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Research in Computational Molecular Biology

11th Annunal International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007, Proceedings

  • Conference proceedings
  • © 2007

Overview

Editors:
  1. Terry Speed
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  2. Haiyan Huang
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 4453)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: RECOMB 2007.

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Table of contents (37 papers)

  1. Front Matter

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  2. QNet: A Tool for Querying Protein Interaction Networks

    • Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
    Pages 1-15

  3. Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology

    • Rohit Singh, Jinbo Xu, Bonnie Berger
    Pages 16-31

  4. Reconstructing the Topology of Protein Complexes

    • Allister Bernard, David S. Vaughn, Alexander J. Hartemink
    Pages 32-46

  5. Network Legos: Building Blocks of Cellular Wiring Diagrams

    • T. M. Murali, Corban G. Rivera
    Pages 47-61

  6. An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments

    • Abhishek Garg, Ioannis Xenarios, Luis Mendoza, Giovanni DeMicheli
    Pages 62-76

  7. A Feature-Based Approach to Modeling Protein-DNA Interactions

    • Eilon Sharon, Eran Segal
    Pages 77-91

  8. Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking

    • Joshua A. Grochow, Manolis Kellis
    Pages 92-106

  9. Nucleosome Occupancy Information Improves de novo Motif Discovery

    • Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink
    Pages 107-121

  10. 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 et al.
    Pages 122-136

  11. Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models

    • Wenyi Wang, Benilton Carvalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry
    Pages 137-150

  12. GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data

    • Yanxin Shi, Fan Guo, Wei Wu, Eric P. Xing
    Pages 151-165

  13. Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions

    • Hiroyuki Kuwahara, Chris Myers
    Pages 166-180

  14. Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding

    • Noah Zaitlen, Manuel Reyes-Gomez, David Heckerman, Nebojsa Jojic
    Pages 181-195

  15. Reconstructing the Phylogeny of Mobile Elements

    • Sean O’Rourke, Noah Zaitlen, Nebojsa Jojic, Eleazar Eskin
    Pages 196-210

  16. Beyond Galled Trees - Decomposition and Computation of Galled Networks

    • Daniel H. Huson, Tobias H. Klöpper
    Pages 211-225

  17. Variational Upper Bounds for Probabilistic Phylogenetic Models

    • Ydo Wexler, Dan Geiger
    Pages 226-237

  18. 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
    Pages 238-252

  19. Support Vector Training of Protein Alignment Models

    • Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy
    Pages 253-267

  20. Tools for Simulating and Analyzing RNA Folding Kinetics

    • Xinyu Tang, Shawna Thomas, Lydia Tapia, Nancy M. Amato
    Pages 268-282
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