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17. PSB 2012: Kohala Coast, Hawaii, USA
- Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Tiffany Murray, Teri E. Klein:
Biocomputing 2012: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2012. World Scientific Publishing 2012, ISBN 978-1-61839-811-6
Identification of Aberrant Pathway and Network Activity from High-Throughput Data
- Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader:
Session Introduction. 1-6 - Nirmalya Bandyopadhyay, Sanjay Ranka, Tamer Kahveci:
SSLPred : Predicting Synthetic Sickness Lethality. 7-18 - Gregory W. Carter, Michelle Hays, Song Li, Timothy Galitski:
Predicting the Effects of Copy-Number Variation in Double and Triple Mutant Combinations. 19-30 - Li Chen, Jianhua Xuan, Jinghua Gu, Yue Wang, Zhen Zhang, Tian-Li Wang, Ie-Ming Shih:
Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer. 31-42 - Shahin Mohammadi, Giorgios Kollias, Ananth Grama:
Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways. 43-54 - Fabio Vandin, Patrick Clay, Eli Upfal, Benjamin J. Raphael:
Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. 55-66
Intrinsically Disordered Proteins: Analysis, Prediction, Simulation, and Biology
- Jianhan Chen, Jianlin Cheng, A. Keith Dunker:
Session introduction. 67-69 - Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanley, Pratul K. Agarwal, Chakra S. Chennubhotla:
Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble. 70-81 - Charles K. Fisher, Orly Ullman, Collin M. Stultz:
Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations. 82-93 - Jianjiong Gao, Dong Xu:
Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein. 94-103 - Xin Guo, Martha L. Bulyk, Alexander J. Hartemink:
Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors. 104-115 - Wei-Lun Hsu, Christopher J. Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, A. Keith Dunker:
Intrinsic Protein Disorder and Protein-Protein Interactions. 116-127 - Fei Huang, Christopher J. Oldfield, Jingwei Meng, Wei-Lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, A. Keith Dunker:
Subclassifying Disordered Proteins by the CH-CDF Plot Method. 128-139 - Chan-seok Jeong, Dongsup Kim:
Coevolved Residues and the Functional Association for Intrinsically Disordered Proteins. 140-151 - Diana M. Mitrea, Richard W. Kriwacki:
Cryptic Disorder: An Order-Disorder Transformation Regulates the Function of Nucleophosmin. 152-163 - Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley:
Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator. 164-175 - Zhenling Peng, Lukasz A. Kurgan:
On the Complementarity of the Consensus-Based Disorder Prediction. 176-187 - Dana Vuzman, Yonit Hoffman, Yaakov Levy:
Modulating Protein-DNA Interactions by Post-Translational Modifications at Disordered Regions. 188-199
Microbiome Studies: Analytical Tools and Techniques
- James A. Foster, Jason H. Moore, Jack A. Gilbert, John Bunge:
Session introduction. 200-202 - John Bunge, Dankmar Böhning, Heather K. Allen, James A. Foster:
Estimating Population Diversity with Unreliable Low Frequency Counts. 203-212 - Julia Fukuyama, Paul J. McMurdie, Les Dethlefsen, David A. Relman, Susan P. Holmes:
Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies. 213-224 - Alys Hugo, Douglas J. Baxter, William R. Cannon, Ananth Kalyanaraman, Gaurav Ramesh Kulkarni, Stephen J. Callister:
Proteotyping of Microbial Communities by Optimization of Tandem Mass Spectrometry Data Interpretation. 225-234 - Paul J. McMurdie, Susan P. Holmes:
phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data. 235-246 - Siavash Mirarab, Nam Nguyen, Tandy J. Warnow:
SEPP: SATe -Enabled Phylogenetic Placement. 247-258 - Quan Zhang, Thomas G. Doak, Yuzhen Ye:
Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads. 259-270 - Yuan Zhang, Yanni Sun:
MetaDomain: A Profile HMM-Based Protein Domain Classification Tool for Short Sequences. 271-282
Modeling Host-Pathogen Interactions: Computational Biology And Bioinformatics For Infectious Disease Research
- Jason E. McDermott, Pascal Braun, Richard Bonneau, Daniel R. Hyduke:
Session introduction. 283-286 - Eric A. Franzosa, Yu Xia:
Structural Models for Host-Pathogen Protein-Protein Interactions: Assessing Coverage and Bias. 287-298 - Raluca Gordân, Saumyadipta Pyne, Martha L. Bulyk:
Identification of Cell Cycle-Regulated, Putative Hyphal Genes in Candida Albicans. 299-310 - Ilia Nouretdinov, Alex Gammerman, Yanjun Qi, Judith Klein-Seetharaman:
Determining Confidence of Predicted Interactions Between HIV-1 and Human Proteins Using Conformal Method. 311-322
Personalized Medicine: From Genotypes and Molecular Phenotypes Towards Computed Therapy
- Oliver Stegle, Frederick P. Roth, Quaid Morris, Jennifer Listgarten:
Session introduction. 323-326 - Ross E. Curtis, Junming Yin, Peter Kinnaird, Eric P. Xing:
Finding Genome-Transcriptome-Phenome Associations with Structured Association Mapping and Visualization in GenAMap. 327-338 - Konrad J. Karczewski, Robert P. Tirrell, Pablo Cordero, Nicholas P. Tatonetti, Joel T. Dudley, Keyan Salari, Michael Snyder, Russ B. Altman, Stuart K. Kim:
Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine. 339-350 - Ranadip Pal, Noah Berlow:
A Kinase Inhibition Map Approach for Tumor Sensitivity Prediction and Combination Therapy Design for Targeted Drugs. 351-362 - David Warde-Farley, Michael Brudno, Quaid Morris, Anna Goldenberg:
Mixture Model for Sub-Phenotyping in GWAS. 363-374
Text and Knowledge Mining for Pharmacogenomics: Genotypephenotype-Drug Relationships
- Kevin Bretonnel Cohen, Yael Garten, Nigam Shah, Udo Hahn:
Session introduction. 375 - Ekaterina Buyko, Elena Beisswanger, Udo Hahn:
The Extraction of Pharmacogenetic and Pharmacogenomic Relations - A Case Study Using PharmGKB. 376-387 - Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos:
Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing. 388-399 - Jyotishman Pathak, Laura C. Weiss, Matthew J. Durski, Qian Zhu, Robert R. Freimuth, Christopher G. Chute:
Integrating VA's NDF-RT Drug Terminology with PharmGKB: Preliminary Results. 400-409 - Bethany Percha, Yael Garten, Russ B. Altman:
Discovery and Explanation of Drug-Drug Interactions via Text Mining. 410-421 - Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu:
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation. 422-433
Workshops
- William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-jun Duan, Yi Mao:
The Structure and Function of Chromatin and Chromosomes. 434-440 - Gregory Hampikian, Eric M. Meslin:
Law, Bioethics and the Current Status of Ownership, Privacy, Informed Consent in the Genomic Age. 441 - Marylyn D. Ritchie, Nancy J. Cox, Cheng Cheng, Scott Weiss, Teri E. Klein, Russ B. Altman:
Systems Pharmacogenomics-Bridging the Gap. 442
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