RECOMB 2009 Proceedings

Tucson, AZ, United States, May 18-21, 2009

PC Chair: Serafim Batzoglou
Organization Committee: John Kececioglu (chair)
Keynote Speakers: Carlos D. Bustamante, Rade Drmanac, Mark Gerstein, Eran Halperin, Michael Hammer, Joanna Mountain, Stephen Quake, Mostafa Ronaghi, Pardis Sabeti, Michael Snyder

List of Publications

• Searching Protein 3-D Structures in Linear Time. Tetsuo Shibuya.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 1-15, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_1
• Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. Zengyou He, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, Weichuan Yu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 16-30, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_2
• Boosting Protein Threading Accuracy. Jian Peng and Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 31-45, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_3
• New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. Cedric Chauve and Nadia El-Mabrouk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 46-58, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_4
• A Probabilistic Graphical Model for Ab Initio Folding. Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 59-73, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_5
• Topology-Free Querying of Protein Interaction Networks. Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 74-89, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_6
• Cross Species Expression Analysis of Innate Immune Response. Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 90-107, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_7
• Haplotype Inference in Complex Pedigrees. Bonnie Kirkpatrick, Javier Rosa, Eran Halperin, Richard M. Karp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 108-120, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_8
• Storage and Retrieval of Individual Genomes. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 121-137, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_9
• An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. Arvind Ramanathan, Pratul K. Agarwal, Maria Kurnikova, Christopher J. Langmead.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 138-154, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_10
• Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology. Alexandre Donzé, Gilles Clermont, Axel Legay, Christopher J. Langmead.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 155-169, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_11
• Spatial Clustering of Multivariate Genomic and Epigenomic Information. Rami Jaschek and Amos Tanay.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 170-183, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_12
• How Many Bootstrap Replicates Are Necessary?. Nicholas D. Pattengale, Masoud Alipour, Olaf R.P. Bininda-Emonds, Bernard M.E. Moret, Alexandros Stamatakis.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 184-200, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_13
• A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. Oliver Stegle, Katherine Denby, David L. Wild, Zoubin Ghahramani, Karsten M. Borgwardt.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 201-216, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_14
• Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation. Tali Raveh-Sadka, Michal Levo, Eran Segal.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 217-217, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_15
• Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 218-219, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_16
• Optimizing PCR Assays for DNA Based Cancer Diagnostics. Ali Bashir, Qing Lu, Dennis Carson, Benjamin Raphael, Yu-Tsueng Liu, Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 220-235, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_17
• The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. Dan Gusfield.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 236-252, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_18
• COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study. Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 253-269, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_19
• Overlapping Pools for High Throughput Targeted Resequencing. Snehit Prabhu and Itsik Pe’er.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 270-270, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_20
• Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 271-284, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_21
• Lifting Prediction to Alignment of RNA Pseudoknots. Mathias Möhl, Sebastian Will, Rolf Backofen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 285-301, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_22
• Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 302-320, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_23
• Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 321-338, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_24
• Simultaneous Alignment and Folding of Protein Sequences. Jérôme Waldispühl, Charles W. O’Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 339-355, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_25
• Shared Peptides in Mass Spectrometry Based Protein Quantification. Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 356-371, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_26
• Evaluating Between-Pathway Models with Expression Data. Benjamin J. Hescott, Maek D.M. Leiserson, Lenore J. Cowen, Donna K. Slonim.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 372-385, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_27
• Sorting Signed Permutations by Inversions in O(n log n) Time. Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M.E. Moret.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 386-399, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_28
• Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. Saket Navlakha, James White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 400-417, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_29
• Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. Suzanne S. Sindi and Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 418-433, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_30
• On the Relationship between DNA Periodicity and Local Chromatin Structure. Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 434-450, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_31
• Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep. Constantinos Daskalakis, Elchanan Mossel, Sebastien Roch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 451-465, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_32
• Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples. Eun Yong Kang, Ilya Shpitser, Chun Ye, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 466-481, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_33
• An Adaptive and Memory Efficient Algorithm for Genotype Imputation. Hyun Min Kang, Noah A. Zaitlen, Buhm Han, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 482-495, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_34
• A Statistical Framework for the Functional Analysis of Metagenomes. Itai Sharon, Amrita Pati, Victor M. Markowitz, Ron Y. Pinter.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 496-511, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_35
• Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. Eagu Kim, Travis Wheeler, John Kececioglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 512-532, Springer, Cham.
    • DOI: 10.1007/978-3-642-02008-7_36