Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009 Tucson, AZ, USA, May 18-21, 2009 Proceedings

by Batzoglou, Serafim

• ISBN13: 9783642020070
• ISBN10: 3642020070
• Edition: 1st
• Format: Paperback
• Copyright: 2009-05-01
• Publisher: SPRINGER

Summary

This book constitutes the refereed proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009, held in Tucson, Arisona, USA in May 2009.The 37 revised full papers presented were carefully reviewed and selected from 166 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

Searching Protein 3-D Structures in Linear Time	p. 1
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification	p. 16
Boosting Protein Threading Accuracy	p. 31
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees	p. 46
A Probabilistic Graphical Model for Ab Initio Folding	p. 59
Topology-Free Querying of Protein Interaction Networks	p. 74
Cross Species Expression Analysis of Innate Immune Response	p. 90
Haplotype Inference in Complex Pedigrees	p. 108
Storage and Retrieval of Individual Genomes	p. 121
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations	p. 138
Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology	p. 155
Spatial Clustering of Multivariate Genomic and Epigenomic Information	p. 170
How Many Bootstrap Replicates Are Necessary?	p. 184
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series	p. 201
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation	p. 217
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes	p. 218
Optimizing PCR Assays for DNA Based Cancer Diagnostics	p. 220
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory	p. 236
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study	p. 253
Overlapping Pools for High Throughput Targeted Resequencing	p. 270
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction	p. 271
Lifting Prediction to Alignment of RNA Pseudoknots	p. 285
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks	p. 302
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination	p. 321
Simultaneous Alignment and Folding of Protein Sequences	p. 339
Shared Peptides in Mass Spectrometry Based Protein Quantification	p. 356
Evaluating Between-Pathway Models with Expression Data	p. 372
Sorting Signed Permutations by Inversions in O(n log n) Time	p. 386
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information	p. 400
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data	p. 418
On the Relationship between DNA Periodicity and Local Chromatin Structure	p. 434
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep (Extended Abstract)	p. 451
Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples	p. 466
An Adaptive and Memory Efficient Algorithm for Genotype Imputation	p. 482
A Statistical Framework for the Functional Analysis of Metagenomes	p. 496
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure	p. 512
Author Index	p. 533
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