwartz and Jian Ma. Allele-Specific Quantification of Structural Variations in Cancer Genomes
  1. Yunan Luo, Jianyang Zeng, Bonnie Berger and Jian Peng. Low-density locality-sensitive hashing boosts metagenomic binning
  1. Constantinos Tsirogiannis and Brody Sandel. Fast Phylogenetic Biodiversity Computations Under a Non-Uniform Random Distribution
  1. Andreas Dwi Maryanto Gunawan, Bhaskar Dasgupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time
  1. Katharina Jahn, Jack Kuipers and Niko Beerenwinkel. Tree inference for single-cell data
  1. Victoria Popic and Serafim Batzoglou. Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting