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Biocomputing 2017 - Proceedings Of The Pacific Symposium [Kõva köide]

Edited by (Indiana Univ, Usa), Edited by (Univ Of Colorado Health Sciences Center, Usa), Edited by (Univ Of Pennsylvania, Usa), Edited by (Stanford Univ, Usa), Edited by (Stanford Univ, Usa), Edited by (Stanford Univ, Usa)
  • Formaat: Hardback, 668 pages
  • Ilmumisaeg: 23-Jan-2017
  • Kirjastus: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9813207809
  • ISBN-13: 9789813207806
Teised raamatud teemal:
  • Formaat: Hardback, 668 pages
  • Ilmumisaeg: 23-Jan-2017
  • Kirjastus: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9813207809
  • ISBN-13: 9789813207806
Teised raamatud teemal:
The Pacific Symposium on Biocomputing (PSB) 2017 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 2017 will be held on January 4 – 8, 2017 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2017 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 vii
Computational Approaches To Understanding The Evolution Of Molecular Function
Session Introduction
1(2)
Yana Bromberg
Matthew W. Hahn
Predrag Radivojac
Identification and Analysis of Bacterial Genomic Metabolic Signatures
3(12)
Nathan Bowerman
Nathan Tintle
Matthew DeJongh
Aaron A. Best
When should we NOT transfer functional annotation between sequence paralogs?
15(12)
Mengfei Cao
Lenore J. Cowen
ProSNet: integrating homology with molecular networks for protein function prediction
27(12)
Sheng Wang
Meng Qu
Jian Peng
On the power and limits of sequence similarity based clustering of proteins into families
39(12)
Christian Wiwie
Richard Rottger
Imaging Genomics
Session Introduction
51(7)
Li Shen
Lee A.D. Cooper
Adaptive testing of SNP-brain functional connectivity association via a modular network analysis
58(12)
Chen Gao
Junghi Kim
Wei Pan
Exploring Brain Transcriptomic Patterns: A Topological Analysis Using Spatial Expression Networks
70(12)
Zhana Kuncheva
Michelle L. Krishnan
Giovanni Montana
Integrative Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated with Genetic Variations
82(12)
Chao Wang
Hai Su
Lin Yang
Kun Huang
Identification of Discriminative Imaging Proteomics Associations in Alzheimer's Disease via a Novel Sparse Correlation Model
94(11)
Jingwen Yan
Shannon L. Risacher
Kwangsik Nho
Andrew J. Saykin
Li Shen
Enforcing Co-expression in Multimodal Regression Framework
105(12)
Pascal Zille
Vince D. Calhoun
Yu-Ping Wang
Methods To Ensure The Reproducibility Of Biomedical Research
Session Introduction
117(3)
Konrad J. Karczewski
Nicholas P. Tatonetti
Chirag J. Patel
Arjun K. Manrai
C. Titus Brown
John P.A. Ioannidis
Exploring the Reproducibility of Probabilistic Causal Molecular Network Models
120(12)
Ariella Cohain
Apama A. Divaraniya
Kuixi Zhu
Joseph R. Scarpa
Andrew Kasarskis
Jun Zhu
Rui Chang
Joel T. Dudley
Eric E. Schadt
Reproducible Drug Repurposing: When Similarity Does Not Suffice
132(12)
Emre Guney
Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility
144(10)
Winston A. Haynes
Francesco Vallania
Charles Liu
Erika Bongen
Aurelie Tomczak
Marta Andres-Terre
Shane Lofgren
Andrew Tam
Cole A. Deisseroth
Matthew D. Li
Timothy E. Sweeney
Purvesh Khatri
Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions
154(12)
Gaurav Kaushik
Sinisa Ivkovic
Janko Simonovic
Nebojsa Tijanic
Brandi Davis-Dusenbery
Deniz Kural
Data Sharing and Reproducible Clinical Genetic Testing: Successes and Challenges
166(11)
Shan Yang
Melissa Cline
Can Zhang
Benedict Paten
Stephen E. Lincoln
Patterns In Biomedical Data-How Do We Find Them?
