Systems Biology and Computational Proteomics [electronic resource] : Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers / edited by Trey Ideker, Vineet Bafna.

Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation -- Probabilistic Paths for Protein Complex Inference -- Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting -- A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells -- Identification and Evaluation of Functional Modules in Gene Co-expression Networks -- A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast -- A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry -- De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis -- Alignment of Mass Spectrometry Data by Clique Finding and Optimization.

The RECOMB Satellite Conferences on Systems Biology and Computational Proteomics were held December 1–3, 2006, at La Jolla, California. The S- tems Biology meeting brought researchers together on various aspects of s- tems biology, including integration of genome-wide microarray, proteomic, and metabolomic data, inference and comparison of biological networks, and model testing through design of experiments. Speci?c 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 – Identi?cation and modeling of cis-regulatory regions – Modeling the structure and function of regulatory regions – Comparative genomics of regulation Withthesequencingofthegenome,andsubsequentidenti?cationoftheparts list (the gene and their protein products), there is a renewed emphasis on stu- ing the proteome. This year, the computational proteomics meeting focused on on computational mass spectrometry. Mass spectrometry is emerging as a key technology for proteomics. The last few years have seen tremendous impro- ment in the quality and quantity of available peptide mass spectrometry data, as well asthe realizationthat advanced computational approachesarecritical to thesuccessofthis technology. Theconferenceexploredtheuseofthis technology in various proteomic applications, including, but not limited to: protein ident- cation and quanti?cation in speci?c cellular environments; structural genomics; networks of protein interaction; post-translational modi?cations; and others. We received approximately 50 full paper submissions to the joint workshops.