14. RECOMB 2010: Lisbon, Portugal

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

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