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14. PSB 2009: Kohala Coast, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein:
Biocomputing 2009: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, 5-9 January 2009. 2009, ISBN 978-981-283-692-2 - 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 D. Riedel:
Stochastic Transient Analysis of Biochemical Systems and Its Application to the Design of Biochemical Logic Gates. 4-14 - James C. Costello, Daniel R. 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 Martínez:
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 P. 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, Ivan 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 - Vincent A. Voelz, Paula 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 F. 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 L. 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 - Pinal N. Kanabar, Charles J. Vaske, Chen-Hsiang Yeang, Fitnat 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 - Öznur 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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