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Systems Biology and Regulatory Genomics

Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA, December 2-4, 2005, Revised Selected Papers

  • Conference proceedings
  • © 2006

Overview

Editors:
  1. Eleazar Eskin
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  2. Trey Ideker
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  3. Ben Raphael
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  4. Christopher Workman
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 4023)

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

Included in the following conference series:

Conference proceedings info: RRG 2005, RSB 2005.

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Table of contents (21 papers)

  1. Front Matter

    Download chapter PDF

  2. An Interactive Map of Regulatory Networks of Pseudomonas aeruginosa Genome

    • Weihui Wu, Yongling Song, Shouguang Jin, Su-Shing Chen
    Pages 1-10

  3. The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways

    • David L. Dill, Merrill A. Knapp, Pamela Gage, Carolyn Talcott, Keith Laderoute, Patrick Lincoln
    Pages 11-22

  4. Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations

    • Elena Zotenko, Katia S. Guimarães, Raja Jothi, Teresa M. Przytycka
    Pages 23-38

  5. Comparison of Protein-Protein Interaction Confidence Assignment Schemes

    • Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker
    Pages 39-50

  6. Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs

    • Michal Lapidot, Yitzhak Pilpel
    Pages 51-61

  7. Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes

    • Michiel de Hoon, Dennis Vitkup
    Pages 62-69

  8. Improvement of Computing Times in Boolean Networks Using Chi-square Tests

    • Haseong Kim, Jae K. Lee, Taesung Park
    Pages 70-79

  9. Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements

    • Guandong Wang, Weixiong Zhang
    Pages 80-94

  10. Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes

    • David Kulp, Manjunatha Jagalur
    Pages 95-106

  11. Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels

    • Orna Man, Joel L. Sussman, Yitzhak Pilpel
    Pages 107-118

  12. Improved Duplication Models for Proteome Network Evolution

    • Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, S. Cenk Sahinalp
    Pages 119-137

  13. Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis

    • Chih-Yu Chen, Von-Wun Soo, Chi-Li Kuo
    Pages 138-149

  14. Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data

    • Elissa J. Chesler, Michael A. Langston
    Pages 150-165

  15. Topological Robustness of the Protein-Protein Interaction Networks

    • Chien-Hung Huang, Jywe-Fei Fang, Jeffrey J. P. Tsai, Ka-Lok Ng
    Pages 166-177

  16. A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data

    • Sudhakar Jonnalagadda, Rajagopalan Srinivasan
    Pages 178-187

  17. Probabilistic in Silico Prediction of Protein-Peptide Interactions

    • Wolfgang Lehrach, Dirk Husmeier, Christopher K. I. Williams
    Pages 188-197

  18. Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences

    • Sing-Hoi Sze, Xiaoyan Zhao
    Pages 198-211

  19. Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties

    • Huiquan Wang, Craig J. Benham
    Pages 212-224

  20. An Interaction-Dependent Model for Transcription Factor Binding

    • Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli
    Pages 225-234
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