Research in Computational Molecular Biology: 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006. Proceedings

Balaji S. Srinivasan, Antal F. Novak (auth.), Alberto Apostolico, Concettina Guerra, Sorin Istrail, Pavel A. Pevzner, Michael Waterman (eds.)3540332952, 9783540332954

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.

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Table of contents :
Front Matter….Pages –
Integrated Protein Interaction Networks for 11 Microbes….Pages 1-14
Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially–Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination….Pages 15-29
Biological Networks: Comparison, Conservation, and Evolutionary Trees….Pages 30-44
Assessing Significance of Connectivity and Conservation in Protein Interaction Networks….Pages 45-59
Clustering Short Gene Expression Profiles….Pages 60-68
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies….Pages 69-82
Global Interaction Networks Probed by Mass Spectrometry….Pages 83-83
Statistical Evaluation of Genome Rearrangement….Pages 84-84
An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets….Pages 85-98
Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization….Pages 99-113
Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data….Pages 114-129
RNA Secondary Structure Prediction Via Energy Density Minimization….Pages 130-142
Structural Alignment of Pseudoknotted RNA….Pages 143-158
Stan Ulam and Computational Biology….Pages 159-159
CONTRAlign: Discriminative Training for Protein Sequence Alignment….Pages 160-174
Clustering Near-Identical Sequences for Fast Homology Search….Pages 175-189
New Methods for Detecting Lineage-Specific Selection….Pages 190-205
A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer….Pages 206-220
A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric….Pages 221-230
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations….Pages 231-245
Inferring Common Origins from mtDNA….Pages 246-247
Efficient Enumeration of Phylogenetically Informative Substrings….Pages 248-264
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes….Pages 265-280
Maximal Accurate Forests from Distance Matrices….Pages 281-295
Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction….Pages 296-308
Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence….Pages 309-320
An Important Connection Between Network Motifs and Parsimony Models….Pages 321-335
Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human Genome….Pages 336-337
Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data….Pages 338-347
Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes….Pages 348-362
A New Approach to Protein Identification….Pages 363-378
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics….Pages 379-393
Simulating Protein Motions with Rigidity Analysis….Pages 394-409
Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation….Pages 410-424
An Outsider’s View of the Genome….Pages 425-425
Alignment Statistics for Long-Range Correlated Genomic Sequences….Pages 426-440
Simple and Fast Inverse Alignment….Pages 441-455
Revealing the Proteome Complexity by Mass Spectrometry….Pages 456-457
Motif Yggdrasil: Sampling from a Tree Mixture Model….Pages 458-472
A Study of Accessible Motifs and RNA Folding Complexity….Pages 473-487
A Parameterized Algorithm for Protein Structure Alignment….Pages 488-499
Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction….Pages 500-515
A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem….Pages 516-529
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….Pages 530-545
10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB)….Pages 546-562
Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions….Pages 563-577
A Parsimony Approach to Genome-Wide Ortholog Assignment….Pages 578-594
Detecting the Dependent Evolution of Biosequences….Pages 595-609
Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data….Pages E1-E3
Back Matter….Pages –