Research in Computational Molecular Biology: 12th Annual International Conference, Recomb 2008, Singapore, March 30 - April 2, 2008, Proceedings

by Vingron, Martin; Wong, Limsoon

• ISBN13: 9783540788386
• ISBN10: 3540788387
• Format: Paperback
• Copyright: 2008-05-21
• Publisher: Springer Verlag

Summary

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.

Table of Contents

Computational Biology: Its Challenges Past, Present, and Future (Keynote)	p. 1
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast	p. 3
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads	p. 17
Reconstructing the Evolutionary History of Complex Human Gene Clusters	p. 29
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads	p. 50
Orchestration of DNA Methylation (Keynote)	p. 65
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes	p. 66
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors	p. 82
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery	p. 98
The Statistical Power of Phylogenetic Motif Models	p. 112
Transcriptional Regulation and Cancer Genomics (Keynote)	p. 127
Automatic Recognition of Cells (ARC) for 3D Images of C. elegans	p. 128
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing	p. 140
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry	p. 154
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics	p. 167
De Novo Sequencing of Nonribosomal Peptides	p. 181
Systems Metabolic Engineering (Keynote)	p. 196
Protein Function Prediction Based on Patterns in Biological Networks	p. 197
Automatic Parameter Learning for Multiple Network Alignment	p. 214
An Integrative Network Approach to Map the Transcriptome to the Phenome	p. 232
Fast and Accurate Alignment of Multiple Protein Networks	p. 246
High-Resolution Modeling of Cellular Signaling Networks	p. 257
At the Origin of Life: How Did Folded Proteins Evolve? (Keynote)	p. 272
Locating Multiple Gene Duplications through Reconciled Trees	p. 273
Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information	p. 285
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins	p. 300
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework	p. 315
Computation of Median Gene Clusters	p. 331
BCL-2: From Translocation to Therapy (Keynote)	p. 346
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles	p. 347
Constructing Treatment Portfolios Using Affinity Propagation	p. 360
Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs	p. 372
More Efficient Algorithms for Closest String and Substring Problems	p. 396
Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia (Keynote)	p. 410
Accounting for Non-genetic Factors Improves the Power of eQTL Studies	p. 411
Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA	p. 423
On the Inference of Ancestries in Admixed Populations	p. 424
Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information	p. 434
Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information	p. 435
Constructing Level-2 Phylogenetic Networks from Triplets	p. 450
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony	p. 463
Author Index	p. 479
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