RECOMB 2016 Proceedings

Santa Monica, CA, United States, April 17-21, 2016

PC Chair: Mona Singh
Organization Committee: Eleazar Eskin (chair)
Keynote Speakers: Peter S. Kim, Rob Knight, Leonid Kruglyak, Phil Bradley, Teresa Przytycka, Karen Adelman

List of Publications

• A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets. Chandler Zuo, Kailei Chen, Sündüz Keleş.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 19-36, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_2
• Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. Hao Wang, Joel McManus, Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 37-52, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_3
• Multitask Matrix Completion for Learning Protein Interactions Across Diseases. Meghana Kshirsagar, Jaime G. Carbonell, Judith Klein-Seetharaman, Keerthiram Murugesan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 53-64, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_4
• pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. Simona Cristea, Jack Kuipers, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 65-82, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_5
• Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data. Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 83-94, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_6
• Flexible Modelling of Genetic Effects on Function-Valued Traits. Nicolo Fusi and Jennifer Listgarten.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 95-110, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_7
• MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. Ahmed Sobih, Alexandru I. Tomescu, Veli Mäkinen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 111-121, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_8
• LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency. Mark A. Hallen, Jonathan D. Jou, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 122-136, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_9
• Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters. David Pellow, Darya Filippova, Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 137-151, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_10
• Safe and Complete Contig Assembly Via Omnitigs. Alexandru I. Tomescu and Paul Medvedev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 152-163, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_11
• 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.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 164-175, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_12
• Structural Variation Detection with Read Pair Information-An Improved Null-Hypothesis Reduces Bias. Kristoffer Sahlin, Mattias Frånberg, Lars Arvestad.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 176-188, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_13
• On Computing Breakpoint Distances for Genomes with Duplicate Genes. Mingfu Shao and Bernard M.E. Moret.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 189-203, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_14
• New Genome Similarity Measures Based on Conserved Gene Adjacencies. Luis Antonio B. Kowada, Daniel Doerr, Simone Dantas, Jens Stoye.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 204-224, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_15
• Fast Phylogenetic Biodiversity Computations Under a Non-uniform Random Distribution. Constantinos Tsirogiannis and Brody Sandel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 225-238, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5_16
• SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data. Joshua D. Welch, Ziqing Liu, Li Wang, Junjie Lu, Paul Lerou, Jeremy Purvis, Li Qian, Alexander Hartemink, Jan F. Prins.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 239-240, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Multi-track Modeling for Genome-Scale Reconstruction of 3D Chromatin Structure from Hi-C Data. Chenchen Zou, Yuping Zhang, Zhengqing Ouyang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 241-241, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Revealing the Genetic Basis of Immune Traits in the Absence of Experimental Immunophenotyping. Yael Steuerman and Irit Gat-Viks.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 242-243, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments. Emre Sefer and Ziv-Bar Joseph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 244-245, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. Sean Simmons, Cenk Sahinalp, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 246-247, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting. Victoria Popic and Serafim Batzoglou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 248-249, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Finding Mutated Subnetworks Associated with Survival in Cancer. Tommy Hansen and Fabio Vandin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 250-250, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 251-251, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Tree Inference for Single-Cell Data. Katharina Jahn, Jack Kuipers, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 252-252, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• mLDM: A New Hierarchical Bayesian Statistical Model for Sparse Microbial Association Discovery. Yuqing Yang, Ning Chen, Ting Chen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 253-254, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 255-257, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• metaSPAdes: A New Versatile de novo Metagenomics Assembler. Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 258-258, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Distributed Gradient Descent in Bacterial Food Search. Shashank Singh, Sabrina Rashid, Saket Navlakha, Ziv Bar-Joseph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 259-260, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• 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.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 261-262, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Fast Bayesian Inference of Copy Number Variants Using Hidden Markov Models with Wavelet Compression. John Wiedenhoeft, Eric Brugel, Alexander Schliep.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 263-263, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Allele-Specific Quantification of Structural Variations in Cancer Genomes. Yang Li, Shiguo Zhou, David C. Schwartz, Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 264-264, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Assembly of Long Error-Prone Reads Using de Bruijn Graphs. Yu Lin, Max W. Shen, Jeffrey Yuan, Mark Chaisson, Pavel P. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 265-265, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Locating a Tree in a Reticulation-Visible Network in Cubic Time. Andreas D.M. Gunawan, Bhaskar Das Gupta, Louxin Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 266-266, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization. Somaye Hashemifar, Qixing Huang, Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 267-269, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5
• Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining. Xiuli Ma, Guangyu Zhou, Jingjing Wang, Jian Peng, Jiawei Han.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649, pp 270-272, Springer, Cham.
    • DOI: 10.1007/978-3-319-31957-5