Author details

Full Name

John H Morris

Affiliation

University of California san francisco

ORCID

Career Start Year

1985

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36759942	The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.	Bioinformatics	2023
37020209	clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape.	BMC Bioinformatics	2023
37035036	Translating desktop success to the web in the cytoscape project.	Front Bioinform	2023
36512705	Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks.	J Proteome Res	2023
34987108	Hemin-Induced Death Models Hemorrhagic Stroke and Is a Variant of Classical Neuronal Ferroptosis.	J Neurosci	2022
36040253	U-CIE [/juË 'siË/]: Color encoding of high-dimensional data.	Protein Sci	2022
32881101	UCSF ChimeraX: Structure visualization for researchers, educators, and developers.	Protein Sci	2021
34912541	scNetViz: from single cells to networks using Cytoscape.	F1000Res	2021
33303586	Genetic interaction mapping informs integrative structure determination of protein complexes.	Science	2020
30476243	STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.	Nucleic Acids Res	2019
28710774	UCSF ChimeraX: Meeting modern challenges in visualization and analysis.	Protein Sci	2018
29983926	The Cytoscape Automation app article collection.	F1000Res	2018
29377793	Prediction of enzymatic pathways by integrative pathway mapping.	Elife	2018
27924014	The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.	Nucleic Acids Res	2017
28365730	Biocuration in the structure-function linkage database: the anatomy of a superfamily.	Database (Oxford)	2017
28187133	An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.	PLoS Comput Biol	2017
28605775	Biocuration in the structure-function linkage database: the anatomy of a superfamily.	Database (Oxford)	2017
28054422	An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.	Protein Sci	2017
27835946	DASP3: identification of protein sequences belonging to functionally relevant groups.	BMC Bioinformatics	2016
25212755	cddApp: a Cytoscape app for accessing the NCBI conserved domain database.	Bioinformatics	2015
24271399	The Structure-Function Linkage Database.	Nucleic Acids Res	2014
25580224	The Cytoscape app article collection.	F1000Res	2014
25237389	Integrative visual analysis of protein sequence mutations.	BMC Proc	2014
25285206	enhancedGraphics: a Cytoscape app for enhanced node graphics.	F1000Res	2014
25199793	Biological network exploration with Cytoscape 3.	Curr Protoc Bioinformatics	2014
25275790	Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.	Nat Protoc	2014
24861624	Enhancing UCSF Chimera through web services.	Nucleic Acids Res	2014
23932120	From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.	Cell	2013
21118823	Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.	Bioinformatics	2011
22070249	clusterMaker: a multi-algorithm clustering plugin for Cytoscape.	BMC Bioinformatics	2011
22190034	Global landscape of HIV-human protein complexes.	Nature	2011
20525940	Computational tools for the interactive exploration of proteomic and structural data.	Mol Cell Proteomics	2010
21123224	GLay: community structure analysis of biological networks.	Bioinformatics	2010
20875130	Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection.	BMC Bioinformatics	2010
20508635	Partitioning biological data with transitivity clustering.	Nat Methods	2010
19190775	Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.	PLoS One	2009
17623706	structureViz: linking Cytoscape and UCSF Chimera.	Bioinformatics	2007
17947979	Integration of biological networks and gene expression data using Cytoscape.	Nat Protoc	2007
16381950	The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.	Nucleic Acids Res	2006
16489747	Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.	Biochemistry	2006
15759632	Enhancing data sharing in collaborative research projects with DASH.	Pac Symp Biocomput	2005
2441974	The 3-channel Lissajous' trajectory of the auditory brain-stem response.	Electroencephalogr Clin Neurophysiol	1987
3981219	Effects of acute nerve compression on conduction of impulse trains of increasing frequency.	J Neurol Sci	1985

1 - 43 of 43

Jeremy Goecks

Oregon Health & Science University

Career Start Year 2010

Number of shared co-authors 1

Anna Ritz

Reed College

Career Start Year 2007

Number of shared co-authors 0

Aleksandar Stojmirovic

Janssen Research & Development LLC

Career Start Year 2007

Number of shared co-authors 6

Fidel Ram??rez

Max Planck Institute of Immunobiology and Epigenetics

Career Start Year 2007

Number of shared co-authors 3

Atanas Kamburov

Broad Institute of Harvard and MIT

Career Start Year 2007

Number of shared co-authors 2

Augustin Luna

Harvard Medical School

Career Start Year 2006

Number of shared co-authors 7

Avi Ma'ayan

Icahn School of Medicine at Mount Sinai

Career Start Year 2005

Number of shared co-authors 2

Alberto Paccanaro

University of London

Career Start Year 2005

Number of shared co-authors 8

Tanusya M Murali

Yong Loo Lin School of Medicine, National University of Singapore

Career Start Year 2003

Number of shared co-authors 0

Max Kotlyar

Schroeder Arthritis Institute

Career Start Year 2002

Number of shared co-authors 2

Christopher Churas (CM4AI)

