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Biocomputing 2015 - Proceedings Of The Pacific Symposium [Kietas viršelis]

Edited by (Stanford Univ, Usa), Edited by (Stanford Univ, Usa), Edited by (Indiana Univ, Usa), Edited by (Univ Of Colorado Health Sciences Center, Usa), Edited by (Stanford Univ, Usa), Edited by (Univ Of Pennsylvania, Usa)
  • Formatas: Hardback, 516 pages
  • Išleidimo metai: 11-Nov-2014
  • Leidėjas: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9814644722
  • ISBN-13: 9789814644723
Kitos knygos pagal šią temą:
  • Formatas: Hardback, 516 pages
  • Išleidimo metai: 11-Nov-2014
  • Leidėjas: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9814644722
  • ISBN-13: 9789814644723
Kitos knygos pagal šią temą:
The Pacific Symposium on Biocomputing (PSB) 2015 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2015 will be held from January 4 – 8, 2015 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2015 will bring together top researchers from the US, the Asian Pacific nations, and 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 applications in 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.
Preface vi
A Twentieth Anniversary Tribute to PSB
1(7)
Darla Hewett
Michelle Whirl-Carrillo
Lawrence E. Hunter
Russ B. Altman
Teri E. Klein
CANCER PANOMICS: COMPUTATIONAL METHODS AND INFRASTRUCTURE FOR INTEGRATIVE ANALYSIS OF CANCER HIGH-THROUGHPUT "OMICS" DATA
Session Introduction
8(2)
Søren Brunak
Francisco M. De La Vega
Adam Margolin
Benjamin J. Raphael
Gunnar Ratsch
Joshua M. Stuart
Cell Index Database (CELLX): A Web Tool for Cancer Precision Medicine
10(10)
Keith A. Ching
Kai Wang
Zhengyan Kan
Julio Fernandez
Wenyan Zhong
Jarek Kostrowicki
Tao Xie
Zhou Zhu
Jean-Francois Martini
Maria Koehler
Kim Arndt
Paul Rejto
Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors
20(12)
Amit G. Deshwar
Shankar Vembu
Quaid Morris
Stepwise Group Sparse Regression (SGSR): Gene-Set-Based Pharmacogenomic Predictive Models with Stepwise Selection of Functional Priors
32(12)
In Sock Jang
Rodrigo Dienstmann
Adam A. Margolin
Justin Guinney
Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma
44(12)
Kjong-Van Lehmann
Andre Kahles
Cyriac Kandoth
William Lee
Nikolaus Schultz
Oliver Stegle
Gunnar Ratsch
An Integrated Framework for Reporting Clinically Relevant Biomarkers from Paired Tumor/Normal Genomic and Transcriptomic Sequencing Data In Support of Clinical Trials in Personalized Medicine
56(12)
Sara Nasser
Ahmet A. Kurdolgu
Tyler Izatt
Jessica Aldrich
Megan L. Russell
Alexis Christoforides
Wiabhav Tembe
Jeffery A. Keifer
Jason J. Corneveaux
Sara A. Byron
Karen M. Forman
Clarice Zuccaro
Jonathan J. Keats
Patricia M. LoRusso
John D. Carpten
Jeffrey M. Trent
David W. Craig
Characteristics of Drug Combination Therapy in Oncology by Analyzing Clinical Trial Data on Clinicaltrials. Gov
68(12)
Menghua Wu
Marina Sirota
Atul J. Butte
Bin Chen
CANCER PATHWAYS: AUTOMATIC EXTRACTION, REPRESENTATION, AND REASONING IN THE "BIG DATA" ERA
Session Introduction
80(4)
Graciela Gonzalez
Chitta Baral
Jeff Kiefer
Suengchan Kim
Jieping Ye
Identifying Mutation Specific Cancer Pathways Using a Structurally Resolved Protein Interaction Network
84(12)
H. Billur Engin
Matan Hofree
Hannah Carter
Binning Somatic Mutations Based on Biological Knowledge for Predicting Survival: An Application in Renal Cell Carcinoma
96(12)
Dokyoon Kim
Ruowang Li
Scott M. Dudek
John R. Wallace
