RECOMB 2010 Proceedings

Lisbon, Portugal, August 12-15, 2010

PC Chair: Bonnie Berger
Organization Committee: Arlindo Oliveira (co-chair), Ana Teresa Freitas (co-chair), João Carriço, Alexandre Francisco, Paulo Fonseca, José Pereira Leal, Sara Madeira, Luís Rocha, Sara Silva, Susana Vinga
Keynote Speakers: Cecilia Arraiano, David Bartel, Isaac Kohane, Phil Kapranov, Norbert Perrimon, Mona Singh

List of Publications

• An Algorithmic Framework for Predicting Side-Effects of Drugs. Nir Atias and Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 1-14, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_1
• SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. Ferhat Ay and Tamer Kahveci.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 15-30, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_2
• Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA. Sivan Bercovici and Dan Geiger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 31-49, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_3
• Pathway-Based Functional Analysis of Metagenomes. Sivan Bercovici, Itai Sharon, Ron Y. Pinter, Tomer Shlomi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 50-64, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_4
• Hierarchical Generative Biclustering for MicroRNA Expression Analysis. José Caldas and Samuel Kaski.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 65-79, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_5
• Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 80-95, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_6
• Proteome Coverage Prediction for Integrated Proteomics Datasets. Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 96-109, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_7
• Discovering Regulatory Overlapping RNA Transcripts. Timothy Danford, Robin Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David Gifford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 110-122, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_8
• Alignment-Free Phylogenetic Reconstruction. Constantinos Daskalakis and Sebastien Roch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 123-137, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_9
• Inference of Isoforms from Short Sequence Reads. Jianxing Feng, Wei Li, Tao Jiang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 138-157, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_10
• 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.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 158-173, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_11
• A New Algorithm for Improving the Resolution of Cryo-EM Density Maps. Michael Hirsch, Bernhard Schölkopf, Michael Habeck.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 174-188, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_12
• Towards Automated Structure-Based NMR Resonance Assignment. Richard Jang, Xin Gao, Ming Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 189-207, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_13
• Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra. Kyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 208-232, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_14
• naive BayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. Wei-Chun Kao and Yun S. Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 233-247, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_15
• Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. David R. Kelley and Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 248-262, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_16
• Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases. Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 263-280, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_17
• Incremental Signaling Pathway Modeling by Data Integration. Geoffrey Koh, David Hsu, P.S. Thiagarajan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 281-296, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_18
• The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data. Adam Kowalczyk, Justin Bedo, Thomas Conway, Bryan Beresford-Smith.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 297-309, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_19
• Compressing Genomic Sequence Fragments Using SLIMGENE. Christos Kozanitis, Chris Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 310-324, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_20
• On the Genealogy of Asexual Diploids. Fumei Lam, Charles H. Langley, Yun S. Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 325-340, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_21
• Genovo: De Novo Assembly for Metagenomes. Jonathan Laserson, Vladimir Jojic, Daphne Koller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 341-356, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_22
• MOGUL: Detecting Common Insertions and Deletions in a Population. Seunghak Lee, Eric Xing, Michael Brudno.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 357-368, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_23
• Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny. Navodit Misra, Guy Blelloch, R. Ravi, Russell Schwartz.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 369-383, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_24
• Seed Design Framework for Mapping SOLID Reads. Laurent Noé, Marta Gîrdea, Gregory Kucherov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 384-396, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_25
• Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. Bogdan Paşaniuc, Noah Zaitlen, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 397-409, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_26
• Cactus Graphs for Genome Comparisons. Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard Suh, David Haussler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 410-425, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_27
• IDBA A Practical Iterative de Bruijn Graph De Novo Assembler. Yu Peng, Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 426-440, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_28
• Predicting Nucleosome Positioning Using Multiple Evidence Tracks. Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 441-455, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_29
• Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs. Barna Saha, Allison Hoch, Samir Khuller, Louiga Raschid, Xiao-Ning Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 456-472, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_30
• Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. Raheleh Salari, Mathias Möhl, Sebastian Will, S. Cenk Sahinalp, Rolf Backofen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 473-490, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_31
• HLA Type Inference via Haplotypes Identical by Descent. Manu N. Setty, Alexander Gusev, Itsik Pe’er.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 491-505, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_32
• Algorithms for Detecting Significantly Mutated Pathways in Cancer. Fabio Vandin, Eli Upfal, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 506-521, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_33
• Leveraging Sequence Classification by Taxonomy-Based Multitask Learning. Christian Widmer, Jose Leiva, Yasemin Altun, Gunnar Rätsch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 522-534, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_34
• A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using ℓ-Tuples. Yu-Wei Wu and Yuzhen Ye.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 535-549, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_35
• A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. Jianyang Zeng, Pei Zhou, Bruce Randall Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 550-570, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_36
• Genomic DNA k-mer Spectra: Models and Modalities. Benny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 571-571, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_37
• Deciphering the Swine-Flu Pandemics of 1918 and 2009. Richard Goldstein, Mario dos Reis, Asif Tamuri, Alan Hay.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 572-573, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_38
• Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 574-574, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_39
• A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning. Jean-Denis Benazet, Mirko Bischofberger, Eva Tiecke, Alexandre Gonalves, James F. Martin, Aime Zuniga, Felix Naef, Rolf Zeller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 575-576, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_40
• Automated High-Dimensional Flow Cytometric Data Analysis. 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.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 577-577, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_41
• Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences. Yonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 578-580, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_42