RECOMB 2011 Proceedings

Vancouver, BC, Canada, March 28-31, 2011

PC Chair: Vineet Bafna
Organization Committee: S. Cenk Sahinalp (chair), Cedric Chauve, Martin Ester, Inanc Birol, Fiona Brinkman, Steven Jones, Anne Condon, Jack Chen, Artem Cherkasov, Colin Collins, Tamon Stephen, Stas Volik, Wyeth Wasserman, Kay Wiese
Keynote Speakers: Evan Eichler, Daphne Koller, Marco Marra, Karen Nelson, Elaine Mardis, Joseph Nadeau

List of Publications

• Bacterial Community Reconstruction Using Compressed Sensing. Amnon Amir and Or Zuk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 1-15, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_1
• Constrained De Novo Sequencing of Peptides with Application to Conotoxins. Swapnil Bhatia, Yong J. Kil, Beatrix Ueberheide, Brian Chait, Lemmuel L. Tayo, Lourdes J. Cruz, Bingwen Lu, John R. Yates III, Marshall Bern.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 16-30, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_2
• Metabolic Network Analysis Demystified. Leonid Chindelevitch, Aviv Regev, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 31-33, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_3
• Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes. Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch Huang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 34-37, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_4
• Hapsembler: An Assembler for Highly Polymorphic Genomes. Nilgun Donmez and Michael Brudno.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 38-52, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_5
• Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome. Jason Ernst and Manolis Kellis.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 53-53, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_6
• Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks. Sinan Erten, Gurkan Bebek, Mehmet Koyutürk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 54-68, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_7
• Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 69-69, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_8
• Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways. Allison P. Heath, George N. Bennett, Lydia E. Kavraki.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 70-84, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_9
• A Probabilistic Model For Sequence Alignment with Context-Sensitive Indels. Glenn Hickey and Mathieu Blanchette.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 85-103, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_10
• Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 104-105, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_11
• Variable Selection through Correlation Sifting. Jim C. Huang and Nebojsa Jojic.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 106-123, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_12
• Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions. Shuai Jiang and Max A. Alekseyev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 124-133, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_13
• PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling. Jaebum Kim and Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 134-135, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_14
• Pedigree Reconstruction Using Identity by Descent. Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 136-152, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_15
• A Quantitative Model of Glucose Signaling in Yeast Reveals an Incoherent Feed Forward Loop Leading to a Specific, Transient Pulse of Transcription. Sooraj KuttyKrishnan, Jeffrey Sabina, Laura Langton, Mark Johnston, Michael R. Brent.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 153-153, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_16
• Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut. Mark D.M. Leiserson, Diana Tatar, Lenore J. Cowen, Benjamin J. Hescott.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 154-167, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_17
• IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. Wei Li, Jianxing Feng, Tao Jiang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 168-188, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_18
• Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals. Xin Li and Jing Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 189-203, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_19
• Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 204-221, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_20
• A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs. Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 222-237, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_21
• Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. Paul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler, Pavel Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 238-251, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_22
• An Optimization-Based Sampling Scheme for Phylogenetic Trees. Navodit Misra, Guy Blelloch, R. Ravi, Russell Schwartz.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 252-266, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_23
• Multiplex De Novo Sequencing of Peptide Antibiotics. Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudêncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 267-281, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_24
• Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk (Invited Talk). Joe Nadeau.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 282-282, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_25
• AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization. Daniel Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 283-297, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_26
• Blocked Pattern Matching Problem and Its Applications in Proteomics. Julio Ng, Amihood Amir, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 298-319, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_27
• A Three-Dimensional Model of the Yeast Genome. William Noble, Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 320-320, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_28
• Optimization of Combinatorial Mutagenesis. Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 321-335, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_29
• Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets. Hanchuan Peng and Fuhui Long.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 336-336, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_30
• T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome. Yu Peng, Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 337-338, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_31
• Experiment Specific Expression Patterns. Tobias Petri, Robert Küffner, Ralf Zimmer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 339-354, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_32
• Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. Yosef Prat, Menachem Fromer, Michal Linial, Nathan Linial.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 355-357, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_33
• A Ribosome Flow Model for Analyzing Translation Elongation. Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 358-360, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_34
• Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm. Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 361-376, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_35
• Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data. Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 377-391, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_36
• Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction. Emre Sefer and Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 392-407, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_37
• Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. Solomon Shenker, Charles W. O’Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 408-423, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_38
• Optimally Orienting Physical Networks. Dana Silverbush, Michael Elberfeld, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 424-436, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_39
• Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. Song Gao, Niranjan Nagarajan, Wing-Kin Sung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 437-451, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_40
• Increasing Power of Groupwise Association Test with Likelihood Ratio Test. Jae Hoon Sul, Buhm Han, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 452-467, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_41
• Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection. Ryan Tarpine, Fumei Lam, Sorin Istrail.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 468-482, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_42
• Protein Loop Closure Using Orientational Restraints from NMR Data. Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 483-498, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_43
• De Novo Discovery of Mutated Driver Pathways in Cancer. Fabio Vandin, Eli Upfal, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 499-500, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_44
• An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. Jérôme Waldispühl and Yann Ponty.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 501-515, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_45
• Nonparametric Combinatorial Sequence Models. Fabian L. Wauthier, Michael I. Jordan, Nebojsa Jojic.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 516-530, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_46
• Algorithms for MDC-Based Multi-locus Phylogeny Inference. Yun Yu, Tandy Warnow, Luay Nakhleh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 531-545, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_47
• Rich Parameterization Improves RNA Structure Prediction. Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 546-562, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_48
• A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 563-578, Springer, Cham.
    • DOI: 10.1007/978-3-642-20036-6_49