Marylyn D. Ritchie
Topological Features in Cancer Gene Expression Data
108(12)
Svetlana Lockwood
Bala Krishnamoorthy
Distant Supervision for Cancer Pathway Extraction from Text
120(12)
Hoifung Poon
Kristina Toutanova
Chris Quirk
Unsupervised Feature Construction and Knowledge Extraction from Genome-Wide Assays of Breast Cancer with Denoising Autoencoders
132(12)
Jie Tan
Matthew Ung
Chao Cheng
Casey S. Greene
Automated Gene Expression Pattern Annotation in the Mouse Brain
144(12)
Tao Yang
Xinlin Zhao
Binbin Lin
Tao Zeng
Shuiwang Ji
Jieping Ye
CHARACTERIZING THE IMPORTANCE OF ENVIRONMENTAL EXPOSURES, INTERACTIONS BETWEEN THE ENVIRONMENT AND GENETIC ARCHTECTURE, AND GENETC INTERACTIONS: NEW METHODS FOR UNDERSTANDING THE ETIOLOGY OF COMPLEX TRAITS AND DISEASE
Session Introduction
156(5)
Molly Hall
Shefali Setia Verma
Dennis P. Wall
Jason H. Moore
Brendan Keating
Daniel B. Campbell
Gregory Gibson
Folkert W. Asselbergs
Sarah A. Pendergrass
Measures of Exposure Impact Genetic Association Studies: An Example in Vitamin K Levels and VKORC1
161(10)
Dana C. Crawford
Kristin Brown-Gentry
Mark J. Rieder
A Bipartite Network Approach to Inferring Interactions Between Environmental Exposures and Human Diseases
171(12)
Christian Darabos
Emily D. Grussing
Maria E. Cricco
Kenzie A. Clark
Jason H. Moore
A Screening-Testing Approach for Detecting Gene-Environment Interactions Using Sequential Penalized and Unpenalized Multiple Logistic Regression
183(12)
H. Robert Frost
Angeline S. Andrew
Margaret R. Karagas
Jason H. Moore
Variable Selection Method for the Identification of Epistatic Models
195(12)
Emily Rose Holzinger
Silke Szymczak
Abhijit Dasgupta
James Malley
Qing Li
Joan E. Bailey-Wilson
Genome-Wide Genetic Interaction Analysis of Glaucoma Using Expert Knowledge Derived from Human Phenotype Networks
207(12)
Ting Hu
Christian Darabos
Maria E. Cricco
Emily Kong
Jason H. Moore
Identification of Gene-Gene and Gene-Environment Interactions Within the Fibrinogen Gene Cluster for Fibrinogen Levels in Three Ethnically Diverse Populations
219(12)
Janina M. Jeff
Kristin Brown-Gentry
Dana C. Crawford
Development of Exposome Correlations Globes to Map Out Environment-Wide Associations
231(12)
Chirag J. Patel
Arjun K. Manrai
Mitochondrial Variation and the Risk of Age-Related Macular Degeneration Across Diverse Populations
243(12)
Nicole A. Restrepo
Sabrina L. Mitchell
Robert J. Goodloe
Deborah G. Murdock
Jonathan L. Haines
Dana C. Crawford
iPINBPA: An Integrative Network-Based Functional Module Discovery Tool for Genome-Wide Association Studies
255(12)
Lili Wang
Parvin Mousavi
Sergio E. Baranzini
CROWDSOURCING AND MINING CROWD DATA
Session Introduction
267(3)
Robert Leaman
Benjamin M. Good
Andrew I. Su
Zhiyong Lu
Reputation-Based Collaborative Network Biology
270(12)
Jean Binder
Stephanie Boue
Anselmo Di Fabio
R. Brett Fields
William Hayes
Julia Hoeng
Jennifer S. Park
Manuel C. Peitsch
Microtask Crowdsourcing for Disease Mention Annotation in PubMed Abstracts
282(12)
Benjamin M. Good
Max Nanis
Chunlei Wu
Andrew I. Su
Crowdsourcing Image Annotation for Nucleus Detection and Segmentation in Computational Pathology: Evaluating Experts, Automated Methods, and the Crowd
294(12)
Humayun Irshad
Laleh Montaser-Kouhsari
Gail Waltz
Octavian Bucur
Jonathan A. Nowak
Fei Dong
Nicholas W. Knoblauch
Andrew H. Beck
Analyzing Search Behavior of Healthcare Professionals for Drug Safety Surveillance
306(12)
David J. Odgers
