RECOMB 2007 Proceedings

Oakland, CA, United States, April 21 - 25, 2007

PC Chair: Terry Speed
Organization Committee: Sandrine Dudoit
Keynote Speakers: Elizabeth H. Blackburn, Jennifer Marshall Graves, Yishi Jin, Jay D. Keasling, Harry F. Noller, Patrick O. Brown, Abby Dernburg, Aviv Regev
Website: https://recomb.org/recomb2007
Export: JSON | BibTeX

List of Publications

• QNet: A Tool for Querying Protein Interaction Networks. Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 1-15, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_1
  • Journal: QNet: A Tool for Querying Protein Interaction Networks. Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan. Journal of Computational Biology, 15(7): 913-925, 2008.
    • DOI: 10.1089/cmb.2007.0172
• Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. Rohit Singh, Jinbo Xu, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 16-31, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_2
• Reconstructing the Topology of Protein Complexes. Allister Bernard, David S. Vaughn, Alexander J. Hartemink.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 32-46, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_3
• Network Legos: Building Blocks of Cellular Wiring Diagrams. T.M. Murali and Corban G. Rivera.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 47-61, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_4
  • Journal: Network Legos: Building Blocks of Cellular Wiring Diagrams. T. M. Murali, Corban G. Rivera. Journal of Computational Biology, 15(7): 829-844, 2008.
    • DOI: 10.1089/cmb.2007.0139
• An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments. Abhishek Garg, Ioannis Xenarios, Luis Mendoza, Giovanni DeMicheli.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 62-76, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_5
• A Feature-Based Approach to Modeling Protein-DNA Interactions. Eilon Sharon and Eran Segal.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 77-91, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_6
  • Journal: A Feature-Based Approach to Modeling Protein–DNA Interactions. Eilon Sharon, Shai Lubliner, Eran Segal. PLoS Computational Biology, 4(8): e1000154, 2008.
    • DOI: 10.1371/journal.pcbi.1000154
• Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking. Joshua A. Grochow and Manolis Kellis.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 92-106, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_7
• Nucleosome Occupancy Information Improves de novo Motif Discovery. Leelavati Narlikar, Raluca Gordan, Alexander J. Hartemink.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 107-121, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_8
• Framework for Identifying Common Aberrations in DNA Copy Number Data. Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael T. Barrett, John N. Weinstein, Anne-Lise Børresen-Dale, Zohar Yakhini.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 122-136, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_9
• Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models. Wenyi Wang, Benilton Carvalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 137-150, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_10
  • Journal: Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models. Wenyi Wang, Benilton S. Carvalho, Nathaniel D. Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry. Journal of Computational Biology, 15(7): 857-866, 2008.
    • DOI: 10.1089/cmb.2007.0148
• GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data. Yanxin Shi, Fan Guo, Wei Wu, Eric P. Xing.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 151-165, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_11
• Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. Hiroyuki Kuwahara and Chris Myers.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 166-180, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_12
  • Journal: Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. Hiroyuki Kuwahara, Chris J. Myers. Journal of Computational Biology, 15(7): 779-792, 2008.
    • DOI: 10.1089/cmb.2007.0135
• Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding. Noah Zaitlen, Manuel Reyes-Gomez, David Heckerman, Nebojsa Jojic.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 181-195, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_13
  • Journal: Shift-Invariant Adaptive Double Threading: Learning MHC II–Peptide Binding. Noah Zaitlen, Manuel Reyes Gomez, David Heckerman, Nebojša Jojić. Journal of Computational Biology, 15(7): 927-942, 2008.
    • DOI: 10.1089/cmb.2007.0183
• Reconstructing the Phylogeny of Mobile Elements. Sean O’Rourke, Noah Zaitlen, Nebojsa Jojic, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 196-210, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_14
• Beyond Galled Trees Decomposition and Computation of Galled Networks. Daniel H. Huson and Tobias H. Klöpper.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 211-225, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_15
• Variational Upper Bounds for Probabilistic Phylogenetic Models. Ydo Wexler and Dan Geiger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 226-237, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_16
  • Journal: Variational Upper and Lower Bounds for Probabilistic Graphical Models. Ydo Wexler, Dan Geiger. Journal of Computational Biology, 15(7): 721-735, 2008.
    • DOI: 10.1089/cmb.2007.0129
• Heuristics for the Gene-Duplication Problem: A Θ(n) Speed-Up for the Local Search. Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 238-252, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_17
• Support Vector Training of Protein Alignment Models. Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 253-267, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_18
  • Journal: Support Vector Training of Protein Alignment Models. Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jarosław Pillardy. Journal of Computational Biology, 15(7): 867-880, 2008.
    • DOI: 10.1089/cmb.2007.0152
• Tools for Simulating and Analyzing RNA Folding Kinetics. Xinyu Tang, Shawna Thomas, Lydia Tapia, Nancy M. Amato.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 268-282, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_19
• Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. Yue Lu and Sing-Hoi Sze.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 283-295, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_20
  • Journal: Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. Yue Lu, Sing-Hoi Sze. Journal of Computational Biology, 15(7): 767-777, 2008.
