This book constitutes the refereed proceedings of the 19th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2015, held in Warsaw, Poland, in April 2015. The 36 extended abstracts were carefully reviewed and selected from 170 submissions. They report on original research in all areas of computational molecular biology and bioinformatics.
This book constitutes the refereed proceedings of the 19th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2015, held in Warsaw, Poland, in April 2015. The 36 extended abstracts were carefully reviewed and selected from 170 submissions. They report on original research in all areas of computational molecular biology and bioinformatics.
Efficient Alignment Free Sequence Comparison with Bounded Mismatches.- DockStar: A Novel ILP Based Integrative Method for Structural Modelling of Multimolecular Protein Complexes.- CRISPR Detection from Short Reads Using Partial Overlap Graphs.- Hap Tree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data.- Read Clouds Uncover Variation in Complex Regions of the Human Genome.- Learning Microbial Interaction Networks from Metagenomic Count Data.- Immunoglobulin Classification Using the Colored Antibody Graph.- CIDANE: Comprehensive Isoform Discovery and Abundance Estimation.- Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.- Fragmentation Trees Reloaded.- KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids.- Locating a Tree in a Phylogenetic Network in Quadratic Time.- Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data.- COMETS (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence.- Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure.- BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design.- An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations.- Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models.- CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer.- Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters.- Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning.- ScaffMatch: Scaffolding Algorithm Basedon Maximum Weight Matching.- Symmetric Length-Aware Enrichment Test.- Functional Alignment of Metabolic Networks.- Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples.- Ultra-Large Alignments Using Ensembles of Hidden Markov Models.- Topological Signatures for Population Admixture.- Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele.- Gap Filling as Exact Path Length Problem.- Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.- A Fast and Exact Algorithm for the Exemplar Breakpoint Distance.- Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions.- On the Sample Complexity of Cancer Pathways Identification.- A Novel Probabilistic Methodology for eQTL Analysis of Signaling Networks.- Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.- Computational Protein Design Using AND/OR Branch-and-Bound Search.
Efficient Alignment Free Sequence Comparison with Bounded Mismatches.- DockStar: A Novel ILP Based Integrative Method for Structural Modelling of Multimolecular Protein Complexes.- CRISPR Detection from Short Reads Using Partial Overlap Graphs.- Hap Tree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data.- Read Clouds Uncover Variation in Complex Regions of the Human Genome.- Learning Microbial Interaction Networks from Metagenomic Count Data.- Immunoglobulin Classification Using the Colored Antibody Graph.- CIDANE: Comprehensive Isoform Discovery and Abundance Estimation.- Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks.- Fragmentation Trees Reloaded.- KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids.- Locating a Tree in a Phylogenetic Network in Quadratic Time.- Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data.- COMETS (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence.- Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure.- BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design.- An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations.- Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models.- CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer.- Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters.- Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning.- ScaffMatch: Scaffolding Algorithm Basedon Maximum Weight Matching.- Symmetric Length-Aware Enrichment Test.- Functional Alignment of Metabolic Networks.- Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples.- Ultra-Large Alignments Using Ensembles of Hidden Markov Models.- Topological Signatures for Population Admixture.- Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele.- Gap Filling as Exact Path Length Problem.- Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations.- A Fast and Exact Algorithm for the Exemplar Breakpoint Distance.- Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions.- On the Sample Complexity of Cancer Pathways Identification.- A Novel Probabilistic Methodology for eQTL Analysis of Signaling Networks.- Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.- Computational Protein Design Using AND/OR Branch-and-Bound Search.
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