Author details

Full Name

James Christopher Bare

Affiliation

Institute for Systems Biology

ORCID

Career Start Year

2007

Papers

H Index

Expertise

CM4AI Collaborator

Timothy Clark (CM4AI)

PMID	Paper Title	Journal Title	Published Year
29385983	Germline contamination and leakage in whole genome somatic single nucleotide variant detection.	BMC Bioinformatics	2018
30400818	Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.	Genome Biol	2018
27864015	Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.	Lancet Oncol	2017
30657384	A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.	JCO Clin Cancer Inform	2017
27079753	Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.	Alzheimers Dement	2016
26938265	The mPower study, Parkinson disease mobile data collected using ResearchKit.	Sci Data	2016
25984700	Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.	Nat Methods	2015
26448092	Erratum: Prediction of human population responses to toxic compounds by a collaborative competition.	Nat Biotechnol	2015
26258538	Prediction of human population responses to toxic compounds by a collaborative competition.	Nat Biotechnol	2015
23235920	Architecture for interoperable software in biology.	Brief Bioinform	2014
25289666	Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting.	PLoS One	2014
24675517	Global optimization of somatic variant identification in cancer genomes with a global community challenge.	Nat Genet	2014
24271392	Network portal: a database for storage, analysis and visualization of biological networks.	Nucleic Acids Res	2014
21750103	Parallel evolution of transcriptome architecture during genome reorganization.	Genome Res	2011
22108796	Niche adaptation by expansion and reprogramming of general transcription factors.	Mol Syst Biol	2011
21602264	miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.	Nucleic Acids Res	2011
20642854	Integration and visualization of systems biology data in context of the genome.	BMC Bioinformatics	2010
20626906	GTC: A web server for integrating systems biology data with web tools and desktop applications.	Source Code Biol Med	2010
19536208	Prevalence of transcription promoters within archaeal operons and coding sequences.	Mol Syst Biol	2009
18160043	A predictive model for transcriptional control of physiology in a free living cell.	Cell	2007
18021453	The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.	BMC Bioinformatics	2007

1 - 21 of 21

Jeremy Goecks

Oregon Health & Science University

Career Start Year 2010

Number of shared co-authors 3

H??ctor Corrada Bravo

University of Maryland College Park, College Park

Career Start Year 2009

Number of shared co-authors 3

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 0

Geir Kjetil Sandve

University of Oslo

Career Start Year 2006

Number of shared co-authors 0

Joshua W K Ho

The University of Hong Kong

Career Start Year 2006

Number of shared co-authors 0

Daniel Blankenberg

Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Career Start Year 2005

Number of shared co-authors 1

James Taylor

Johns Hopkins University

Career Start Year 2004

Number of shared co-authors 1

Shannan J Ho Sui

Harvard T.H. Chan School of Public Health

Career Start Year 2004

Number of shared co-authors 6

Stephen A Ramsey

Oregon State University

Career Start Year 2004

Number of shared co-authors 4

Ted Liefeld

Moores Cancer Center, University of California San Diego

Career Start Year 2003

Number of shared co-authors 2

Chunlei Wu

The Scripps Research Institute

Career Start Year 2002

Number of shared co-authors 5

Johan Rung

Uppsala University

Career Start Year 2001

Number of shared co-authors 0

Pjotr Prins

Wageningen University & Research

Career Start Year 2001

Number of shared co-authors 1

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Career Start Year 2001

Number of shared co-authors 2

Gary D Bader

University of Toronto

Career Start Year 2000

Number of shared co-authors 7

Ana Conesa

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC)

Career Start Year 2000

Number of shared co-authors 1

Fabien Campagne

Weill Cornell Medical College

Career Start Year 1998

Number of shared co-authors 1

Jessica Severin

Center for Integrative Medical Sciences

Career Start Year 1996

Number of shared co-authors 0

Ralf Zimmer

Ludwig-Maximilians-Universitat Munchen

Career Start Year 1995

Number of shared co-authors 0

Christopher T Workman

Technical University of Denmark

Career Start Year 1995

Number of shared co-authors 1

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 0

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 5

Joel S Bader

Johns Hopkins University

Career Start Year 1993

Number of shared co-authors 4

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 2

Jason E McDermott

Pacific Northwest National Laboratory

Career Start Year 1993

Number of shared co-authors 0

Jill P Mesirov

University of California San Diego

Career Start Year 1992

Number of shared co-authors 4

Robert Gentleman

Center for Computational Biomedicine, Harvard Medical School

Career Start Year 1991

Number of shared co-authors 4

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 11

John Quackenbush

Harvard T. H. Chan School of Public Health

Career Start Year 1989

Number of shared co-authors 4

Martin Kuiper

Norwegian University of Science and Technology

Career Start Year 1983

Number of shared co-authors 3

row(s) 1 - 30 of 30

Nitin S Baliga

Institute for Systems Biology

Co-authored papers 10

Thea Norman

Bill & Melinda Gates Foundation

Co-authored papers 9

Stephen H Friend

University of Oxford

Co-authored papers 8

Gustavo Stolovitzky

IBM T.J. Watson Research Center

Co-authored papers 7

Michael R Kellen

University of Washington

Co-authored papers 6

Adam A Margolin

Icahn School of Medicine

Co-authored papers 5

Paul C Boutros

University of California los angeles

Co-authored papers 5

Elias Chaibub Neto

University of Wisconsin-Madison.

Co-authored papers 5

Cristian Caloian

Ontario Institute for Cancer Research

Co-authored papers 4

Adam D Ewing

Mater Research Institute - University of Queensland

Co-authored papers 4

Kyle Ellrott

Oregon Health & Science University

Co-authored papers 4

Joshua M Stuart

University of California at Santa Cruz

Co-authored papers 4

Takafumi N Yamaguchi

University of California los angeles

Co-authored papers 3

Yin Hu

Co-authored papers 3

Justin Guinney

University of Washington

Co-authored papers 3

Xiaowei Zhan

Southwestern Medical Center, University of Texas

Co-authored papers 3

Yang Xie

Quantitative Biomedical Research Center

Co-authored papers 3

Dan Tenenbaum

Fred Hutchinson Cancer Research Center

Co-authored papers 3

Kathleen E Houlahan

University of California los angeles

Co-authored papers 3

Tao Wang

University of Texas Southwestern Medical Center

Co-authored papers 3

Lara M Mangravite

Children's Hospital Oakland Research Institute

Co-authored papers 3

Guanghua Xiao

The University of Texas Southwestern Medical Center

Co-authored papers 3

Allen Dearry

National Institute of Environmental Health Sciences

Co-authored papers 2

David Haussler

Genomics Institute, University of California Santa Cruz

Co-authored papers 2

Stephen R Piccolo

Brigham Young University

Co-authored papers 2

Arno Klein

Child Mind Institute

Co-authored papers 2

Kristen K Dang

Benaroya Research Institute at Virginia Mason

Co-authored papers 2

Paul Shannon

Institute for Systems Biology

Co-authored papers 2

James C Costello

University of Colorado Anschutz Medical Campus

Co-authored papers 2

Ivan Rusyn

Co-authored papers 2

1 - 30

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