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
Website: https://recomb.org/recomb2016/
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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
  • Journal: 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. Journal of Computational Biology, 24(6): 472-485, 2017.
    • DOI: 10.1089/cmb.2016.0138
• 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
  • Journal: Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. Hao Wang, Joel McManus, Carl Kingsford. Journal of Computational Biology, 24(6): 486-500, 2017.
    • DOI: 10.1089/cmb.2016.0147
• 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
  • Journal: Multitask Matrix Completion for Learning Protein Interactions Across Diseases. Meghana Kshirsagar, Keerthiram Murugesan, Jaime G. Carbonell, Judith Klein-Seetharaman. Journal of Computational Biology, 24(6): 501-514, 2017.
    • DOI: 10.1089/cmb.2016.0201
• 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
  • Journal: pathTiMEx: joint inference of mutually exclusive cancer pathways and their progression dynamics. Simona Cristea, Jack Kuipers, Niko Beerenwinkel. Journal of Computational Biology, 24(6): 603-615, 2017.
    • DOI: 10.1089/cmb.2016.0171
• 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
  • Journal: 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. Journal of Computational Biology, 24(6): 515-523, 2017.
    • DOI: 10.1089/cmb.2016.0148
• 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
  • Journal: Flexible Modeling of Genetic Effects on Function-Valued Traits. Nicolò Fusi, Jennifer Listgarten. Journal of Computational Biology, 24(6): 524-535, 2017.
    • DOI: 10.1089/cmb.2016.0174
• 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
  • Preprint: bioRxiv 038208
• 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
  • Journal: 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. Journal of Computational Biology, 24(6): 536-546, 2017.
    • DOI: 10.1089/cmb.2016.0136
• 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
  • Journal: Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters. David Pellow, Darya Filippova, Carl Kingsford. Journal of Computational Biology, 24(6): 547-557, 2017.
    • DOI: 10.1089/cmb.2016.0155
• 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
  • Preprint: arXiv:1601.02932
  • Journal: Safe and complete contig assembly through omnitigs. Alexandru I. Tomescu, Paul Medvedev. Journal of Computational Biology, 24(6): 590-602, 2017.
    • DOI: 10.1089/cmb.2016.0141
• 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
  • Preprint: bioRxiv 036392
  • Journal: 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. Journal of Computational Biology, 24(6): 558-570, 2017.
    • DOI: 10.1089/cmb.2016.0146
• 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
  • Preprint: bioRxiv 036707
  • Journal: Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias. Kristoffer Sahlin, Mattias Frånberg, Lars Arvestad. Journal of Computational Biology, 24(6): 581-589, 2017.
    • DOI: 10.1089/cmb.2016.0124
• 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
  • Journal: On Computing Breakpoint Distances for Genomes with Duplicate Genes. Mingfu Shao, Bernard M.E. Moret. Journal of Computational Biology, 24(6): 571-580, 2017.
    • DOI: 10.1089/cmb.2016.0149
• 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
  • Journal: New Genome Similarity Measures Based on Conserved Gene Adjacencies. Daniel Doerr, Luis Antonio B. Kowada, Francisco Eloi Soares de Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye. Journal of Computational Biology, 24(6): 616-634, 2017.
    • DOI: 10.1089/cmb.2017.0065
• 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
  • Preprint: bioRxiv 047845
  • Journal: 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. Genome Biology, 17(1): 106, 2016.
    • DOI: 10.1186/s13059-016-0975-3
• 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
  • Journal: Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments. Emre Sefer, Ziv Bar-Joseph. Cell Systems, 3(1): 35-42, 2016.
    • DOI: 10.1016/j.cels.2016.06.007
• 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
  • Preprint: arXiv:1604.04484
  • Journal: Enabling Privacy-Preserving GWASs in Heterogeneous Human Populations. Sean Simmons, Cenk Sahinalp, Bonnie Berger. Cell Systems, 3(1):54-61, 2016.
    • DOI: 10.1016/j.cels.2016.04.013
• 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
  • Preprint: arXiv:1604.02467
• 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
  • Preprint: arXiv:1604.02605
  • Journal: Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures. Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael. Cell Systems, 3(1):43-53, 2016.
    • DOI: 10.1016/j.cels.2016.07.004
• 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
  • Preprint: bioRxiv 047795
  • Journal: Tree Inference for Single-Cell Data. Katharina Jahn, Jack Kuipers, Niko Beerenwinkel. Genome Biology, 17(1): 86, 2016.
    • DOI: 10.1186/s13059-016-0936-x
• 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
  • Preprint: bioRxiv 042630
• 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
  • Preprint: arXiv:1604.02699
  • Journal: Metagenomic binning through low-density hashing. Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng. Bioinformatics, 35(2): 219-226, 2018.
    • DOI: 10.1093/bioinformatics/bty611
• 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
  • Preprint: arXiv:1604.03071
  • Journal: metaSPAdes: a new versatile metagenomic assembler. Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov, Pavel A Pevzner. Genome Research, 27(5) 824-834, 2017.
    • DOI: 10.1101/gr.213959.116
• 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
  • Preprint: arXiv:1604.03052
• 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
  • Preprint: bioRxiv 047357
• 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
  • Preprint: bioRxiv 023705
  • Journal: Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. John Wiedenhoeft, Eric Brugel, Alexander Schliep. PLoS Computational Biology, 12(5): e1004871, 2016.
    • DOI: 10.1371/journal.pcbi.1004871
• 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
  • Preprint: bioRxiv 048207
  • Journal: Allele-Specific Quantification of Structural Variations in Cancer Genomes. Yang Li, Shiguo Zhou, David C. Schwartz, Jian Ma. Cell Systems, 3(1): 21-34, 2016.
    • DOI: 10.1016/j.cels.2016.05.007
• 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
  • Preprint: bioRxiv 048413
  • Journal: Assembly of Long Error-Prone Reads Using de Bruijn Graphs. Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner. Proceedings of the National Academy of Sciences, 113(52): E8396-E8405, 2016.
    • DOI: 10.1073/pnas.1604560113
• 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
  • Preprint: arXiv:1507.02119
• 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
  • Journal: Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization. Somaye Hashemifar, Qixing Huang, Jinbo Xu. Journal of Computational Biology, 23(11): 903-911, 2016.
    • DOI: 10.1089/cmb.2016.0025
• 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
  • Preprint: arXiv:1604.03244
  • Journal: Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining. Xiuli Ma, Guangyu Zhou, Jingjing Wang, Jian Peng, Jiawei Han. Journal of Computational Biology, 24(9): 923-941, 2017.
    • DOI: 10.1089/cmb.2017.0037