Session Introduction
177(7)
Anna Okula Basile
Anurag Verma
Marta Byrska-Bishop
Sarah P. Pendergrass
Christian Darabos
H. Lester Kirchner
Learning Attributes of Disease Progression from Trajectories of Sparse Lab Values
184(11)
Vibhu Agarwal
Nigam H. Shah
Computer Aided Image Segmentation and Classification for Viable and Non-Viable Tumor Identification in Osteosarcoma
195(12)
Harish Babu Arunachalam
Rashika Mishra
Bogdan Armaselu
Ovidiu Daescu
Maria Martinez
Patrick Leavey
Dinesh Rakheja
Kevin Cederberg
Anita Sengupta
Molly Ni'suilleabhain
Missing Data Imputation in the Electronic Health Record Using Deeply Learned Autoencoders
207(12)
Brett K. Beaulieu-Jones
Jason H. Moore
he Pooled Resource Open-Access ALS Clinical Trials Consortium, A Deep Learning Approach for Cancer Detection and Relevant Gene Identification
219(11)
Padideh Danaee
Reza Ghaeini
David Hendrix
Development and Performance of Text-Mining Algorithms to Extract Socioeconomic Status from De-Identified Electronic Health Records
230(12)
Brittany M. Hollister
Nicole A. Restrepo
Eric Farber-Eger
Dana C. Crawford
Melinda C. Aldrich
Amy Non
Genome-Wide Interaction with Selected Type 2 Diabetes Loci Reveals Novel Loci for Type 2 Diabetes in African Americans
242(12)
Jacob M. Keaton
Jacklyn N. Hellwege
Maggie C.Y. Ng
Nicholette D. Palmer
James S. Pankow
Myriam Fornage
James G. Wilson
Adolfo Correa
Laura J. Rasmussen-Torvik
Jerome I. Rotter
Yii-Der I. Chen
Kent D. Taylor
Stephen S. Rich
Lynne E. Wagenknecht
Barry I. Freedman
Donald W. Bowden
Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks
254(12)
Jack Lanchantin
Ritambhara Singh
Beilun Wang
Yanjun Qi
Meta-Analysis of Continuous Phenotypes Identifies a Gene Signature that Correlates with COPD Disease Status
266(10)
Madeleine Scott
Francesco Vallania
and Purvesh Khatri
Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort
276(12)
Khader Shameer
Kipp W. Johnson
Alexandre Yahi
Riccardo Miotto
Li Li
Doran Ricks
Jebakumar Jebakaran
Patricia Kovatch
Partho P. Sengupta
Annetine Gelijns
Alan Moskovitz
Bruce Darrow
David L. Reich
Andrew Kasarskis
Nicholas P. Tatonetti
Sean Pinney
Joel T. Dudley
Learning Parsimonious Ensembles for Unbalanced Computational Genomics Problems
288(12)
Ana Stanescu
Gaurav Pandey
Methods for Clustering Time Series Data Acquired from Mobile Health Apps
300(12)
Nicole Tignor
Pei Wang
Nicholas Genes
Linda Rogers
Steven G. Hershman
Erick R. Scott
Micol Zweig
Yu-Feng Yvonne Chan
Eric E. Schadt
A New Relevance Estimator for the Compilation and Visualization of Disease Patterns and Potential Drug Targets
312(12)
Modest von Korff
Tobias Fink
Thomas Sander
Network Map of Adverse Health Effects Among Victims of Intimate Partner Violence
324(12)
Kathleen Whiting
Larry Y. Liu
Mehmet Koyuturk
Gunnur Karakurt
Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks
336(12)
Stephen J. Wilson
Angela D. Wilkins
Chih-Hsu Lin
Rhonald C. Lua
Olivier Lichtarge
Precision Medicine: Data And Discovery For Improved Health And Therapy
Session Introduction
348(8)
Alexander A. Morgan
Dana C. Crawford
Josh C. Denny
Sean D. Mooney
Bruce J. Aronow
Steven E. Brenner
Opening the Door to the Large Scale Use of Clinical Lab Measures for Association Testing: Exploring Different Methods for Defining Phenotypes
356(12)
Christopher R. Bauer
Daniel Lavage
John Snyder
Joseph Leader
J. Matthew Mahoney
Sarah A. Pendergrass
A Powerful Method for Including Genotype Uncertainty in Tests of Hardy-Weinberg Equilibrium
368(12)
Andrew Beck
Alexander Luedtke
Keli Liu
Nathan Tintle
Temporal Order of Disease Pairs Affects Subsequent Disease Trajectories: The Case of Diabetes and Sleep Apnea
380(10)
Mette Beck
David Westergaard
Leif Groop
Soren Brunak
MicroRNA-Augmented Pathways (mirAP) and Their Applications to Pathway Analysis and Disease Subtyping
390(12)
Diana Diaz
Michele Donato
Tin Nguyen
Sorin Draghici
Frequent Subgraph Mining of Personalized Signaling Pathway Networks Groups Patients with Frequently Dysregulated Disease Pathways and Predicts Prognosis
402(12)
Arda Dunnaz
Tim A.D. Henderson
Douglas Brubaker
Gurkan Bebek
Human Kinases Display Mutational Hotspots at Cognate Positions Within Cancer
414(12)
Jonathan Gallion
Angela D. Wilkins
Olivier Lichtarge
