Research in Computational Molecular Biology: 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings

Front Matter....Pages -
Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss....Pages 1-13
SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation....Pages 14-29
Dissecting Cancer Heterogeneity with a Probabilistic Genotype-Phenotype Model....Pages 30-31
eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data....Pages 32-44
Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models....Pages 45-57
Detecting Protein Conformational Changes in Interactions via Scaling Known Structures....Pages 58-74
IPED: Inheritance Path Based Pedigree Reconstruction Algorithm Using Genotype Data....Pages 75-87
An Optimal Algorithm for Building the Majority Rule Consensus Tree....Pages 88-99
UniNovo : A Universal Tool for de Novo Peptide Sequencing....Pages 100-117
Efficiently Identifying Significant Associations in Genome-Wide Association Studies....Pages 118-131
Identification of Ultramodified Proteins Using Top-Down Spectra....Pages 132-144
Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors....Pages 145-157
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads....Pages 158-170
Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data....Pages 171-172
NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources....Pages 173-185
High Resolution Modeling of Chromatin Interactions....Pages 186-198
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs....Pages 199-211
An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test....Pages 212-229
Learning Natural Selection from the Site Frequency Spectrum....Pages 230-233
Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks....Pages 234-248
Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery....Pages 249-263
Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches....Pages 264-265
MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods....Pages 266-268
Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data....Pages 269-270
Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure....Pages 271-284
Genome-Wide Survival Analysis of Somatic Mutations in Cancer....Pages 285-286
Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance....Pages 287-288
SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics....Pages 289-290
An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees....Pages 291-303
Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform....Pages 304-316
Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data....Pages 317-332
Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties....Pages 333-344
Back Matter....Pages -