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Biocomputing 2012 - Proceedings Of The Pacific Symposium [Kõva köide]

Edited by (Stanford Univ, Usa), Edited by (Indiana Univ, Usa), Edited by (Stanford Univ, Usa), Edited by (Stanford Univ, Usa), Edited by (Univ Of Colorado Health Sciences Center, Usa)
  • Formaat: Hardback, 452 pages
  • Ilmumisaeg: 31-Dec-2011
  • Kirjastus: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 981459637X
  • ISBN-13: 9789814596374
Teised raamatud teemal:
  • Formaat: Hardback, 452 pages
  • Ilmumisaeg: 31-Dec-2011
  • Kirjastus: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 981459637X
  • ISBN-13: 9789814596374
Teised raamatud teemal:
The Pacific Symposium on Biocomputing (PSB) 2012 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in the problems of biological significance. Presentations are rigorously peer-reviewed and are published in an archival proceedings volume. PSB 2012 will be held on January 3 – 7, 2012 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2012 will bring together top researchers from the US, the Asian Pacific nations, and countries around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods as applied to biological problems, with emphasis on the applications in the data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's “hot topics.” In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.
IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA
Session Introduction
1(6)
Rachel Karchin
Michael F. Ochs
Joshua M. Stuart
Joel S. Bader
SSLPred: Predicting Synthetic Sickness Lethality
7(12)
Nirmalya Bandyopadhyayy
Sanjay Ranka
Tamer Kahveci
Predicting the Effects of Copy-Number Variation in Double and Triple Mutant Combinations
19(12)
Gregory W. Carter
Michelle Hays
Song Li
Timothy Galitski
Integrative Network Analysis to Identify Aberrant Pathway Networks in Ovarian Cancer
31(12)
Li Chen
Jianhua Xuan
Jinghua Gu
Yue Wang
Li Chen
Zhen Zhang
Tian-Li Wang
Ie-Ming Shih
Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among Pathways
43(12)
Shahin Mohammadi
Giorgos Kollias
Ananth Grama
Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer
55(12)
Fabio Vandin
Patrick Clay
Eli Upfal
Benjamin J. Raphael
INTRINSICALLY DISORDERED PROTEINS: ANALYSIS, PREDICTION, SIMULATION, AND BIOLOGY
Session Introduction
67(3)
Jianhan Chen
Jianlin Cheng
A. Keith Dunker
Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble
70(12)
Virginia M. Burger
Arvind Ramanathan
Andrej J. Savol
Christopher B. Stanley
Pratul K. Agarwal
Chakra S. Chennubhotla
Efficient Construction of Disordered Protein Ensembles in a Bayesian Framework with Optimal Selection of Conformations
82(12)
Charles K. Fisher
Orly Ullman
Collin M. Stultz
Correlation Between Posttranslational Modification and Intrinsic Disorder in Protein
94(10)
Jianjiong Gao
Dong Xu
Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors
104(12)
Xin Guo
Martha L. Bulyk
Alexander J. Hartemink
Intrinsic Protein Disorder and Protein-Protein Interactions
116(12)
Wei-Lun Hsu
Christopher Oldfield
Jingwei Meng
Fei Huang
Bin Xue
Vladimir N. Uversky
Pedro Romero
A. Keith Dunker
Subclassifying Disordered Proteins by the CH-CDF Plot Method
128(12)
Fei Huang
Christopher Oldfield
Jingwei Meng
Weilun Hsu
Bin Xue
Vladimir N. Uversky
Pedro Romero
A. Keith Dunker
Coevolved Residues and the Functional Association for Intrinsically Disordered Proteins
140(12)
Chan-Seok Jeong
Dongsup Kim
Cryptic Disorder: An Order-Disorder Transformation Regulates the Function of Nucleophosmin
152(12)
Diana M. Mitrea
Richard W. Kriwacki
Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator
164(12)
Ashwini Patil
Shunsuke Teraguchi
Huy Dinh
Kenta Nakai
Daron M. Standley
On the Complementarity of the Consensus-Based Disorder Prediction
176(12)
Zhenling Peng
Lukasz Kurgan