Rave Harpaz
Alison Callahan
Gregor Stiglic
Nigam H. Shah
Refining Literature Curated Protein Interactions Using Expert Opinions
318(12)
Oznur Tastan
Yanjun Qi
Jaime G. Carbonell
Judith Klein-Seetharaman
Crowdsourcing RNA Structural Alignments with an Online Computer Game
330(12)
Jerome Waldispuhl
Arthur Kam
Paul P. Gardner
PERSONALIZED MEDICINE: FROM GENOTYPES, MOLECULAR PHENOTYPES AND THE QUANTIFIED SELF, TOWARDS IMPROVED MEDICINE
Session Introduction
342(5)
Joel T. Dudley
Jennifer Listgarten
Oliver Stegle
Steven E. Brenner
Leopold Parts
KLEAT: Cleavage Site Analysis of Transcriptomes
347(12)
Inanc Birol
Anthony Raymond
Readman Chiu
Ka Ming Nip
Shaun D. Jackman
Maayan Kreitzman
T. Roderick Docking
Catherine A. Ennis
A. Gordon Robertson
Aly Karsan
Causal Inference in Biology Networks with Integrated Belief Propagation
359(12)
Rui Chang
Jonathan R. Karr
Eric E. Schadt
Machine Learning from Concept to Clinic: Reliable Detection of BRAF V600E DNA Mutations in Thyroid Nodules Using High-Dimensional RNA Expression Data
371(12)
James Diggans
Su Yeon Kim
Zhanzhi Hu
Daniel Pankratz
Mei Wong
Jessica Reynolds
Ed Tom
Moraima Pagan
Robert Monroe
Juan Rosai
Virginia A. Livolsi
Richard B. Lanman
Richard T. Kloos
P. Sean Walsh
Giulia C. Kennedy
A Systematic Assessment of Linking Gene Expression with Genetic Variants for Prioritizing Candidate Targets
383(12)
Hua Fan-Minogue
Bin Chen
Weronika Sikora-Wohlfeld
Marina Sirota
Atul J. Butte
Drug-induced mRNA Signatures Are Enriched for the Minority of Genes that Are Highly Heritable
395(12)
Tianxiang Gao
Petter Brodin
Mark M. Davis
Vladimir Jojic
An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships
407(12)
Benjamin S. Glicksberg
Li Li
Wei-Yi Cheng
Khader Shameer
Jorg Hakenberg
Rafael Castellanos
Meng Ma
Lisong Shi
Hardik Shah
Joel T. Dudley
Rong Chen
PEAX: Interactive Visual Analysis and Exploration of Complex Clinical Phenotype and Gene Expression Association
419(12)
Michael A. Hinterberg
David P. Kao
Michael R. Bristow
Lawrence E. Hunter
J. David Port
Carsten Gorg
T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes
431(12)
Grace T. Huang
Ioannis Tsamardinos
Vineet Raghu
Naftali Kaminski
Panayiotis V. Benos
Meta-Analysis of Differential Gene Co-Expression: Application to Lupus
443(12)
Sumit B. Makashir
Leah C. Kottyan
Matthew T. Weirauch
Melancholic Depression Prediction by Identifying Representative Features in Metabolic and Microarray Profiles with Missing Values
455(12)
Zhi Nie
Tao Yang
Yashu Liu
Binbin Lin
Qingyang Li
Vaibhav A. Narayan
Gayle Wittenberg
Jieping Ye
BayClone: Bayesian Nonparametric Inference of Tumor Subclones Using NGS Data
467(12)
Subhajit Sengupta
Jin Wang
Juhee Lee
Peter Muller
Kamalakar Gulukota
Arunava Banerjee
Yuan Ji
WORKSHOPS
Human Evolutionary Genomics and the Search for the Genes that Made Us Human
479(3)
James M. Sikela
Discovery Informatics in Biological and Biomedical Sciences: Research Challenges and Opportunities
482(1)
Vasant Honavar
Inviting the Public: The Impact on Informatics Arising from Emerging Global Health Research Paradigms
483(5)
Richard Gayle
Mark Minie
Erik Nilsson
Training the Next Generation of Quantitative Biologists in the Era of Big Data
488(5)
Kristine A. Pattin
Anna C. Greene
Russ B. Altman
Kevin B. Cohen
Elizabeth Wethington
Carsten Gorg
Lawrence E. Hunter
Spencer V. Muse
Predrag Radivojac
Jason H. Moore
ERRATUM: Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX Toolkit 493