Table of Contents

• Session IntroductionGil Alterovitz, Judith A. Blake, Jonathan M. Dreyfuss, Drew Endy, Marco Ramoni. 1-3 [doi]
• Stochastic Transient Analysis of Biochemical Systems and Its Application to the Design of Biochemical Logic GatesBin Cheng, Marc Riedel. 4-14 [doi]
• Data-Driven OntologiesJames C. Costello, Dan Schrider, Jeff Gehlhausen, Mehmet M. Dalkilic. 15-26 [doi]
• Identification of Discriminating Biomarkers for Human Disease Using Integrative Network BiologyJoel Dudley, Atul J. Butte. 27-38 [doi]
• Learning the Structure of Protein-Protein Interaction NetworksOleksii Kuchaiev, Natasa Przulj. 39-50 [doi]
• Inference of Functional Networks of Condition-Specific Response--A Case Study Of Quiescence In YeastSushmita Roy, Terran Lane, Margaret Werner-Washburne, Diego Martinez. 51-62 [doi]
• Learning Cyclic Signaling Pathway Structures While Minimizing Data RequirementsKaren Sachs, S. Itani, J. Fitzgerald, L. Wille, Birgit Schoeberl, M. A. Dahleh, Garry P. Nolan. 63-74 [doi]
• Context-Specific Gene Regulations in Cancer Gene Expression DataIna Sen, Michael P. Verdicchio, Sungwon Jung, Robert Trevino, Michael L. Bittner. 75-86 [doi]
• Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular NetworksLuis Tari, Jörg Hakenberg, Graciela Gonzalez, Chitta Baral. 87-98 [doi]
• Pairwise Alignment of Interaction Networks by Fast Identification of Maximal Conserved PatternsWenhong Tian, Nagiza F. Samatova. 99-110 [doi]
• Session IntroductionBernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff. 111-113 [doi]
• Identifying Parent-Daughter Relationships Among Duplicated GenesMira V. Han, Matthew W. Hahn. 114-125 [doi]
• A Parsimony Approach to Analysis of Human Segmental DuplicationsCrystal L. Kahn, Benjamin J. Raphael. 126-137 [doi]
• An Exact Solver for the DCJ Median ProblemMeng Zhang, William Arndt, Jijun Tang. 138-149 [doi]
• Inferring Genome-Wide Mosaic StructureQi Zhang, Wei Wang, Leonard McMillan, Fernando Pardo-Manuel de Villena, David Threadgill. 150-161 [doi]
• Simultaneous History Reconstruction for Complex Gene Clusters in Multiple SpeciesYu Zhang, Giltae Song, Chih-Hao Hsu, Webb Miller. 162-173 [doi]
• Session IntroductionTanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh. 174-177 [doi]
• Dense Graphlet Statistics of Protein Interaction and Random NetworksRecep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp. 178-189 [doi]
• Reverse Engineering the Evolution of Protein Interaction NetworksTodd A. Gibson, Debra Goldberg. 190-202 [doi]
• Identifying Dynamic Network Modules with Temporal and Spatial ConstraintsRuoming Jin, Scott McCallen, Chun-Chi Liu, Yang Xiang, Eivind Almaas, Xianghong Jasmine Zhou. 203-214 [doi]
• Efficient and Robust Prediction Algorithms for Protein Complexes Using Gomory-Hu TreesAntonina Mitrofanova, Martin Farach-Colton, Bud Mishra. 215-226 [doi]
• Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale ComputingKazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi. 227-238 [doi]
• From ODES to Language-Based, Executable Models of Biological SystemsAlida Palmisano, I. Mura, Corrado Priami. 239-250 [doi]
• Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome NetworksYoshinori Tamada, Hiromitsu Araki, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Yukiko Nakanishi, Yuki Tomiyasu, Kaori Yasuda, Ben Dunmore, Deborah Sanders, Sally Humphreys, Cristin G. Print, Stephen D. Charnock-Jones, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano. 251-263 [doi]
• Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B CellsKai Wang, Mariano J. Alvarez, Brygida C. Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera, Andrea Califano. 264-275 [doi]
• Session IntroductionRoy Kerckhoffs, James B. Bassingthwaighte, Jeff Reinbolt, Peter W. Arzberger. 276-280 [doi]
• Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 NeuraminidaseYuhui Cheng, Michael J. Holst, James Andrew McCammon. 281-292 [doi]
