Author details

Full Name

Paul Shannon

Affiliation

Institute for Systems Biology

ORCID

Career Start Year

1998

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
37585474	cyjShiny: A cytoscape.js R Shiny Widget for network visualization and analysis.	PLoS One	2023
37585474	cyjShiny: A cytoscape.js R Shiny Widget for network visualization and analysis.	PLoS One	2023
32814038	Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.	Cell Rep	2020
32024856	Integrative network modeling reveals mechanisms underlying T cell exhaustion.	Sci Rep	2020
32814038	Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.	Cell Rep	2020
32024856	Integrative network modeling reveals mechanisms underlying T cell exhaustion.	Sci Rep	2020
30880026	Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate.	Cell Stem Cell	2019
30772379	Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.	Cell Syst	2019
30880026	Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate.	Cell Stem Cell	2019
30772379	Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.	Cell Syst	2019
29937276	Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus.	Neuron	2018
30158685	Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape.	Nat Genet	2018
29937276	Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus.	Neuron	2018
30158685	Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape.	Nat Genet	2018
25633503	Orchestrating high-throughput genomic analysis with Bioconductor.	Nat Methods	2015
25633503	Orchestrating high-throughput genomic analysis with Bioconductor.	Nat Methods	2015
26672762	CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.	F1000Res	2015
26672762	CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.	F1000Res	2015
24681907	VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.	Bioinformatics	2014
24681907	VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.	Bioinformatics	2014
23300999	Wrangling phosphoproteomic data to elucidate cancer signaling pathways.	PLoS One	2013
23837656	RCytoscape: tools for exploratory network analysis.	BMC Bioinformatics	2013
23300999	Wrangling phosphoproteomic data to elucidate cancer signaling pathways.	PLoS One	2013
23837656	RCytoscape: tools for exploratory network analysis.	BMC Bioinformatics	2013
21182202	The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage.	Proteomics	2011
21182202	The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage.	Proteomics	2011
19915526	Exome sequencing identifies the cause of a mendelian disorder.	Nat Genet	2010
20395639	Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.	Mol Cell Proteomics	2010
20220176	Analysis of genetic inheritance in a family quartet by whole-genome sequencing.	Science	2010
19915526	Exome sequencing identifies the cause of a mendelian disorder.	Nat Genet	2010
20220176	Analysis of genetic inheritance in a family quartet by whole-genome sequencing.	Science	2010
20395639	Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.	Mol Cell Proteomics	2010
18635572	The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.	Bioinformatics	2008
20157627	Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform.	Clin Proteomics	2008
18635572	The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.	Bioinformatics	2008
20157627	Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform.	Clin Proteomics	2008
17360575	General transcription factor specified global gene regulation in archaea.	Proc Natl Acad Sci U S A	2007
17940529	PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.	Mol Syst Biol	2007
17360575	General transcription factor specified global gene regulation in archaea.	Proc Natl Acad Sci U S A	2007
18021453	The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.	BMC Bioinformatics	2007
18160043	A predictive model for transcriptional control of physiology in a free living cell.	Cell	2007
17940529	PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.	Mol Syst Biol	2007
18021453	The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.	BMC Bioinformatics	2007
18160043	A predictive model for transcriptional control of physiology in a free living cell.	Cell	2007
16686963	The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.	Genome Biol	2006
16569235	The Gaggle: an open-source software system for integrating bioinformatics software and data sources.	BMC Bioinformatics	2006
16686963	The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.	Genome Biol	2006
16569235	The Gaggle: an open-source software system for integrating bioinformatics software and data sources.	BMC Bioinformatics	2006
15833125	Derivation of genetic interaction networks from quantitative phenotype data.	Genome Biol	2005
15833837	Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease.	Cancer Res	2005

1 - 50 of 68

Atanas Kamburov

Broad Institute of Harvard and MIT

Career Start Year 2007

Number of shared co-authors 2

Joshua W K Ho

The University of Hong Kong

Career Start Year 2006

Number of shared co-authors 0

Andrey Alexeyenko

Karolinska Institutet

Career Start Year 2006

Number of shared co-authors 3

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 2

Dexter Pratt (CM4AI)

