15. RECOMB 2011: Vancouver, BC, Canada

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

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