14. PSB 2009: Kohala Coast, Hawaii, USA

• Preface.
  

Biomolecular Networks: From Analysis to Synthesis

• Gil Alterovitz, Judith A. Blake, Jonathan M. Dreyfuss, Drew Endy, Marco Ramoni:
  Session Introduction. 1-3
  
• Bin Cheng, Marc Riedel:
  Stochastic Transient Analysis of Biochemical Systems and Its Application to the Design of Biochemical Logic Gates. 4-14
  
• James C. Costello, Dan Schrider, Jeff Gehlhausen, Mehmet M. Dalkilic:
  Data-Driven Ontologies. 15-26
  
• Joel Dudley, Atul J. Butte:
  Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology. 27-38
  
• Oleksii Kuchaiev, Natasa Przulj:
  Learning the Structure of Protein-Protein Interaction Networks. 39-50
  
• Sushmita Roy, Terran Lane, Margaret Werner-Washburne, Diego Martinez:
  Inference of Functional Networks of Condition-Specific Response--A Case Study Of Quiescence In Yeast. 51-62
  
• Karen Sachs, Sleiman Itani, J. Fitzgerald, L. Wille, Birgit Schoeberl, Munther A. Dahleh, Garry P. Nolan:
  Learning Cyclic Signaling Pathway Structures While Minimizing Data Requirements. 63-74
  
• Ina Sen, Michael P. Verdicchio, Sungwon Jung, Robert Trevino, Michael L. Bittner:
  Context-Specific Gene Regulations in Cancer Gene Expression Data. 75-86
  
• Luis Tari, Jörg Hakenberg, Graciela Gonzalez, Chitta Baral:
  Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular Networks. 87-98
  
• Wenhong Tian, Nagiza F. Samatova:
  Pairwise Alignment of Interaction Networks by Fast Identification of Maximal Conserved Patterns. 99-110
  

Computational Challenges in Comparative Genomics: Gene Family Evolution, Ancestral Genome Reconstruction, and Applications to Human Genetics

• Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff:
  Session Introduction. 111-113
  
• Mira V. Han, Matthew W. Hahn:
  Identifying Parent-Daughter Relationships Among Duplicated Genes. 114-125
  
• Crystal L. Kahn, Benjamin J. Raphael:
  A Parsimony Approach to Analysis of Human Segmental Duplications. 126-137
  
• Meng Zhang, William Arndt, Jijun Tang:
  An Exact Solver for the DCJ Median Problem. 138-149
  
• Qi Zhang, Wei Wang, Leonard McMillan, Fernando Pardo-Manuel de Villena, David Threadgill:
  Inferring Genome-Wide Mosaic Structure. 150-161
  
• Yu Zhang, Giltae Song, Chih-Hao Hsu, Webb Miller:
  Simultaneous History Reconstruction for Complex Gene Clusters in Multiple Species. 162-173
  

Dynamics of Biological Networks

• Tanya Y. Berger-Wolf, Teresa M. Przytycka, Mona Singh:
  Session Introduction. 174-177
  
• Recep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp:
  Dense Graphlet Statistics of Protein Interaction and Random Networks. 178-189
  
• Todd A. Gibson, Debra Goldberg:
  Reverse Engineering the Evolution of Protein Interaction Networks. 190-202
  
• Ruoming Jin, Scott McCallen, Chun-Chi Liu, Yang Xiang, Eivind Almaas, Xianghong Jasmine Zhou:
  Identifying Dynamic Network Modules with Temporal and Spatial Constraints. 203-214
  
• Antonina Mitrofanova, Martin Farach-Colton, Bud Mishra:
  Efficient and Robust Prediction Algorithms for Protein Complexes Using Gomory-Hu Trees. 215-226
  
• Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi:
  Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing. 227-238
  
• Alida Palmisano, I. Mura, Corrado Priami:
  From ODES to Language-Based, Executable Models of Biological Systems. 239-250
  
• Yoshinori 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:
  Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks. 251-263
  
• Kai Wang, Mariano J. Alvarez, Brygida C. Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera, Andrea Califano:
  Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells. 264-275
  

Emerging Challenges in Multi-Scale Modeling in Biology

• Roy Kerckhoffs, James B. Bassingthwaighte, Jeff Reinbolt, Peter W. Arzberger:
  Session Introduction. 276-280
  
• Yuhui Cheng, Michael J. Holst, James Andrew McCammon:
  Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 Neuraminidase. 281-292
  
• Senthil K. Eswaran, Aaron J. Fields, Prem Nagarathnam, Tony M. Keaveny:
  Multi-Scale Modeling of the Human Vertebral Body: Comparison of Micro-CT Based High-Resolution and Continuum-Level Models. 293-303
  
• Maxwell Lewis Neal, John H. Gennari, Theo Arts, Daniel L. Cook:
  Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models. 304-315
  
• Amina A. Qutub, Gang Liu, Prakash Vempati, Aleksander S. Popel:
  Integration of Angiogenesis Modules at Multiple Scales: From Molecular to Tissue. 316-327
  
• Frank B. Sachse, Eleonora Savio-Galimberti, Joshua I. Goldhaber, John H. B. Bridge:
  Towards Computational Modeling of Excitation-Contraction Coupling in Cardiac Myocytes: Reconstruction of Structures and Proteins from Confocal Imaging. 328-339
  
• V. A. Voelz, P. Petrone, Vijay S. Pande:
  A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel. 340-352
  

Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data

• Michael Ochs, John Quackenbush, Ramana Davuluri, Habtom W. Ressom:
  Session Introduction. 353-355
  
• Ghislain Bidaut, Christian J. Stoeckert Jr.:
  Characterization of Unknown Adult Stem Cell Samples by Large Scale Data Integration and Artificial Neural Networks. 356-367
  
• William S. Bush, Scott M. Dudek, Marylyn D. Ritchie:
  Biofilter: A Knowledge-Integration System for the Multi-Locus Analysis of Genome-Wide Association Studies. 368-379
  
• Vincent J. Carey, Robert Gentleman:
  Interpreting Genetics Of Gene Expression: Integrative Architecture In Bioconductor. 380-390
  
• Andrew D. Fox, D. Taylor, Donna K. Slonim:
  High Throughput Interaction Data Reveals Degree Conservation of Hub Proteins. 391-402
  
• Reece K. Hart, Kiran Mukhyala:
  Unison: An Integrated Platform for Computational Biology Discovery. 403-414
  
• Feng Pan, Leonard McMillan, Fernando Pardo-Manuel de Villena, David Threadgill, Wei Wang:
  TreeQA: Quantitative Genome Wide Association Mapping Using Local Perfect Phylogeny Trees. 415-426
  
• John H. Phan, Qiqin Yin-Goen, Andrew N. Young, May D. Wang:
  Improving the Efficiency of Biomarker Identification Using Biological Knowledge. 427-438
  
• Shai Shen-Orr, Ofir Goldberger, Yael Garten, Yael Rosenberg-Hasson, Patricia A. Lovelace, David Hirschberg, Russ B. Altman, Mark M. Davis, Atul J. Butte:
  Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System. 439-450
  
• Bobbie-Jo M. Webb-Robertson, Lee Ann McCue, Nathaniel Beagley, Jason E. McDermott, David S. Wunschel, Susan M. Varnum, Jian Zhi Hu, Nancy G. Isern, Garry W. Buchko, Kathleen Mcateer, Joel G. Pounds:
  A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections. 451-463
  

Molecular Bioinformatics for Disease

• Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann:
  Session Introduction. 464-466
  
• Anneleen Daemen, Olivier Gevaert, Karin Leunen, Eric Legius, Ignace Vergote, Bart De Moor:
  Supervised Classification of Array CGH Data with HMM-Based Feature Selection. 468-479
  
• P. N. Kanabar, Charles J. Vaske, Chen-Hsiang Yeang, F. H. Yildiz, Joshua M. Stuart:
  Inferring Disease-Related Pathways Using A Probabilistic Epistasis Model. 480-491
  
• Peter M. Kasson, Vijay S. Pande:
  Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin. 492-503
  
• Wei Keat Lim, Eugenia Lyashenko, Andrea Califano:
  Master Regulators Used As Breast Cancer Metastasis Classifier. 504-515
  
• Oznur Tastan, Yanjun Qi, Jaime G. Carbonell, Judith Klein-Seetharaman:
  Prediction of Interactions Between HIV-1 and Human Proteins by Information Integration. 516-527
  
• Xiang Zhang, Fei Zou, Wei Wang:
  FastChi: An Efficient Algorithm for Analyzing Gene-Gene Interactions. 528-539
  

Workshops

• Cameron Neylon, Shirley Wu:
  Open Science: Tools, Approaches, and Implications. 540-544
  
• Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris:
  Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. 545-548
  

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