Research in Computational Molecular Biology: 12th Annual International Conference, RECOMB 2008, Singapore, March 30 – April 2, 2008. Proceedings

Temple F. Smith (auth.), Martin Vingron, Limsoon Wong (eds.)3540788387, 9783540788386

This book constitutes the refereed proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008, held in Singapore, in March/April 2008.

The 34 revised full papers presented together with the abstracts of 7 keynote talks were carefully reviewed and selected from 193 submissions. As the top conference in computational molecular biology, RECOMB addresses all current issues in algorithmic, theoretical, and experimental bioinformatics such as molecular sequence analysis, recognition of genes and regulatory elements, molecular evolution, protein structure, structural genomics, gene expression, gene networks, drug design, combinatorial libraries, computational proteomics, as well as structural and functional genomics.

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Table of contents :
Front Matter….Pages –
Computational Biology: Its Challenges Past, Present, and Future….Pages 1-2
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast….Pages 3-16
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads….Pages 17-28
Reconstructing the Evolutionary History of Complex Human Gene Clusters….Pages 29-49
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads….Pages 50-64
Orchestration of DNA Methylation….Pages 65-65
BayCis : A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes….Pages 66-81
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors….Pages 82-97
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery….Pages 98-111
The Statistical Power of Phylogenetic Motif Models….Pages 112-126
Transcriptional Regulation and Cancer Genomics….Pages 127-127
Automatic Recognition of Cells (ARC) for 3D Images of C. elegans ….Pages 128-139
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing….Pages 140-153
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry….Pages 154-166
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics….Pages 167-180
De Novo Sequencing of Nonribosomal Peptides….Pages 181-195
Systems Metabolic Engineering….Pages 196-196
Protein Function Prediction Based on Patterns in Biological Networks….Pages 197-213
Automatic Parameter Learning for Multiple Network Alignment….Pages 214-231
An Integrative Network Approach to Map the Transcriptome to the Phenome….Pages 232-245
Fast and Accurate Alignment of Multiple Protein Networks….Pages 246-256
High-Resolution Modeling of Cellular Signaling Networks….Pages 257-271
At the Origin of Life: How Did Folded Proteins Evolve?….Pages 272-272
Locating Multiple Gene Duplications through Reconciled Trees….Pages 273-284
Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information….Pages 285-299
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins….Pages 300-314
DLIGHT – Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework….Pages 315-330
Computation of Median Gene Clusters….Pages 331-345
BCL-2: From Translocation to Therapy….Pages 346-346
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles….Pages 347-359
Constructing Treatment Portfolios Using Affinity Propagation….Pages 360-371
Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs….Pages 372-395
More Efficient Algorithms for Closest String and Substring Problems….Pages 396-409
Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia….Pages 410-410
Accounting for Non-genetic Factors Improves the Power of eQTL Studies….Pages 411-422
Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA….Pages 423-423
On the Inference of Ancestries in Admixed Populations….Pages 424-433
Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information….Pages 434-434
Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information….Pages 435-449
Constructing Level-2 Phylogenetic Networks from Triplets….Pages 450-462
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony….Pages 463-477
Back Matter….Pages –