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

This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.

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This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.

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This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.
Content:
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 -

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This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.
Content:
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 -
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