Table of Contents

• An Algorithmic Framework for Predicting Side-Effects of DrugsNir Atias, Roded Sharan. 1-14 [doi]
• SubMAP: Aligning Metabolic Pathways with Subnetwork MappingsFerhat Ay, Tamer Kahveci. 15-30 [doi]
• Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNASivan Bercovici, Dan Geiger. 31-49 [doi]
• Pathway-Based Functional Analysis of MetagenomesSivan Bercovici, Itai Sharon, Ron Y. Pinter, Tomer Shlomi. 50-64 [doi]
• Hierarchical Generative Biclustering for MicroRNA Expression AnalysisJosé Caldas, Samuel Kaski. 65-79 [doi]
• Subnetwork State Functions Define Dysregulated Subnetworks in CancerSalim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk. 80-95 [doi]
• Proteome Coverage Prediction for Integrated Proteomics DatasetsManfred Claassen, Ruedi Aebersold, Joachim M. Buhmann. 96-109 [doi]
• Discovering Regulatory Overlapping RNA TranscriptsTimothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford. 110-122 [doi]
• Alignment-Free Phylogenetic ReconstructionConstantinos Daskalakis, Sébastien Roch. 123-137 [doi]
• Inference of Isoforms from Short Sequence ReadsJianxing Feng, Wei Li, Tao Jiang. 138-157 [doi]
• The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWASBjarni V. Halldórsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail. 158-173 [doi]
• A New Algorithm for Improving the Resolution of Cryo-EM Density MapsMichael Hirsch, Bernhard Schölkopf, Michael Habeck. 174-188 [doi]
• Towards Automated Structure-Based NMR Resonance AssignmentRichard Jang, Xin Gao, Ming Li. 189-207 [doi]
• Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass SpectraKyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner. 208-232 [doi]
• naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput SequencingWei-Chun Kao, Yun S. Song. 233-247 [doi]
• Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph CompressionDavid R. Kelley, Carl Kingsford. 248-262 [doi]
• Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex DiseasesYoo Ah Kim, Stefan Wuchty, Teresa M. Przytycka. 263-280 [doi]
• Incremental Signaling Pathway Modeling by Data IntegrationGeoffrey Koh, David Hsu, P. S. Thiagarajan. 281-296 [doi]
• The Poisson Margin Test for Normalisation Free Significance Analysis of NGS DataAdam Kowalczyk, Justin Bedo, Thomas Conway, Bryan Beresford-Smith. 297-309 [doi]
• Compressing Genomic Sequence Fragments Using SlimGeneChristos Kozanitis, Chris Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese. 310-324 [doi]
• On the Genealogy of Asexual DiploidsFumei Lam, Charles H. Langley, Yun S. Song. 325-340 [doi]
• Genovo: ::::De Novo:::: Assembly for MetagenomesJonathan Laserson, Vladimir Jojic, Daphne Koller. 341-356 [doi]
• MoGUL: Detecting Common Insertions and Deletions in a PopulationSeunghak Lee, Eric Xing, Michael Brudno. 357-368 [doi]
• Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state PhylogenyNavodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz. 369-383 [doi]
• Seed Design Framework for Mapping SOLiD ReadsLaurent Noé, Marta Gîrdea, Gregory Kucherov. 384-396 [doi]
• Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq ExperimentsBogdan Pasaniuc, Noah Zaitlen, Eran Halperin. 397-409 [doi]
• Cactus Graphs for Genome ComparisonsBenedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler. 410-425 [doi]
• IDBA - A Practical Iterative de Bruijn Graph De Novo AssemblerYu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin. 426-440 [doi]
• Predicting Nucleosome Positioning Using Multiple Evidence TracksSheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble. 441-455 [doi]
• Dense Subgraphs with Restrictions and Applications to Gene Annotation GraphsBarna Saha, Allison Hoch, Samir Khuller, Louiqa Raschid, Xiao-Ning Zhang. 456-472 [doi]
• Time and Space Efficient RNA-RNA Interaction Prediction via Sparse FoldingRaheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen. 473-490 [doi]
• HLA Type Inference via Haplotypes Identical by DescentManu N. Setty, Alexander Gusev, Itsik Pe er. 491-505 [doi]
• Algorithms for Detecting Significantly Mutated Pathways in CancerFabio Vandin, Eli Upfal, Benjamin J. Raphael. 506-521 [doi]
• Leveraging Sequence Classification by Taxonomy-Based Multitask LearningChristian Widmer, Jose Leiva, Yasemin Altun, Gunnar Rätsch. 522-534 [doi]
• A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using ::::l::::-TuplesYu-Wei Wu, Yuzhen Ye. 535-549 [doi]
• A Markov Random Field Framework for Protein Side-Chain Resonance AssignmentJianyang Zeng, Pei Zhou, Bruce Randall Donald. 550-570 [doi]
• Genomic DNA ::::k::::-mer Spectra: Models and ModalitiesBenny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham. 571 [doi]
• Deciphering the Swine-Flu Pandemics of 1918 and 2009Richard Goldstein, Mario dos Reis, Asif U. Tamuri, Alan Hay. 572-573 [doi]
• Distinguishing Direct versus Indirect Transcription Factor-DNA InteractionsRaluca Gordån, Alexander J. Hartemink, Martha L. Bulyk. 574 [doi]
• A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb PatterningJean-Denis Benazet, Mirko Bischofberger, Eva Tiecke, Alexandre Gonalves, James F. Martin, Aime Zuniga, Felix Naef, Rolf Zeller. 575-576 [doi]
• Automated High-Dimensional Flow Cytometric Data AnalysisSaumyadipta Pyne, Xinli Hu, Kui Wang, Elizabeth Rossin, Tsung I. Lin, Lisa Maier, Clare Baecher-Allan, Geoffrey J. McLachlan, Pablo Tamayo, David Hafler, Philip L. De Jager, Jill P. Mesirov. 577 [doi]
• Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory SequencesYonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir. 578-579 [doi]