Biomolecular networks: from analysis to synthesis. Session introduction / Gil Alterovitz [and others]. Stochastic transient analysis of biochemical systems and its application to the design of biochemical logic gates / Bin Cheng and Marc Riedel. Data-driven ontologies / James C. Costello [and others]. Identification of discriminating biomarkers for human disease using integrative network biology / Joel T. Dudley and Atul J. Butte. Learning the structure of protein-protein interaction networks / Oleksii Kuchaiev and Nataša Pržulj. Inference of functional networks of condition-specific response -- a case study of quiescence in yeast / Sushmita Roy [and others]. Learning cyclic signaling pathway structures while minimizing data requirements / K. Sachs [and others]. Context-specific gene regulations in cancer gene expression data / Ina Sen [and others]. Querying parse tree database of Medline text to synthesize user-specific biomolecular networks / Luis Tari [and others]. Pairwise alignment of interaction networks by fast identification of maximal conserved patterns / Wenhong Tian and Nagiza F. Samatova -- Computational challenges in comparative genomics: gene family evolution, ancestral genome reconstruction, and applications to human genetics. Session introduction / Bernard M.E. Moret [and others]. Identifying parent-daughter relationships among duplicated genes / Mira V. Han and Matthew W Hahn. A parsimony approach to analysis of human segmental duplications / Crystal L. Kahn and Benjamin J. Raphael. An exact solver for the DCJ median problem / Meng Zhang, William Arndt, and Jijun Tang. Inferring genome-wide mosaic structure / Qi Zhang [and others]. Simultaneous history reconstruction for complex gene clusters in multiple species / Yi Zhang [and others] -- Dynamics of biological networks. Session introduction / Tanya Y. Berger-Wolf, Teresa M. Przytycka, and Mona Singh. Dense graphlet statistics of protein interaction and random networks / R. Colak [and others]. Reverse engineering the evolution of protein interaction networks / Todd A. Gibson and Debra S. Goldberg. Identifying dynamic network modules with temporal and spatial constraints / Ruoming Jin [and others]. Efficient and robust prediction algorithms for protein complexes using Gomory-Hu trees / A. Mitrofanova, M. Farach-Colton, and B. Mishra. Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing / Kazuyuki Nakamura [and others]. From ODES to language-based, executable models of biological systems / A. Palmisano, I. Mura, and C. Priami. Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks / Yoshinori Tamada [and others]. Dissecting the interface between signaling and transcriptional regulation in human B cells / Kai Wang [and others] -- Emerging challenges in multi-scale modeling in biology. Session introduction / Roy Kerckhoffs [and others]. Finite element analysis of drug electrostatic diffusion: inhibition rate studies in Nl neuraminidase / Yuhui Cheng, Michael J. Holst, and J.A. McCammon. Multi-scale modeling of the human vertebral body: comparison of micro-CT based high-resolution and continuum-level models / Senthil K. Eswaran [and others]. Advances in semantic representation for multiscale biosimulation: a case study in merging models / Maxwell Lewis Neal [and others]. Integration of angiogenesis modules at multiple scales: from molecular to tissue / Amina A. Qutub [and others]. Towards computational modeling of excitation-contraction coupling in cardiac myocytes: reconstruction of structures and proteins from confocal imaging / Frank B. Sachse [and others]. A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel / V.A. Voelz, P. Petrone, and V.S. Pande -- Knowledge-driven analysis and data integration for high-throughput biological data. Session introduction / Michael Ochs [and others]. Characterization of unknown adult stem cell samples by large scale data integration and artificial neural networks / G. Bidaut and C.J. Stoeckert Jr. Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies / William S. Bush, Scott M. Dudek, and Marylyn D. Ritchie. Interpreting genetics of gene expression: integrative architecture in bioconductor / V.J. Carey and R. Gentleman. High throughput interaction data reveals degree conservation of hub proteins / A. Fox, D. Taylor, and D.K. Slonim. Unison: an integrated platform for computational biology discovery / Reece K. Hart and Kiran Mukhyala. TreeQA: quantitative genome wide association mapping using local perfect phylogeny trees / Feng Pan [and others]. Improving the efficiency of biomarker identification using biological knowledge / John H. Phan [and others]. Towards a cytokine-cell interaction knowledgebase of the adaptive immune system / Shai S. Shen-Orr [and others]. A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections / Bobbie-Jo M. Webb-Robertson [and others] -- Molecular bioinformatics for disease. Session introduction / Yves A. Lussier [and others]. Molecular interaction network based discovery of master regulator genes / Andrea Califano. Supervised classification of array CGH data with HMM-based feature selection / Anneleen Daemen [and others]. Inferring disease-related pathways using a probabilistic epistasis model / P.N. Kanabar [and others]. Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin / Peter M. Kasson and Vijay S. Pande. Master regulators used as breast cancer metastasis classifier / Wei Keat Lim, Eugenia Lyashenko, and Andrea Califano. Prediction of interactions between HIV -1 and human proteins by information integration / Oznur Tastan [and others]. FastChi: an efficient algorithm for analyzing gene-gene interactions / Xiang Zhang, Fei Zou, and Wei Wang. Open science: tools, approaches, and implications / Cameron Neylon and Shirley Wu. Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization / Benjamin Blencowe [and others].