• Multi-Scale Modeling of the Human Vertebral Body: Comparison of Micro-CT Based High-Resolution and Continuum-Level ModelsSenthil K. Eswaran, Aaron J. Fields, Prem Nagarathnam, Tony M. Keaveny. 293-303 [doi]
• Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging ModelsMaxwell Lewis Neal, John H. Gennari, Theo Arts, Daniel L. Cook. 304-315 [doi]
• Integration of Angiogenesis Modules at Multiple Scales: From Molecular to TissueAmina A. Qutub, Gang Liu, Prakash Vempati, Aleksander S. Popel. 316-327 [doi]
• Towards Computational Modeling of Excitation-Contraction Coupling in Cardiac Myocytes: Reconstruction of Structures and Proteins from Confocal ImagingFrank B. Sachse, Eleonora Savio-Galimberti, Joshua I. Goldhaber, John H. B. Bridge. 328-339 [doi]
• A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit TunnelV. A. Voelz, P. Petrone, Vijay S. Pande. 340-352 [doi]
• Session IntroductionMichael Ochs, John Quackenbush, Ramana Davuluri, Habtom W. Ressom. 353-355 [doi]
• Characterization of Unknown Adult Stem Cell Samples by Large Scale Data Integration and Artificial Neural NetworksGhislain Bidaut, Christian J. Stoeckert Jr.. 356-367 [doi]
• Biofilter: A Knowledge-Integration System for the Multi-Locus Analysis of Genome-Wide Association StudiesWilliam S. Bush, Scott M. Dudek, Marylyn D. Ritchie. 368-379 [doi]
• Interpreting Genetics Of Gene Expression: Integrative Architecture In BioconductorVincent J. Carey, Robert Gentleman. 380-390 [doi]
• High Throughput Interaction Data Reveals Degree Conservation of Hub ProteinsA. Fox, D. Taylor, Donna K. Slonim. 391-402 [doi]
• Unison: An Integrated Platform for Computational Biology DiscoveryReece K. Hart, Kiran Mukhyala. 403-414 [doi]
• TreeQA: Quantitative Genome Wide Association Mapping Using Local Perfect Phylogeny TreesFeng Pan, Leonard McMillan, Fernando Pardo-Manuel de Villena, David Threadgill, Wei Wang. 415-426 [doi]
• Improving the Efficiency of Biomarker Identification Using Biological KnowledgeJohn H. Phan, Qiqin Yin-Goen, Andrew N. Young, May D. Wang. 427-438 [doi]
• Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune SystemShai Shen-Orr, Ofir Goldberger, Yael Garten, Yael Rosenberg-Hasson, Patricia A. Lovelace, David Hirschberg, Russ B. Altman, Mark M. Davis, Atul J. Butte. 439-450 [doi]
• A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial InfectionsBobbie-Jo M. Webb-Robertson, Lee Ann McCue, Nathaniel Beagley, Jason McDermott, David S. Wunschel, Susan M. Varnum, Jian Zhi Hu, Nancy G. Isern, Garry W. Buchko, Kathleen Mcateer, Joel G. Pounds. 451-463 [doi]
• Session IntroductionYves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann. 464-466 [doi]
• Supervised Classification of Array CGH Data with HMM-Based Feature SelectionAnneleen Daemen, Olivier Gevaert, Karin Leunen, Eric Legius, Ignace Vergote, Bart De Moor. 468-479 [doi]
• Inferring Disease-Related Pathways Using A Probabilistic Epistasis ModelP. N. Kanabar, Charles J. Vaske, Chen-Hsiang Yeang, F. H. Yildiz, Joshua M. Stuart. 480-491 [doi]
• Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza HemagglutininPeter M. Kasson, Vijay S. Pande. 492-503 [doi]
• Master Regulators Used As Breast Cancer Metastasis ClassifierWei Keat Lim, Eugenia Lyashenko, Andrea Califano. 504-515 [doi]
• Prediction of Interactions Between HIV-1 and Human Proteins by Information IntegrationOznur Tastan, Yanjun Qi, Jaime G. Carbonell, Judith Klein-Seetharaman. 516-527 [doi]
• FastChi: An Efficient Algorithm for Analyzing Gene-Gene InteractionsXiang Zhang, Fei Zou, Wei Wang. 528-539 [doi]
• Open Science: Tools, Approaches, and ImplicationsCameron Neylon, Shirley Wu. 540-544 [doi]
• Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and LocalizationBenjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris. 545-548 [doi]