MUSE: A Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait Prediction
426(12)
Dan He
Laxmi Panda
ceRNA Search Method Identified a MET-activated Subgroup Among EGFR DNA Amplified Lung Adenocarcinoma Patients
438(11)
Halla Kabat
Leo Tunkle
Inhan Lee
Improved Performance of Gene Set Analysis on Genome-Wide Transcriptomics Data when Using Gene Activity State Estimates
449(12)
Thomas Kamp
Micah Adams
Craig Disselkoen
Nathan Tintle
methylDMV: Simultaneous Detection of Differential DNA Methylation and Variability with Confounder Adjustment
461(12)
Pei Fen Kuan
Junyan Song
Shuyao He
Identifying Cancer Driver Genes Through Shared Mendelian Disease Pathogenic Variants and Cancer Somatic Mutations
473(12)
Meng Ma
Changchang Wang
Benjamin Glicksberg
Eric Schadt
Shuyu D. Li
Rong Chen
Identifying Cancer Specific Metabolic Signatures Using Constraint-Based Models
485(12)
Andre Schultz
Sanket Mehta
Chenyue W. Hu
Fieke W Hoff
Terzah M. Horton
Steven M. Kornblau
Amina A. Qutub
Differential Pathway Dependency Discovery Associated with Drug Response across Cancer Cell Lines
497(12)
Gil Speyer
Divya Mahendra
Hai J. Tran
Jeff Kiefer
Stuart L. Schreiber
Paul A. Clemons
Harshil Dhruv
Michael Berens
Seungchan Kim
A Methylation-to-Expression Feature Model for Generating Accurate Prognostic Risk Scores and Identifying Disease Targets in Clear Cell Kidney Cancer
509(12)
Jeffrey A. Thompson
Carmen J. Marsit
De Novo Mutations in Autism Implicate the Synaptic Elimination Network
521(12)
Guhan Ram Venkataraman
Chloe O'Connell
Fumiko Egawa
Dorna Kashef-Haghighi
Dennis Paul Wall
Identifying Genetic Associations with Variability in Metabolic Health and Blood Count Laboratory Values: Diving into the Quantitative Traits by Leveraging Longitudinal Data from an EHR
533(12)
Shefali S. Verma
Anastasia M. Lucas
Daniel R. Lavage
Joseph B. Leader
Raghu Metpally
Sarathbabu Krishnamurthy
Frederick Dewey
Ingrid Borecki
Alexander Lopez
John Overton
John Penn
Jeffrey Reid
Sarah A. Pendergrass
Gerda Breitwieser
Marylyn D. Ritchie
Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population
545(12)
Laura Wiley
Jacob VanHouten
David Samuels
Melinda Aldrich
Dan Roden
Josh Peterson
Joshua Denny
Single-Cell Analysis And Modelling Of Cell Population Heterogeneity
Session Introduction
557(7)
Nikolay Samusik
Nima Aghaeepour
Sean Bendall
Production of a Preliminary Quality Control Pipeline for Single Nuclei RNA-Seq and Its Application in the Analysis of Cell Type Diversity of Post-Mortem Human Brain Neocortex
564(12)
Brian Aevermann
Jamison McCorrison
Pratap Venepally
Rebecca Hodge
Trygve Bakken
Jeremy Miller
Mark Novotny
Danny N. Tran
Francisco Diez-Fuertes
Lena Christiansen
Fan Zhang
Frank Steemers
Roger S. Lasken
Ed Lein
Nicholas Schork
Richard H. Scheuermann
Tracing Co-Regulatory Network Dynamics in Noisy, Single-Cell Transcriptome Trajectories
576(12)
Pablo Cordero
Joshua M. Stuart
An Updated Debarcoding Tool for Mass Cytometry with Cell Type-Specific and Cell Sample-Specific Stringency Adjustment
588(11)
Kristin I. Fread
William D. Strickland
Garry P. Nolan
Eli R. Zunder
Mapping Neuronal Cell Types Using Integrative Multi-Species Modeling of Human and Mouse Single Cell RNA Sequencing
599(12)
Travis Johnson
Zachary Abrams
Yan Zhang
Kun Huang
A Spatiotemporal Model to Simulate Chemotherapy Regimens for Heterogeneous Bladder Cancer Metastases to the Lung
611(12)
Kimberly R. Kanigel Winner
James C. Costello
Scalable Visualization for High-dimensional Single-cell Data
623(12)
Juho Kim
Nate Russell
Jian Peng
Workshops
Harnessing Big Data for Precision Medicine: Infrastructures and Applications
635(5)
Kun-Hsing Yu
Steven N. Hart
Rachel Goldfeder
Qiangfeng Cliff Zhang
Stephen C.J. Parker
Michael Snyder
The Training of Next Generation Data Scientists in Biomedicine
640(6)
Lana Garmire
Stephen Gliske
Quynh C Nguyen
Jonathan H. Chen
Shamim Nemati
John D. Van Horn
Jason H. Moore
Carol Shreffler
Michelle Dunn
No-Boundary Thinking in Bioinformatics
646(3)
Jason H. Moore
Steven F. Jennings
Casey S. Greene
Lawrence E. Hunter
Andy D. Perkins
Clarlynda Williams-Devane
Donald C. Wunsch
Zhongming Zhao
Xiuzhen Huang
Open Data for Discovery Science
649
Philip R.O. Payne
Kun Huang
Nigam H. Shah
Jessica Tenenbaum