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

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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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