    • DOI: 10.1089/cmb.2007.0132
• Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data. Joël Pradines, Vlado Dančík, Alan Ruttenberg, Victor Farutin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 296-310, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_21
• Multivariate Segmentation in the Analysis of Transcription Tiling Array Data. Antonio Piccolboni.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 311-324, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_22
  • Journal: Multivariate Segmentation in the Analysis of Transcription Tiling Array Data. Antonio Piccolboni. Journal of Computational Biology, 15(7): 845-856, 2008.
    • DOI: 10.1089/cmb.2007.0141
• A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements. Anitha Kannan, Andrew Emili, Brendan J. Frey.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 325-338, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_23
• Rearrangements in Genomes with Centromeres Part I: Translocations. Michal Ozery-Flato and Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 339-353, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_24
  • Journal: Sorting Genomes with Centromeres by Translocations. Michal Ozery-Flato, Ron Shamir. Journal of Computational Biology, 15(7): 793-812, 2008.
    • DOI: 10.1089/cmb.2007.0136
• Identification of Deletion Polymorphisms from Haplotypes. Erik Corona, Benjamin Raphael, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 354-365, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_25
• Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation. Hetunandan Kamisetty, Eric P. Xing, Christopher J. Langmead.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 366-380, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_26
  • Journal: Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation. Hetunandan Kamisetty, Eric P. Xing, Christopher J. Langmead. Journal of Computational Biology, 15(7): 755-766, 2008.
    • DOI: 10.1089/cmb.2007.0131
• Minimizing and Learning Energy Functions for Side-Chain Prediction. Chen Yanover, Ora Schueler-Furman, Yair Weiss.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 381-395, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_27
  • Journal: Minimizing and Learning Energy Functions for Side-Chain Prediction. Chen Yanover, Ora Schueler‐Furman, Yair Weiss. Journal of Computational Biology, 15(7): 899-911, 2008.
    • DOI: 10.1089/cmb.2007.0158
• Protein Conformational Flexibility Analysis with Noisy Data. Anshul Nigham and David Hsu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 396-411, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_28
  • Journal: Protein Conformational Flexibility Analysis with Noisy Data. Anshul Nigham, David Hsu. Journal of Computational Biology, 15(7): 813-828, 2008.
    • DOI: 10.1089/cmb.2007.0138
• Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules. Yuval Inbar, Dina Schneidman-Duhovny, Oranit Dror, Ruth Nussinov, Haim J. Wolfson.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 412-429, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_29
  • Journal: Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules. Dina Schneidman‐Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson. Journal of Computational Biology, 15(7): 737-754, 2008.
    • DOI: 10.1089/cmb.2007.0130
• Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 430-443, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_30
  • Journal: Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. Anthony Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk. Journal of Computational Biology, 15(7): 655-665, 2008.
    • DOI: 10.1089/cmb.2007.0114
• Improved Ranking Functions for Protein and Modification-Site Identifications. Marshall Bern and David Goldberg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 444-458, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_31
  • Journal: Improved Ranking Functions for Protein and Modification-Site Identifications. Marshall Bern, David Theo Goldberg. Journal of Computational Biology, 15(7): 705-719, 2008.
    • DOI: 10.1089/cmb.2007.0119
• Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions. Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss, William Stafford Noble.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 459-472, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_32
  • Journal: Improving Tandem Mass Spectrum Identification Using Peptide Retention Time Prediction across Diverse Chromatography Conditions. Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss, William Stafford Noble. Analytical Chemistry, 79(16): 6111-6118, 2007.
    • DOI: 10.1021/ac070262k
• A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data. Ole Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Hildebrandt, Knut Reinert.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 473-487, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_33
  • Journal: Computational Quantification of Peptides from LC-MS Data. Ole Schulz-Trieglaff, René Hussong, Clemens Gröpl, Andreas Leinenbach, Andreas Hildebrandt, Christian G. Huber, Knut Reinert. Journal of Computational Biology, 15(7): 685-704, 2008.
    • DOI: 10.1089/cmb.2007.0117
• Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms. Yufeng Wu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 488-502, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_34
  • Journal: Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms. Yufeng Wu. Journal of Computational Biology, 15(7): 667-684, 2008.
    • DOI: 10.1089/cmb.2007.0116
• An Efficient and Accurate Graph-Based Approach to Detect Population Substructure. Srinath Sridhar, Satish Rao, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 503-517, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_35
• RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints. Wah-Heng Lee and Wing-Kin Sung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 518-532, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_36
  • Journal: RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints. Wah-Heng Lee, Wing‐Kin Sung. Journal of Computational Biology, 15(7): 881-898, 2008.
    • DOI: 10.1089/cmb.2007.0154
• Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs. Cyrus L. Harmon, Parvez Ahammad, Ann Hammonds, Richard Weiszmann, Susan E. Celniker, S. Shankar Sastry, Gerald M. Rubin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science, vol 4453, pp 533-548, Springer, Cham.
    • DOI: 10.1007/978-3-540-71681-5_37