Research in Computational Molecular Biology

This volume contains the papers presented at RECOMB 2010: the 14th Annual International Conference on Research in Computational Molecular Biology held in Lisbon, Portugal, during April 25-28, 2010. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner, and Michael Waterman. RECOMB 2010 was hosted by INESC-ID and Instituto Superior Tecnico, or- nized by a committee chaired by Arlindo Oliveira and took place at the Int- national Fair of Lisbon Meeting Centre. This year, 36 papers were accepted for presentation out of 176 submissions. The papers presented were selected by the Program Committee (PC) assisted by a number of external reviewers. Each paper was reviewed by three members of the PC, or by external reviewers, and there was an extensive Web-based discussion over a period of two weeks, leading to the ?nal decisions. RECOMB 2010 also introduced a Highlights Track, in which six additional presentations by senior authors were chosen from papers published in 2009. The RECOMB conferenceseriesiscloselyassociatedwiththeJournalofComputational Biology, which traditionally publishes special issues devoted to presenting full versions of selected conference papers.

Inhalt

An Algorithmic Framework for Predicting Side-Effects of Drugs.- SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings.- Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA.- Pathway-Based Functional Analysis of Metagenomes.- Hierarchical Generative Biclustering for MicroRNA Expression Analysis.- Subnetwork State Functions Define Dysregulated Subnetworks in Cancer.- Proteome Coverage Prediction for Integrated Proteomics Datasets.- Discovering Regulatory Overlapping RNA Transcripts.- Alignment-Free Phylogenetic Reconstruction.- Inference of Isoforms from Short Sequence Reads.- The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS.- A New Algorithm for Improving the Resolution of Cryo-EM Density Maps.- Towards Automated Structure-Based NMR Resonance Assignment.- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra.- naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing.- Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression.- Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases.- Incremental Signaling Pathway Modeling by Data Integration.- The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data.- Compressing Genomic Sequence Fragments Using SlimGene.- On the Genealogy of Asexual Diploids.- Genovo: De Novo Assembly for Metagenomes.- MoGUL: Detecting Common Insertions and Deletions in a Population.- Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny.- Seed Design Framework for Mapping SOLiD Reads.- Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments.- Cactus Graphs for Genome Comparisons.- IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler.- Predicting Nucleosome Positioning Using Multiple Evidence Tracks.- Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs.- Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding.- HLA Type Inference via Haplotypes Identical by Descent.- Algorithms for Detecting Significantly Mutated Pathways in Cancer.- Leveraging Sequence Classification by Taxonomy-Based Multitask Learning.- A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples.- A Markov Random Field Framework for Protein Side-Chain Resonance Assignment.- Genomic DNA k-mer Spectra: Models and Modalities.- Deciphering the Swine-Flu Pandemics of 1918 and 2009.- Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions.- A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning.- Automated High-Dimensional Flow Cytometric Data Analysis.- Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences.