| 2009 | Inference of Functional Networks of Condition-Specific Response--A Case Study Of Quiescence In Yeast. | Sushmita Roy, Terran Lane, Margaret Werner-Washburne, Diego Martnez |
| 2009 | Integration of Angiogenesis Modules at Multiple Scales: From Molecular to Tissue. | Amina A. Qutub, Gang Liu, Prakash Vempati, Aleksander S. Popel |
| 2009 | Improving the Efficiency of Biomarker Identification Using Biological Knowledge. | John H. Phan, Qiqin Yin-Goen, Andrew N. Young, May D. Wang |
| 2009 | TreeQA: Quantitative Genome Wide Association Mapping Using Local Perfect Phylogeny Trees. | Feng Pan, Leonard McMillan, Fernando Pardo-Manuel de Villena, David Threadgill, Wei Wang |
| 2009 | From ODES to Language-Based, Executable Models of Biological Systems. | Alida Palmisano, Ivan Mura, Corrado Priami |
| 2009 | Session Introduction. | Michael F. Ochs, John Quackenbush, Ramana V. Davuluri, Habtom W. Ressom |
| 2009 | Open Science: Tools, Approaches, and Implications. | Cameron Neylon, Shirley Wu |
| 2009 | Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models. | Maxwell Lewis Neal, John H. Gennari, Theo Arts, Daniel L. Cook |
| 2009 | Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing. | Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi |
| 2009 | Session Introduction. | Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff |
| 2009 | Efficient and Robust Prediction Algorithms for Protein Complexes Using Gomory-Hu Trees. | Antonina Mitrofanova, Martin Farach-Colton, Bud Mishra |
| 2009 | Session Introduction. | Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann |
| 2009 | Master Regulators Used As Breast Cancer Metastasis Classifier. | Wei Keat Lim, Eugenia Lyashenko, Andrea Califano |
| 2009 | Learning the Structure of Protein-Protein Interaction Networks. | Oleksii Kuchaiev, Natasa Przulj |
| 2009 | Session Introduction. | Roy Kerckhoffs, James B. Bassingthwaighte, Jeff Reinbolt, Peter W. Arzberger |
| 2009 | Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin. | Peter M. Kasson, Vijay S. Pande |
| 2009 | Inferring Disease-Related Pathways Using A Probabilistic Epistasis Model. | Pinal N. Kanabar, Charles J. Vaske, Chen-Hsiang Yeang, Fitnat H. Yildiz, Joshua M. Stuart |
| 2009 | A Parsimony Approach to Analysis of Human Segmental Duplications. | Crystal L. Kahn, Benjamin J. Raphael |
| 2009 | Identifying Dynamic Network Modules with Temporal and Spatial Constraints. | Ruoming Jin, Scott McCallen, Chun-Chi Liu, Yang Xiang, Eivind Almaas, Xianghong Jasmine Zhou |
| 2009 | Unison: An Integrated Platform for Computational Biology Discovery. | Reece K. Hart, Kiran Mukhyala |
| 2009 | Identifying Parent-Daughter Relationships Among Duplicated Genes. | Mira V. Han, Matthew W. Hahn |
| 2009 | Reverse Engineering the Evolution of Protein Interaction Networks. | Todd A. Gibson, Debra Goldberg |
| 2009 | High Throughput Interaction Data Reveals Degree Conservation of Hub Proteins. | Andrew D. Fox, D. Taylor, Donna K. Slonim |
| 2009 | Multi-Scale Modeling of the Human Vertebral Body: Comparison of Micro-CT Based High-Resolution and Continuum-Level Models. | Senthil K. Eswaran, Aaron J. Fields, Prem Nagarathnam, Tony M. Keaveny |
| 2009 | Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology. | Joel Dudley, Atul J. Butte |