University of California San Diego

Career Start Year 2002

Number of shared co-authors 8

Emek Demir

Knight Cancer Institute, Oregon Health & Science University

Career Start Year 2002

Number of shared co-authors 7

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Career Start Year 2001

Number of shared co-authors 1

Haiyuan Yu

Weill Institute for Cell and Molecular Biology, Cornell University

Career Start Year 2001

Number of shared co-authors 5

Andrew I Su

The Scripps Research Institute

Career Start Year 2001

Number of shared co-authors 7

Paul Shannon

Institute for Systems Biology

Career Start Year 1998

Number of shared co-authors 8

Fabien Campagne

Weill Cornell Medical College

Career Start Year 1998

Number of shared co-authors 0

Igor Jurisica

Schroeder Arthritis Institute

Career Start Year 1998

Number of shared co-authors 2

J Lynn Fink

The University of Queensland Diamantina Institute, The University of Queensland

Career Start Year 1997

Number of shared co-authors 2

Patrick Aloy

Institucio Catalana de Recerca i Estudis Avancats (ICREA)

Career Start Year 1997

Number of shared co-authors 6

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 10

Edward M Marcotte

University of Texas

Career Start Year 1993

Number of shared co-authors 4

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 5

Erik L L Sonnhammer

Stockholm University

Career Start Year 1992

Number of shared co-authors 3

Se??n I O'Donoghue

University of NSW

Career Start Year 1991

Number of shared co-authors 5

Robert Gentleman

Center for Computational Biomedicine, Harvard Medical School

Career Start Year 1991

Number of shared co-authors 1

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 13

Lincoln Stein

Ontario Institute for Cancer Research, University Avenue

Career Start Year 1986

Number of shared co-authors 6

Richard Bonneau

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

Career Start Year 1983

Number of shared co-authors 7

row(s) 1 - 30 of 30

Thomas E Ferrin

Department of Pharmaceutical Chemistry, University of California San Francisco

Co-authored papers 19

Patricia C Babbitt

University of California san francisco

Co-authored papers 11

Conrad C Huang

Department of Pharmaceutical Chemistry, University of California San Francisco

Co-authored papers 11

Elaine C Meng

Department of Pharmaceutical Chemistry, University of California San Francisco

Co-authored papers 11

Alexander R Pico

Institute of Data Science and Biotechnology, Gladstone Institutes

Co-authored papers 7

Gary D Bader

University of Toronto

Co-authored papers 6

Shoshana D Brown

University of California san francisco

Co-authored papers 5

Eyal Akiva

University of California san francisco

Co-authored papers 4

Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Co-authored papers 4

Allan Kuchinsky

Co-authored papers 4

Andrej Sali (CM4AI)

University of California San Francisco

Co-authored papers 3

Gemma L Holliday

European Bioinformatics Institute (EMBL-EBI)

Co-authored papers 3

Keiichiro Ono

university of california san diego

Co-authored papers 3

Michael Shales

University of California, USA Quantitative Biosciences Institute (QBI) san francisco

Co-authored papers 3

Christian von Mering

Co-authored papers 3

Doug Stryke

University of California San Francisco

Co-authored papers 3

Peter Cimermancic

Verily Life Sciences LLC

Co-authored papers 3

Trey Ideker (CM4AI)

University of California San Diego

Co-authored papers 3

Barry Demchak

University of California

Co-authored papers 3

Benno Schwikowski

Center for Bioinformatics, Institut Pasteur CNRS

Co-authored papers 3

Eric F Pettersen

Department of Pharmaceutical Chemistry, University of California San Francisco

Co-authored papers 3

Nevan J Krogan (CM4AI)

University of California San Francisco

Co-authored papers 3

Shuyi Wang

Fudan University

Co-authored papers 2

William J R Longabaugh

Institute for Systems Biology

Co-authored papers 2

Jeffrey R Johnson

Gladstone Institutes

Co-authored papers 2

Thomas D Goddard

Department of Pharmaceutical Chemistry, University of California San Francisco

Co-authored papers 2

Peer Bork

University of Wurzburg

Co-authored papers 2

Bruce R Conklin

Gladstone Institutes

Co-authored papers 2

Hannes Braberg

University of California San Francisco

Co-authored papers 2

Miljan Simonovi??

University of Illinois at Chicago

Co-authored papers 2

1 - 30

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