This book constitutes the refereed proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2010, held in Lisbon, Portugal, in April 2010. The 36 revised full papers were carefully reviewed and selected from 176 submissions. The papers cover all areas of computational molecular biology such as molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; population genetics; systems biology; imaging; computational proteomics; and molecular structural biology.
An Algorithmic Framework for Predicting Side-Effects of Drugs Nir Atias Roded Sharan 1
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings Ferhat Ay Tamer Kahveci 15
Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA Sivan Bercovici Dan Geiger 31
Pathway-Based Functional Analysis of Metagenomes Sivan Bercovici Itai Sharon Ron Y. Pinter Tomer Shlomi 50
Hierarchical Generative Biclustering for MicroRNA Expression Analysis José Caldas Samuel Kaski 65
Subnetwork State Functions Define Dysregulated Subnetworks in Cancer Salim A. Chowdhury Rod K. Nibbe Mark R. Chance Mehmet Koyutürk 80
Proteome Coverage Prediction for Integrated Proteomics Datasets Manfred Claassen Ruedi Aebersold Joachim M. Buhmann 96
Discovering Regulatory Overlapping RNA Transcripts Timothy Danford Robin Dowell Sudeep Agarwala Paula Grisafi Gerald Fink David Gifford 110
Alignment-Free Phylogenetic Reconstruction Constantinos Daskalakis Sebastien Roch 123
Inference of Isoforms from Short Sequence Reads (Extended Abstract) Jianxing Feng Wei Li Tao Jiang 138
The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS Bjarni V. Halldórsson Derek Aguiar Ryan Tarpine Sorin Istrail 158
A New Algorithm for Improving the Resolution of Cryo-EM Density Maps Michael Hirsch Bernhard Schölkopf Michael Habeck 174
Towards Automated Structure-Based NMR Resonance Assignment Richard Jang Xin Gao Ming Li 189
Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra Kyowon Jeong Sangtae Kim Nuno Bandeira Pavel A. Pevzner 208
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing Wei-Chun Kao Yun S. Song 233
Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression David R. Kelley Carl Kingsford 248
Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases Yoo-Ah Kim Stefan Wuchty Teresa M. Przytycka 263
Incremental Signaling Pathway Modeling by Data Integration Geoffrey Koh David Hsu P.S. Thiagarajan 281
The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data Adam Kowalczyk Justin Bedo Thomas Conway Bryan Beresford-Smith 297
Compressing Genomic Sequence Fragments Using SLIMGENE Christos Kozanitis Chris Saunders Semyon Kruglyak Vineet Bafna George Varghese 310
On the Genealogy of Asexual Diploids Fumei Lam Charles H. Langley Yun S. Song 325
Genovo: De Novo Assembly for Metagenomes Jonathan Laserson Vladimir Jojic Daphne Koller 341
MoGUL: Detecting Common Insertions and Deletions in a Population Seunghak Lee Eric Xing Michael Brudno 357
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phytogeny Navodit Misra Guy Blelloch R. Ravi Russell Schwartz 369
Seed Design Framework for Mapping SOLiD Reads Laurent Noé Marta Gîrdea Gregory Kucherov 384
Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments Bogdan Pasaniuc Noah Zaitlen Eran Halperin 397
Cactus Graphs for Genome Comparisons Benedict Paten Mark Diekhans Dent Earl John St. John Jian Ma Bernard Suh David Haussler 410
IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler Yu Peng Henry C.M. Leung S.M. Yiu Francis Y.L. Chin 426
Predicting Nucleosome Positioning Using Multiple Evidence Tracks Sheila M. Reynolds Zhiping Weng Jeff A. Bilmes William Stafford Noble 441
Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs Barna Saha Allison Hoch Samir Khuller Louiqa Raschid Xiao-Ning Zhang 456
Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding Raheleh Salari Mathias Möhl Sebastian Will S. Cenk Sahinalp Rolf Backofen 473
HLA Type Inference via Haplotypes Identical by Descent Manu N. Setty Alexander Gusev Itsik Pe'er 491
Algorithms for Detecting Significantly Mutated Pathways in Cancer Fabio Vandin Eli Upfal Benjamin J. Raphael 506
Leveraging Sequence Classification by Taxonomy-Based Multitask Learning Christian Widmer Jose Leiva Yasemin Altun Gunnar Rätsch 522
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples Yu-Wei Wu Yuzhen Ye 535
A Markov Random Field Framework for Protein Side-Chain Resonance Assignment Jianyang Zeng Pei Zhou Bruce Randall Donald 550
Genomic DNA k-mer Spectra: Models and Modalities (Abstract) Benny Chor David Horn Nick Goldman Yaron Levy Tim Massingham 571
Deciphering the Swine-Flu Pandemics of 1918 and 2009 (Abstract) Richard Goldstein Mario dos Reis Asif Tamuri Alan Hay 572
Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions (Abstract) Raluca Gordân Alexander J. Hartemink Martha L. Bulyk 574
A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning (Abstract) Jean-Denis Benazet Mirko Bischofberger Eva Tiecke Alexandre Gonalves James F. Martin Aime Zuniga Felix Naef Rolf Zeller 575
Automated High-Dimensional Flow Cytometric Data Analysis (Abstract) Saumyadipta Pyne Xinli Hu Kui Wang Elizabeth Rossin Tsung-I Lin Lisa Maier Clare Baecher-Allan Geoffrey McLachlan Pablo Tamayo David Hafler Philip De Jager Jill Mesirov 577
Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences (Abstract) Yonit Halperin Chaim Linhart Igor Ulitsky Ron Shamir 578
Author Index 581
Overview
This book constitutes the refereed proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2010, held in Lisbon, Portugal, in April 2010. The 36 revised full papers were carefully reviewed and selected from 176 submissions. The papers cover all areas of computational molecular biology such as molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping ...