Systems Biology and Computational Proteomics: Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers

Fereydoun Hormozdiari, Petra Berenbrink (auth.), Trey Ideker, Vineet Bafna (eds.)3540730591, 9783540730590

The RECOMB Satellite Conferences on Systems Biology and Computational Proteomics were held December 1–3, 2006, at La Jolla, California. The Systems Biology meeting brought researchers together on various aspects of systems biology, including integration of genome-wide microarray, proteomic, and metabolomic data, inference and comparison of biological networks, and model testing through design of experiments. Specific topics included:– Pathway mapping and evolution in protein interaction networks– Inference of protein signaling networks for understanding cellular responses and developmental programs– Model prediction of drug mechanism of action and toxicity– Multi-scale methods which bridge abstract and detailed models– Systematic design of genome-scale experiments– Modeling and recognition of regulatory elements– Identification and modeling of cis-regulatory regions– Modeling the structure and function of regulatory regions– Comparative genomics of regulation

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Table of contents :
Front Matter….Pages –
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation….Pages 1-13
Probabilistic Paths for Protein Complex Inference….Pages 14-28
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting….Pages 29-41
A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells….Pages 42-56
Identification and Evaluation of Functional Modules in Gene Co-expression Networks….Pages 57-76
A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast….Pages 77-95
A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry….Pages 96-107
De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis….Pages 108-118
Alignment of Mass Spectrometry Data by Clique Finding and Optimization….Pages 119-129
Back Matter….Pages –