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
Website: https://recomb.org/recomb2009
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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
  • Journal: Searching Protein 3-D Structures in Linear Time. Tetsuo Shibuya. Journal of Computational Biology, 17(3): 203-219, 2010.
    • DOI: 10.1089/cmb.2009.0148
• 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
  • Journal: Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. Zengyou He, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, Weichuan Yu. Journal of Computational Biology, 17(3): 221-235, 2010.
    • DOI: 10.1089/cmb.2009.0160
• 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
  • Journal: Torque: topology-free querying of protein interaction networks. Stefan Brückner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan. Nucleic Acids Research, 37(Web Server): W106-W108, 2009.
    • DOI: 10.1093/nar/gkp474
• 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
  • Journal: Cross Species Expression Analysis of Innate Immune Response. Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar‐Joseph. Journal of Computational Biology, 17(3): 253-268, 2010.
    • DOI: 10.1089/cmb.2009.0147
• 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
  • Journal: Haplotype Inference in Complex Pedigrees. Bonnie Kirkpatrick, Eran Halperin, Richard M. Karp. Journal of Computational Biology, 17(3): 269-280, 2010.
    • DOI: 10.1089/cmb.2009.0174
• 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
  • Journal: Storage and Retrieval of Individual Genomes. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki. DROPS (Schloss Dagstuhl – Leibniz Center for Informatics), 0, 2008.
    • DOI: 10.4230/dagsemproc.08261.10
• 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
  • Journal: An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. Arvind Ramanathan, Pratul K. Agarwal, Maria G. Kurnikova, Christopher J. Langmead. Journal of Computational Biology, 17(3): 309-324, 2010.
    • DOI: 10.1089/cmb.2009.0167
• 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
  • Journal: Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology. Alexandre Donzé, Gilles Clermont, Christopher J. Langmead. Journal of Computational Biology, 17(3): 325-336, 2010.
    • DOI: 10.1089/cmb.2009.0172
• 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
  • Journal: How Many Bootstrap Replicates Are Necessary?. Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda‐Emonds, Bernard M. E. Moret, Alexandros Stamatakis. Journal of Computational Biology, 17(3): 337-354, 2010.
    • DOI: 10.1089/cmb.2009.0179
• 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
  • Journal: A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. Oliver Stegle, Katherine Denby, Emma J. Cooke, David L. Wild, Zoubin Ghahramani, Karsten Borgwardt. Journal of Computational Biology, 17(3): 355-367, 2010.
    • DOI: 10.1089/cmb.2009.0175
• 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
  • Journal: Incorporating nucleosomes into thermodynamic models of transcription regulation. Tali Raveh-Sadka, Michal Levo, Eran Segal. Genome Research, 19(8): 1480-1496, 2009.
    • DOI: 10.1101/gr.088260.108
• 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
  • Journal: Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp. Genome Research, 19(7): 1270-1278, 2009.
    • DOI: 10.1101/gr.088633.108
• 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
  • Journal: Optimizing PCR Assays for DNA-Based Cancer Diagnostics. Ali Bashir, Qing Lü, Dennis A. Carson, Benjamin J. Raphael, Yu‐Tsueng Liu, Vineet Bafna. Journal of Computational Biology, 17(3): 369-381, 2010.
    • DOI: 10.1089/cmb.2009.0203
• 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
  • Journal: The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. Dan Gusfield. Journal of Computational Biology, 17(3): 383-399, 2010.
    • DOI: 10.1089/cmb.2009.0200
• 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
  • Journal: 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. Journal of Computational Biology, 17(3): 401-415, 2010.
    • DOI: 10.1089/cmb.2009.0155
• 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
  • Journal: Overlapping pools for high-throughput targeted resequencing. Snehit Prabhu, Itsik Pe’er. Genome Research, 19(7): 1254-1261, 2009.
    • DOI: 10.1101/gr.088559.108
• 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
  • Journal: Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. Osvaldo Zagordi, Lukas Geyrhofer, Volker Röth, Niko Beerenwinkel. Journal of Computational Biology, 17(3): 417-428, 2010.
    • DOI: 10.1089/cmb.2009.0164
• 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
  • Journal: Lifting Prediction to Alignment of RNA Pseudoknots. Mathias Möhl, Sebastian Will, Rolf Backofen. Journal of Computational Biology, 17(3): 429-442, 2010.
    • DOI: 10.1089/cmb.2009.0168
• 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
  • Journal: Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. Mathieu Lavallée‐Adam, Benoit Coulombe, Mathieu Blanchette. Journal of Computational Biology, 17(3): 443-457, 2010.
    • DOI: 10.1089/cmb.2009.0165
• 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
  • Journal: Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. Wei Zheng, Karl E. Griswold, Chris Bailey‐Kellogg. Journal of Computational Biology, 17(3): 459-475, 2010.
    • DOI: 10.1089/cmb.2009.0189
• 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
  • Journal: Simultaneous Alignment and Folding of Protein Sequences. Jérôme Waldispühl, Charles W. O’Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger. Journal of Computational Biology, 21(7): 477-491, 2014.
    • DOI: 10.1089/cmb.2013.0163
• 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
  • Journal: Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides. Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steven P. Briggs, Vineet Bafna. Journal of Computational Biology, 19(4): 337-348, 2012.
    • DOI: 10.1089/cmb.2009.0267
• 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
  • Journal: Evaluating Between-Pathway Models with Expression Data. Benjamin Hescott, Mark D.M. Leiserson, Thuc Duy Le, Donna K. Slonim. Journal of Computational Biology, 17(3): 477-487, 2010.
    • DOI: 10.1089/cmb.2009.0178
• 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
  • Journal: Sorting Signed Permutations by Inversions in O ( n log n ) Time. Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret. Journal of Computational Biology, 17(3): 489-501, 2010.
    • DOI: 10.1089/cmb.2009.0184
• 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
  • Journal: Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. Saket Navlakha, James R. White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford. Journal of Computational Biology, 17(3): 503-516, 2010.
    • DOI: 10.1089/cmb.2009.0173
• 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
  • Journal: Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. Suzanne Sindi, Benjamin J. Raphael. Journal of Computational Biology, 17(3): 517-531, 2010.
    • DOI: 10.1089/cmb.2009.0185
• 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
  • Preprint: arXiv:0801.4190
• 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
  • Journal: Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples. Eun Yong Kang, Chun Ye, Ilya Shpitser, Eleazar Eskin. Journal of Computational Biology, 17(3): 533-546, 2010.
    • DOI: 10.1089/cmb.2009.0176
• 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
  • Journal: EMINIM: An Adaptive and Memory-Efficient Algorithm for Genotype Imputation. Hyun Min Kang, Noah Zaitlen, Eleazar Eskin. Journal of Computational Biology, 17(3): 547-560, 2010.
    • DOI: 10.1089/cmb.2009.0199
• 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
  • Journal: Aligning Protein Sequences with Predicted Secondary Structure. John Kececioglu, Eagu Kim, Travis J. Wheeler. Journal of Computational Biology, 17(3): 561-580, 2010.
    • DOI: 10.1089/cmb.2009.0222