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18. PSB 2013: Kohala Coast, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein:
Biocomputing 2013: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2013. World Scientific Publishing 2013, ISBN 978-1-62748-016-1
Computational drug repositioning
- Zhiyong Lu, Pankaj Agarwal, Atul J. Butte:
Session Introduction. 1-4 - Jie Cheng, Qing Xie, Vinod Kumar, Mark Hurle, Johannes M. Freudenberg, Lun Yang, Pankaj Agarwal:
Evaluation of Analytical Methods for Connectivity Map Data. 5-16 - Ramon M. Felciano, Sina Bavari, Daniel R. Richards, Jean-Noel Billaud, Travis Warren, Rekha Panchal, Andreas Krämer:
Predictive Systems Biology Approach to Broad-Spectrum, Host-Directed Drug Target Discovery in Infectious Diseases. 17-28 - Sharangdhar S. Phatak, Shuxing Zhang:
A Novel Multi-Modal Drug Repurposing Approach for Identification of Potent ACK1 Inhibitors. 29-40 - Yi Shi, Xinhua Zhang, Xiaoping Liao, Guohui Lin, Dale Schuurmans:
Protein-chemical Interaction Prediction via Kernelized Sparse Learning SVM. 41-52 - Wenhui Wang, Sen Yang, Jing Li:
Drug Target Predictions Based on Heterogeneous Graph Inference. 53-64
Epigenomics
- Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng:
Session Introduction. 65-68 - Surin Ahn, Tao Wang:
A Powerful Statistical Method for Identifying Differentially Methylated Markers in Complex Diseases. 69-79 - Kaixuan Luo, Alexander J. Hartemink:
Using DNase Digestion Data to Accurately Identify Transcription Factor Binding Sites. 80-91 - Avinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, Sridhar Hannenhalli:
Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association Studies. 92-102
Identification of Aberrant Pathway and Network Activity from High-Throughput Data
- Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader:
Session Introduction. 103-110 - Haitham Gabr, Alin Dobra
, Tamer Kahveci:
From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color Coding. 111-122 - Olivier Gevaert, Sylvia K. Plevritis:
Identifying Master Regulators of Cancer and Their Downstream Targets by Integrating Genomic and Epigenomic Features. 123-134 - Yoo-Ah Kim, Raheleh Salari, Stefan Wuchty, Teresa M. Przytycka:
Module Cover - A New Approach to Genotype-Phenotype Studies. 135-146 - Sarah A. Pendergrass, Shefali S. Verma, Emily Rose Holzinger, Carrie Moore, John R. Wallace, Scott M. Dudek, Wayne Huggins, Terrie E. Kitchner, Carol Waudby, Richard L. Berg, Catherine A. McCarty, Marylyn D. Ritchie:
Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX Toolkit. 147-158 - Alan Perez-Rathke, Haiquan Li, Yves A. Lussier:
Interpreting Personal Transcriptomes: Personalized Mechanism-Scale Profiling of RNA-seq Data. 159-170
Personalized medicine: from genotypes and molecular phenotypes towards therapy
- Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten:
Session introduction. 171-174 - Surojit Biswas, Vladimir Jojic:
AMP: Assembly Matching Pursuit. 175-187 - Samuel Coulbourn Flores, Georgeta Zemora, Christina Waldsich:
Insights into Diseases of Human Telomerase from Dynamical Modeling. 200-211 - Grace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra S. Chennubhotla:
Spectral Clustering Strategies for Heterogeneous Disease Data. 212-223 - Li Li, David Ruau, Rong Chen, Susan C. Weber, Atul J. Butte:
Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical Records. 224-235
Phylogenomics and Population Genomics: Models, Algorithms, and Analytical Tools
- Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow:
Session introduction. 247-249 - Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow:
Inferring Optimal Species Trees Under Gene Duplication and Loss. 250-261 - James H. Degnan:
Evaluating Variations on the STAR Algorithm for Relative Efficiency and Sample Sizes Needed to Reconstruct Species Trees. 262-272 - Naama M. Kopelman, Lewi Stone, Olivier Gascuel, Noah A. Rosenberg:
The Behavior of Admixed Populations in Neighbor-Joining Inference of Population Trees. 273-284 - Yu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret:
Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes. 285-296 - Sébastien Roch:
An Analytical Comparison of Multilocus Methods Under the Multispecies Coalescent: The Three-Taxon Case. 297-306
Post-NGS: Interpretation and Analysis of Next Generation Sequencing Data for Basic and Translational Science
- Gürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance:
Session introduction. 307-309 - Daniel G. Brown, Jakub Truszkowski:
LSHPlace: Fast Phylogenetic Placement Using Locality-Sensitive Hashing. 310-319 - Jun Ding, Xiaohui Cai, Ying Wang, Haiyan Hu, Xiaoman Shawn Li:
ChIPModule: Systematic Discovery of Transcription Factors and Their Cofactors from ChIP-seq Data. 320-331 - Carrie Moore, John R. Wallace, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie:
Using BioBin to Explore Rare Variant Population Stratification. 332-343 - Daniel R. Schrider, David J. Begun, Matthew W. Hahn:
Detecting Highly Differentiated Copy-Number Variants from Pooled Population Sequencing. 344-355 - Angad Pal Singh, Samreen Zafer, Itsik Pe'er:
MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association Studies. 356-367
Text and Data Mining for Biomedical Discovery
- Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S. Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye:
Session introduction. 368-372 - Emily Rose Holzinger, Scott M. Dudek, Alex T. Frase, Ronald M. Krauss, Marisa Wong Medina, Marylyn D. Ritchie:
ATHENA: A Tool for Meta-Dimensional Analysis Applied to Genotypes and Gene Expression Data to Predict HDL Cholesterol Levels. 385-396 - Ting Hu, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore:
Statistical Epistasis Networks Reduce the Computational Complexity of Searching Three-Locus Genetic Models. 397-408 - Artemy Kolchinsky, Anália Lourenço, Lang Li, Luis M. Rocha:
Evaluation of Linear Classifiers on Articles Containing Pharmacokinetic Evidence of Drug-Drug Interactions. 409-420 - Karin Verspoor, Andrew MacKinlay, Judith D. Cohn, Michael E. Wall:
Detection of Protein Catalytic Sites in the Biomedical Literature. 433-444
Workshops
- Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, Damian Wójtowicz:
Modeling cell heterogeneity: from single-cell variations to mixed cells populations. 445-450 - Peter M. Kasson:
Computational Biology in the Cloud: Methods and New Insights from Computing at Scale. 451-453 - Lawrence Hunter:
Computational Challenges of Mass Phenotyping. 454-455 - Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle:
The Future of Genome-Based Medicine. 456-458
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