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

Front Matter....Pages -
Searching Protein 3-D Structures in Linear Time....Pages 1-15
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification....Pages 16-30
Boosting Protein Threading Accuracy....Pages 31-45
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees....Pages 46-58
A Probabilistic Graphical Model for Ab Initio Folding....Pages 59-73
Topology-Free Querying of Protein Interaction Networks....Pages 74-89
Cross Species Expression Analysis of Innate Immune Response....Pages 90-107
Haplotype Inference in Complex Pedigrees....Pages 108-120
Storage and Retrieval of Individual Genomes....Pages 121-137
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations....Pages 138-154
Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology....Pages 155-169
Spatial Clustering of Multivariate Genomic and Epigenomic Information....Pages 170-183
How Many Bootstrap Replicates Are Necessary?....Pages 184-200
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series....Pages 201-216
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation....Pages 217-217
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes....Pages 218-219
Optimizing PCR Assays for DNA Based Cancer Diagnostics....Pages 220-235
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory....Pages 236-252
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study....Pages 253-269
Overlapping Pools for High Throughput Targeted Resequencing....Pages 270-270
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction....Pages 271-284
Lifting Prediction to Alignment of RNA Pseudoknots....Pages 285-301
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks....Pages 302-320
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination....Pages 321-338
Simultaneous Alignment and Folding of Protein Sequences....Pages 339-355
Shared Peptides in Mass Spectrometry Based Protein Quantification....Pages 356-371
Evaluating Between-Pathway Models with Expression Data....Pages 372-385
Sorting Signed Permutations by Inversions in O ( n log n ) Time....Pages 386-399
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information....Pages 400-417
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data....Pages 418-433
On the Relationship between DNA Periodicity and Local Chromatin Structure....Pages 434-450
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep....Pages 451-465
Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples....Pages 466-481
An Adaptive and Memory Efficient Algorithm for Genotype Imputation....Pages 482-495
A Statistical Framework for the Functional Analysis of Metagenomes....Pages 496-511
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure....Pages 512-531
Back Matter....Pages -