Research in Computational Molecular Biology: 15th Annual International Conference, Recomb 2011, Vancouver, Bc, Canada, March 28-31, 2011. Proceedings - Lecture Notes in Computer Science / Lecture Notes in Bioinformatics

Jacket Description/Back: This book constitutes the refereed proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011, held in Vancouver, Canada, in March 2011. The 43 revised full papers were carefully reviewed and selected from 153 submissions. The papers cover a wide range of topics including molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; population, statistical genetics; systems biology; imaging; computational proteomics; molecular structural biology. Table of Contents: Bacterial Community Reconstruction Using Compressed Sensing / Amnon Amir, Or Zuk -- 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 -- Metabolic Network Analysis Demystified / Leonid Chindelevitch, Aviv Regev, Bonnie Berger -- Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes (Extended Abstract) / Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch Huang -- Hapsembler: An Assembler for Highly Polymorphic Genomes / Nilgun Donmez, Michael Brudno -- Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome / Jason Ernst, Manolis Kellis -- Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks / Sinan Erten, Gurkan Bebek, Mehmet KoyutUrk -- Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast / Irit Gat- Viks, Renana Meller, Martin Kupiec, Ron Shamir -- Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways / Allison P. Heath, George N. Bennett, Lydia E. Kavraki -- A Probabilistic Model For Sequence Alignment with Context-Sensitive Indels / Glenn Hickey, Mathieu Blanchette -- Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes / Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp -- Variable Selection through Correlation Sifting / Jim C. Huang, Nebojsa Jojic -- Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions / Shuai Jiang, Max A. Alekseyev -- PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling (Extended Abstract) / Jaebum Kim, Jian Ma -- Pedigree Reconstruction Using Identity by Descent / Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin -- 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 -- 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 -- IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly (Extended Abstract) / Wei Li, Jianxing Feng, Tao Jiang -- Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals / Xin Li, Jing Li -- Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs / Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy -- 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 -- 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 -- An Optimization-Based Sampling Scheme for Phylogenetic Trees / Navodit Misra, Guy Blelloch, R. Ravi, Russell Schwartz -- Multiplex De Novo Sequencing of Peptide Antibiotics / Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. GaudEncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner -- Fractal and Transgenerational Genetic Effects on Phenotypic Variation and Disease Risk (Invited Talk) / Joe Nadeau -- AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization / Daniel Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie -- Blocked Pattern Matching Problem and Its Applications in Proteomics / Julio Ng, Amihood Amir, Pavel A. Pevzner -- 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 -- Optimization of Combinatorial Mutagenesis / Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg -- Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets / Hanchuan Peng, Fuhui Long -- T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome (Extended Abstract) / Yu Peng, Henry C. M. Leung, S. M. Yiu, Francis Y. L. Chin -- Experiment Specific Expression Patterns / Tobias Petri, Robert KUffner, Ralf Zimmer -- Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles / Yosef Prat, Menachem Fromer, Michal Linial, Nathan Linial -- A Ribosome Flow Model for Analyzing Translation Elongation (Extended Abstract) / Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller -- 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 -- Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data / Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian BOcker -- Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction / Emre Sefer, Carl Kingsford -- Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models / Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, JErOme WaldispUhl -- Optimally Orienting Physical Networks / Dana Silverbush, Michael Elberfeld, Roded Sharan -- Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences / Song Gao, Niranjan Nagarajan, Wing-Kin Sung -- Increasing Power of Groupwise Association Test with Likelihood Ratio Test / Jae Hoon Sul, Buhm Han, Eleazar Eskin -- Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection / Ryan Tarpine, Fumei Lam, Sorin Istrail -- Protein Loop Closure Using Orientational Restraints from NMR Data / Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald -- De Novo Discovery of Mutated Driver Pathways in Cancer / Fabio Vandin, Eli Upfal, Benjamin J. Raphael -- An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure / JErOme WaldispUhl, Yann Ponty -- Nonparametric Combinatorial Sequence Models / Fabian L. Wauthier, Michael I. Jordan, Nebojsa Jojic -- Algorithms for MDC-Based Multi-locus Phylogeny Inference / Yun Yu, Tandy Warnow, Luay Nakhleh -- Rich Parameterization Improves RNA Structure Prediction / Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv- Ukelson -- A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data / Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce R. Donald -- Author Index.