Fereydoun Hormozdiari and Petra Berenbrink and Natasa Przulj and Cenk SahinalpHailiang Huang and Lan V. Zhang and Frederick P. Roth and Joel S. BaderHans-Michael Kaltenbach and Sebastian Bocker and Sven RohmannCeline Lefebvre and Wei Keat Lim and Katia Basso and Riccardo Dalla Favera and Andrea CalifanoJianhua Ruan and Weixiong ZhangMingzhou (Joe) Song and Z. Lewis LiuYin Wu and Yehia Mechref and Iveta Klouckova and Milos V. Novotny and Haixu TangDerek Ruths and Jen-Te Tseng and Luay Nakhleh and Prahlad T. RamDaniel Fasulo and Anne-Katrin Emde and Lu-Yong Wang and Karin Noy and Nathan Edwards

Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation	p. 1
Probabilistic Paths for Protein Complex Inference	p. 14
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting	p. 29
A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells	p. 42
Identification and Evaluation of Functional Modules in Gene Co-expression Networks	p. 57
A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast	p. 77
A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry	p. 96
De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Arialysis	p. 108
Alignment of Mass Spectrometry Data by Clique Finding and Optimization	p. 119
Author Index	p. 131