UC San Diego

Career Start Year 2006

Number of shared co-authors 3

Avi Ma'ayan

Icahn School of Medicine at Mount Sinai

Career Start Year 2005

Number of shared co-authors 3

Shannan J Ho Sui

Harvard T.H. Chan School of Public Health

Career Start Year 2004

Number of shared co-authors 0

Tanusya M Murali

Yong Loo Lin School of Medicine, National University of Singapore

Career Start Year 2003

Number of shared co-authors 1

Chunlei Wu

The Scripps Research Institute

Career Start Year 2002

Number of shared co-authors 0

Emek Demir

Knight Cancer Institute, Oregon Health & Science University

Career Start Year 2002

Number of shared co-authors 8

Haiyuan Yu

Weill Institute for Cell and Molecular Biology, Cornell University

Career Start Year 2001

Number of shared co-authors 0

Andrew I Su

The Scripps Research Institute

Career Start Year 2001

Number of shared co-authors 1

Kristina Hanspers

Gladstone Institutes

Career Start Year 2001

Number of shared co-authors 7

Johan Rung

Uppsala University

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 3

Gary D Bader

University of Toronto

Career Start Year 2000

Number of shared co-authors 11

Hedi Peterson

Institute of Computer Science, University of Tartu

Career Start Year 2000

Number of shared co-authors 1

Alexander R Pico

Institute of Data Science and Biotechnology, Gladstone Institutes

Career Start Year 1998

Number of shared co-authors 10

Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Career Start Year 1998

Number of shared co-authors 2

Igor Jurisica

Schroeder Arthritis Institute

Career Start Year 1998

Number of shared co-authors 1

Ralf Zimmer

Ludwig-Maximilians-Universitat Munchen

Career Start Year 1995

Number of shared co-authors 5

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 2

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 8

Joel S Bader

Johns Hopkins University

Career Start Year 1993

Number of shared co-authors 3

Jason E McDermott

Pacific Northwest National Laboratory

Career Start Year 1993

Number of shared co-authors 1

Jill P Mesirov

University of California San Diego

Career Start Year 1992

Number of shared co-authors 5

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 9

John Quackenbush

Harvard T. H. Chan School of Public Health

Career Start Year 1989

Number of shared co-authors 10

Lincoln Stein

Ontario Institute for Cancer Research, University Avenue

Career Start Year 1986

Number of shared co-authors 3

John H Morris

University of California san francisco

Career Start Year 1985

Number of shared co-authors 8

row(s) 1 - 30 of 30

Leroy Hood

Center for Phenomic Health, The Buck Institute for Research on Aging

Co-authored papers 11

Nitin S Baliga

Institute for Systems Biology

Co-authored papers 9

Ruedi Aebersold

Institute of Molecular Systems Biology, ETH Zurich

Co-authored papers 6

Richard Bonneau

Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation

Co-authored papers 6

Nathan D Price

Institute for Systems Biology

Co-authored papers 4

David R Goodlett

University of Victoria

Co-authored papers 4

Cory C Funk

Institute for Systems Biology

Co-authored papers 3

Vesteinn Thorsson

Institute for Systems Biology

Co-authored papers 3

Gustavo Glusman

Institute for Systems Biology

Co-authored papers 3

Chad D Huff

University of Texas M.D. Anderson Cancer Center

Co-authored papers 2

Eric W Deutsch

Institute for Systems Biology

Co-authored papers 2

Peter Tarczy-Hornoch

University of Washington School of Medicine, University of Washington

Co-authored papers 2

Alexander Schmidt

Co-authored papers 2

Jay Shendure

University of Washington

Co-authored papers 2

David S Campbell

Co-authored papers 2

Mark L Grimes

Co-authored papers 2

Seth A Ament

Institute for Genome Sciences, University of Maryland School of Medicine

Co-authored papers 2

Vincent J Carey

Brigham and Women's Hospital, Harvard Medical School

Co-authored papers 2

Michael J Bamshad

University of Washington

Co-authored papers 2

Timothy Galitski

Institute for Systems Biology

Co-authored papers 2

Martin Morgan

Roswell Park Comprehensive Cancer Center

Co-authored papers 2

Lukas N Mueller

Co-authored papers 2

Robert L Moritz

Institute for Systems Biology

Co-authored papers 2

James Christopher Bare

Institute for Systems Biology

Co-authored papers 2

Michael Lawrence

Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School

Co-authored papers 2

Mi-Youn Brusniak

Co-authored papers 2

Valerie Obenchain

Fred Hutchinson Cancer Research Center

Co-authored papers 2

Gregory W Carter

Tufts University School of Medicine

Co-authored papers 1

Nil??fer Ertekin-Taner

Mayo Clinic

Co-authored papers 1

Chris Sander

Broad Institute of MIT and Harvard

Co-authored papers 1

1 - 30

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