Modulating Protein--DNA Interactions by Post-Translational Modifications at Disordered Regions
188(12)
Dana Vuzman
Yonit Hoffman
Yaakov Levy
MICROBIOME STUDIES: ANALYTICAL TOOLS AND TECHNIQUES
Session Introduction
200(3)
James A. Foster
Jason H. Moore
Jack Gilbert
John Bunge
Estimating Population Diversity with Unreliable Low Frequency Counts
203(10)
John Bunge
Dankmar Bohning
Heather Allen
James A. Foster
Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies
213(12)
Julia Fukuyama
Paul J. Mcmurdie
Les Dethlefsen
David A. Relman
Susan Holmes
Proteotyping of Microbial Communities by Optimization of Tandem Mass Spectrometry Data Interpretation
225(10)
Alys Hugo
Douglas J. Baxter
William R. Cannon
Ananth Kalyanaraman
Gaurav Kulkarni
Stephen J. Callister
phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data
235(12)
Paul J. McMurdie
Susan Holmes
SEPP: SATe -Enabled Phylogenetic Placement
247(12)
Siavash Mirarab
Nam Nguyen
Tandy Warnow
Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads
259(12)
Quan Zhang
Thomas G. Doak
Yuzhen Ye
MetaDomain: A Profile HMM-Based Protein Domain Classification Tool for Short Sequences
271(12)
Yuan Zhang
Yanni Sun
MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH
Session Introduction
283(4)
Jason E. Mcdermott
Pascal Braun
Richard Bonneau
Daniel R. Hyduke
Structural Models for Host-Pathogen Protein-Protein Interactions: Assessing Coverage and Bias
287(12)
Eric A. Franzosa
Yu Xia
Identification of Cell Cycle-Regulated, Putative Hyphal Genes in Candida Albicans
299(12)
Raluca Gordan
Saumyadipta Pyne
Martha L. Bulyk
Determining Confidence of Predicted Interactions Between HIV-1 and Human Proteins Using Conformal Method
311(12)
Ilia Nouretdinov
Alex Gammerman
Yanjun Qi
Judith Klein-Seetharaman
PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY
Session Introduction
323(4)
Oliver Stegle
Frederick P. Roth
Quaid Morris
Jennifer Listgarten
Finding Genome-Transcriptome-Phenome Associations with Structured Association Mapping and Visualization in GenAMap
327(12)
Ross E. Curtis
Junming Yin
Peter Kinnaird
Eric P. Xing
Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine
339(12)
Konrad J. Karczewski
Robert P. Tirrell
Pablo Cordero
Nicholas P. Tatonetti
Joel T. Dudley
Keyan Salari
Michael Snyder
Russ B. Altman
Stuart K. Kim
A Kinase Inhibition Map Approach for Tumor Sensitivity Prediction and Combination Therapy Design for Targeted Drugs
351(12)
Ranadip Pal
Noah Berlow
Mixture Model for Sub-Phenotyping in GWAS
363(12)
David Warde-Farley
Michael Brudno
Quaid Morris
Anna Goldenberg
TEXT AND KNOWLEDGE MINING FOR PHARMACOGENOMICS: GENOTYPEPHENOTYPE-DRUG RELATIONSHIPS
Session Introduction
375(1)
Kevin Bretonnel Cohen
Yael Garten
Nigham Shah
Udo Hahn
The Extraction of Pharmacogenetic and Pharmacogenomic Relations -- A Case Study Using PharmGKB
376(12)
Ekaterina Buyko
Elena Beisswanger
Udo Hahn
Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing
388(12)
Robert Hoehndorf
Anika Oellrich
Dietrich Rebholz-Schuhmann
Paul Schofield
Georgios V. Gkoutos
Integrating VA's NDF-RT Drug Terminology with PharmGKB: Preliminary Results
400(10)
Jyotishman Pathak
Laura C. Weiss
Matthew J. Durski
Qian Zhu
Robert R. Freimuth
Christopher G. Chute
Discovery and Explanation of Drug-Drug Interactions via Text Mining
410(12)
Bethany Percha
Yael Garten
Russ B. Altman
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation
422(12)
Yonghui Wu
Mei Liu
W. Jim Zheng
Zhongrning Zhao
Hua Xu
WORKSHOPS
The Structure and Function of Chromatin and Chromosomes
434(7)
William Stafford Noble
C. Anthony Blau
Job Dekker
Zhi-Jun Duan
Yi Mao
Law, Bioethics and the Current Status of Ownership, Privacy, Informed Consent in the Genomic Age
441(1)
Greg Hampikian
Eric M. Meslin
Systems Pharmacogenomics--Bridging the Gap
442
Marylyn Ritchie
Nancy Cox
Cheng Cheng
Scott Weiss
Teri Klein
Russ Altman