Publications by authors named "Barry Demchak"

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R
RCy3: Network biology using Cytoscape from within R.
Julia A Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R Pico

F1000Res· June 2020

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Cytoscape Automation: empowering workflow-based network analysis.
David Otasek, John H Morris, Jorge Bouças, Alexander R Pico, Barry Demchak

Genome Biol· September 2019

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Copycat Layout: Network layout alignment via Cytoscape Automation.
Brett Settle, David Otasek, John H Morris, Barry Demchak

F1000Res· July 2019

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aMatReader: Importing adjacency matrices via Cytoscape Automation.
Brett Settle, David Otasek, John H Morris, Barry Demchak

F1000Res· July 2019

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DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.
Michael Ku Yu, Jianzhu Ma, Keiichiro Ono, Fan Zheng, Samson H Fong, Barry Demchak

Cell Syst· March 2019

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Theory and Application of Network Biology Toward Precision Medicine.
Barry Demchak, Jason F Kreisberg, Juan I Fuxman Bass

J Mol Biol· September 2018

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The Cytoscape Automation app article collection.
Barry Demchak, David Otasek, Alexander R Pico, Gary D Bader, Keiichiro Ono

F1000Res· June 2018

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Using deep learning to model the hierarchical structure and function of a cell.
Jianzhu Ma, Michael Ku Yu, Samson Fong, Keiichiro Ono, Eric Sage, Barry Demchak

Nat Methods· April 2018

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NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.
Dexter Pratt, Jing Chen, Rudolf Pillich, Vladimir Rynkov, Aaron Gary, Barry Demchak

Cancer Res· November 2017

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Network propagation in the cytoscape cyberinfrastructure.
Daniel E Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker

PLoS Comput Biol· October 2017

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Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.
Michael H Kramer, Jean-Claude Farré, Koyel Mitra, Michael Ku Yu, Keiichiro Ono, Barry Demchak

Mol Cell· February 2017

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dot-app: a Graphviz-Cytoscape conversion plug-in.
Braxton Fitts, Ziran Zhang, Massoud Maher, Barry Demchak

F1000Res· October 2016

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Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.
Kun Qu, Sara Garamszegi, Felix Wu, Helga Thorvaldsdottir, Ted Liefeld, Barry Demchak

Nat Methods· March 2016

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cyNeo4j: connecting Neo4j and Cytoscape.
Georg Summer, Thomas Kelder, Keiichiro Ono, Marijana Radonjic, Stephane Heymans, Barry Demchak

Bioinformatics· December 2015

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CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.
Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak

F1000Res· December 2015

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NDEx, the Network Data Exchange.
Dexter Pratt, Jing Chen, David Welker, Ricardo Rivas, Rudolf Pillich, Barry Demchak

Cell Syst· October 2015

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Validity of PALMS GPS scoring of active and passive travel compared with SenseCam.
Jordan A Carlson, Marta M Jankowska, Kristin Meseck, Suneeta Godbole, Loki Natarajan, Barry Demchak

Med Sci Sports Exerc· March 2015

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T
The Cytoscape app article collection.
Alexander R Pico, Gary D Bader, Barry Demchak, Oriol Guitart Pla, Timothy Hull

F1000Res· January 2015

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Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.
Keiichiro Ono, Barry Demchak, Trey Ideker

F1000Res· December 2014

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Cytoscape: the network visualization tool for GenomeSpace workflows.
Barry Demchak, Tim Hull, Michael Reich, Ted Liefeld, Michael Smoot

F1000Res· October 2014

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Biological network exploration with Cytoscape 3.
Gang Su, John H Morris, Barry Demchak, Gary D Bader

Curr Protoc Bioinformatics· September 2014

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Porting and using PanGIA for Cytoscape 3: challenges and solutions.
David Welker, Barry Demchak

F1000Res· July 2014

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NeXO Web: the NeXO ontology database and visualization platform.
Janusz Dutkowski, Keiichiro Ono, Michael Kramer, Michael Yu, Dexter Pratt, Barry Demchak

Nucleic Acids Res· January 2014

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The anatomy of successful computational biology software.
Stephen Altschul, Barry Demchak, Richard Durbin, Robert Gentleman, Martin Krzywinski

Nat Biotechnol· October 2013

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Policy Driven Development: Flexible Policy Insertion for Large Scale Systems.
Barry Demchak, Ingolf Krüger

Proc IEEE Int Symp Policies Distrib Syst Netw· July 2012

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