Research in Computational Molecular Biology: 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings (Lecture Notes in Computer Science, 3909)

Stanislaw Ulam Memorial Computational BiologyLecture was given by Michael S. Wat- man. A special feature presentation was devoted to the 10th anniversary and is included in this volume. ... Papers Presnted At The 10th Annual International Conference On Research In Computational Molecular Biology (recomb 2006) Which Was Held In Venice, Italy On April 2-5, 2006--pref. Integrated Protein Interaction Networks For 11 Microbes / Balaji S. Srinivasan ... [et Al.] -- Hypergraph Model Of Multi-residue Interactions In Proteins : Sequentially-constrained Partitioning Algorithms For Optimization Of Site-directed Protein Recombination / Xiaoduan Ye, Alan M. Friedman And Chris Bailey-kellogg -- Biological Networks: Comparison, Conservation, And Evolutionary Trees / Benny Chor And Tamir Tuller -- Assessing Significance Of Connectivity And Conservation In Protein Interaction Networks / Mehmet Koyuturk, Ananth Grama And Wojciech Szpankowski -- Clustering Short Gene Expression Profiles / Ling Wang, Marco Ramoni And Paola Sebastiani -- A Patient-gene Model For Temporal Expression Profiles In Clinical Studies / Naftali Kaminski And Ziv Bar-joseph -- Global Interaction Networks Probed By Mass Spectrometry / Anne-claude Gavin -- Statistical Evaluation Of Genome Rearrangement / David Sankoff --^ An Improved Statistic For Detecting Over-represented Gene Ontology Annotations In Gene Sets / Steffen Grossmann ... [et Al.] -- Protein Function Annotation Based On Ortholog Clusters Extracted From Incomplete Genomes Using Combinatorial Optimization / Akshay Vashist, Casimir Kulikowski And Ilya Muchnik -- Detecting Microrna Targets By Linking Sequence, Microrna And Gene Expression Data / Jim C. Huang, Quaid D. Morris And Brendan J. Frey -- Rna Secondary Structure Prediction Via Energy Density Minimization / Can Alkan ... [et Al.] -- Structural Alignment Of Pseudoknotted Rna / Banu Dost ... [et Al.] -- Stan Ulam And Computational Biology / Michael S. Waterman -- Contralign: Discriminative Training For Protein Sequence Alignment / Chuong B. Do, Samuel S. Gross And Serafim Batzoglou -- Clustering Near-identical Sequences For Fast Homology Search / Michael Cameron, Yaniv Bernstein And Hugh E. Williams --^ New Methods For Detecting Lineage-specific Selection / Adam Siepel, Katherine S. Pollard And David Haussler -- A Probabilistic Model For Gene Content Evolution With Duplication, Loss, And Horizontal Transfer / Miklos Csuros And Istvan Miklos -- A Sublinear-time Randomized Approximation Scheme For The Robinson-foulds Metric / Nicholas D. Pattengale And Bernard M.e. Moret -- Algorithms To Distinguish The Role Of Gene-conversion From Single-crossover Recombination In The Derivation Of Snp Sequences In Populations / Yun S. Song ... [et Al.] -- A New Approach To Protein Identification / Nuno Bandeira ... [et Al.] -- Markov Methods For Hierarchical Coarse-graining Of Large Protein Dynamics / Chakra Chennubhotla And Ivet Bahar -- Simulating Protein Motions With Rigidity Analysis / Shawna Thomas ... [et Al.] -- Predicting Experimental Quantities In Protein Folding Kinetics Using Stochastic Roadmap Simulation / Tsung-han Chiang ... [et Al.] -- An Outsider's View Of The Genome / Carl Zimmer --^ Alignment Statistics For Long-range Correlated Genomic Sequences / Philipp W. Messer ... [et Al.] -- Simple And Fast Inverse Alignment / John Kececioglu And Eagu Kim -- Revealing The Proteome Complexity By Mass Spectrometry / Roman A. Zubarev -- Motif Yggdrasil : Sampling From A Tree Mixture Model / Samuel A. Andersson And Jens Lagergren -- A Study Of Accessible Motifs And Rna Folding Complexity / Ydo Wexler, Chaya Zilberstein And Michal Ziv-ukelson -- A Parameterized Algorithm For Protein Structure Alignment / Jinbo Xu, Feng Jiao And Bonnie Berger -- Geometric Sieving: Automated Distributed Optimization Of 3d Motifs For Protein Function Prediction / Brian Y. Chen ... [et Al.] -- A Branch-and-reduce Algorithm For The Contact Map Overlap Problem / Wei Xie And Nikolaos V. Sahinidis --^ A Novel Minimized Dead-end Elimination Criterion And Its Application To Protein Redesign In A Hybrid Scoring And Search Algorithm For Computing Partition Functions Over Molecular Ensembles / Ivelin Georgiev, Ryan H. Lilien And Bruce R. Donald --10 Years Of The International Conference On Research In Computational Molecular Biology / Sarah J. Aerni And Eleazar Eskin -- Sorting By Weighted Reversals, Transpositions, And Inverted Transpositions / Martin Bader And Enno Ohlebusch -- A Parsimony Approach To Genome-wide Ortholog Assignment / Zheng Fu ... [et Al.] -- Detecting The Dependent Evolution Of Biosequences / Jeremy Darot, Chen-hsiang Yeang And David Haussler. Alberto Apostolico ... [et Al.] (eds.). Includes Bibliographical References And Index. Frontmatter Integrated Protein Interaction Networks for 11 Microbes Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially--Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination Biological Networks: Comparison, Conservation, and Evolutionary Trees Assessing Significance of Connectivity and Conservation in Protein Interaction Networks Clustering Short Gene Expression Profiles A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies Global Interaction Networks Probed by Mass Spectrometry Statistical Evaluation of Genome Rearrangement An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data RNA Secondary Structure Prediction Via Energy Density Minimization Structural Alignment of Pseudoknotted RNA Stan Ulam and Computational Biology CONTRAlign: Discriminative Training for Protein Sequence Alignment Clustering Near-Identical Sequences for Fast Homology Search New Methods for Detecting Lineage-Specific Selection A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations Inferring Common Origins from mtDNA Efficient Enumeration of Phylogenetically Informative Substrings Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes Maximal Accurate Forests from Distance Matrices Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence An Important Connection Between Network Motifs and Parsimony Models Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human Genome Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes A New Approach to Protein Identification Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics Simulating Protein Motions with Rigidity Analysis Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation An Outsider's View of the Genome Alignment Statistics for Long-Range Correlated Genomic Sequences Simple and Fast Inverse Alignment Revealing the Proteome Complexity by Mass Spectrometry Motif Yggdrasil: Sampling from a Tree Mixture Model A Study of Accessible Motifs and RNA Folding Complexity A Parameterized Algorithm for Protein Structure Alignment Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles 10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB) Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions A Parsimony Approach to Genome-Wide Ortholog Assignment Detecting the Dependent Evolution of Biosequences Backmatter Erratum This book constitutes the refereed proceedings of the 10th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2006, held in Venice, Italy in April 2006. The 40 revised full papers presented together with abstracts of 7 keynote talks were carefully reviewed and selected from 212 submissions. As the top conference in computational molecular biology, RECOMB addresses all current issues in algorithmic, theoretical, and experimental bioinformatics "This volume contains the papers presented at the 10th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006), which was held in Venice, Italy, on April 2-5, 2006."