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.
Author(s): Nir Atias, Roded Sharan (auth.), Bonnie Berger (eds.)
Series: Lecture Notes in Computer Science 6044 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2010
Language: English
Pages: 582
Tags: Algorithm Analysis and Problem Complexity; Computational Biology/Bioinformatics; Database Management; Computation by Abstract Devices; Artificial Intelligence (incl. Robotics); Data Structures
Front Matter....Pages -
An Algorithmic Framework for Predicting Side-Effects of Drugs....Pages 1-14
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings....Pages 15-30
Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA....Pages 31-49
Pathway-Based Functional Analysis of Metagenomes....Pages 50-64
Hierarchical Generative Biclustering for MicroRNA Expression Analysis....Pages 65-79
Subnetwork State Functions Define Dysregulated Subnetworks in Cancer....Pages 80-95
Proteome Coverage Prediction for Integrated Proteomics Datasets....Pages 96-109
Discovering Regulatory Overlapping RNA Transcripts....Pages 110-122
Alignment-Free Phylogenetic Reconstruction....Pages 123-137
Inference of Isoforms from Short Sequence Reads....Pages 138-157
The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS....Pages 158-173
A New Algorithm for Improving the Resolution of Cryo-EM Density Maps....Pages 174-188
Towards Automated Structure-Based NMR Resonance Assignment....Pages 189-207
Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra....Pages 208-232
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing....Pages 233-247
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression....Pages 248-262
Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases....Pages 263-280
Incremental Signaling Pathway Modeling by Data Integration....Pages 281-296
The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data....Pages 297-309
Compressing Genomic Sequence Fragments Using SlimGene ....Pages 310-324
On the Genealogy of Asexual Diploids....Pages 325-340
Genovo: De Novo Assembly for Metagenomes....Pages 341-356
MoGUL: Detecting Common Insertions and Deletions in a Population....Pages 357-368
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny....Pages 369-383
Seed Design Framework for Mapping SOLiD Reads....Pages 384-396
Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments....Pages 397-409
Cactus Graphs for Genome Comparisons....Pages 410-425
IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler....Pages 426-440
Predicting Nucleosome Positioning Using Multiple Evidence Tracks....Pages 441-455
Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs....Pages 456-472
Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding....Pages 473-490
HLA Type Inference via Haplotypes Identical by Descent....Pages 491-505
Algorithms for Detecting Significantly Mutated Pathways in Cancer....Pages 506-521
Leveraging Sequence Classification by Taxonomy-Based Multitask Learning....Pages 522-534
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l -Tuples....Pages 535-549
A Markov Random Field Framework for Protein Side-Chain Resonance Assignment....Pages 550-570
Genomic DNA k -mer Spectra: Models and Modalities....Pages 571-571
Deciphering the Swine-Flu Pandemics of 1918 and 2009....Pages 572-573
Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions....Pages 574-574
A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning....Pages 575-576
Automated High-Dimensional Flow Cytometric Data Analysis....Pages 577-577
Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences....Pages 578-579
Back Matter....Pages -
