All Stories

  1. RCy3: Network Biology using Cytoscape from within R

    Article • October 2019, Cold Spring Harbor Laboratory Press

    Dr Alexander Pico, Dr Barry Demchak

  2. Cytoscape Automation: empowering workflow-based network analysis

    Article • September 2019, Springer Science + Business Media

    Dr Barry Demchak

  3. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies

    Article • Cell Systems, March 2019, Elsevier

    Dr Barry Demchak

  4. Theory and Application of Network Biology Toward Precision Medicine

    Article • Journal of Molecular Biology, July 2018, Elsevier

    Dr Barry Demchak

  5. Copycat Layout: Network layout alignment via Cytoscape Automation

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Dr Barry Demchak

  6. aMatReader: Importing adjacency matrices via Cytoscape Automation

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Dr Barry Demchak

  7. The Cytoscape Automation app article collection

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Dr Barry Demchak, Professor Gary D Bader

  8. Using deep learning to model the hierarchical structure and function of a cell

    Article • Nature Methods, March 2018, Springer Science + Business Media

    Dr Barry Demchak

  9. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways

    Article • Cancer Research, October 2017, American Association for Cancer Research (AACR)

    Dr Barry Demchak

  10. Network propagation in the cytoscape cyberinfrastructure

    Article • PLoS Computational Biology, October 2017, PLOS

    Dr Barry Demchak

  11. dot-app: a Graphviz-Cytoscape conversion plug-in

    Article • F1000Research, July 2017, Faculty of 1000, Ltd.

    Dr Barry Demchak

  12. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy

    Article • Molecular Cell, February 2017, Elsevier

    Dr Barry Demchak

  13. dot-app

    Article • F1000Research, October 2016, Faculty of 1000, Ltd.

    Ziran Zhang, Dr Barry Demchak

  14. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

    Article • Nature Methods, January 2016, Springer Science + Business Media

    Dr Barry Demchak

  15. cyNeo4j: connecting Neo4j and Cytoscape: Fig. 1.

    Article • Bioinformatics, August 2015, Oxford University Press (OUP)

    Dr Barry Demchak

  16. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

    Article • F1000Research, August 2015, Faculty of 1000, Ltd.

    Dr Barry Demchak

  17. Validity of PALMS GPS Scoring of Active and Passive Travel Compared with SenseCam

    Article • Medicine & Science in Sports & Exercise, March 2015, Wolters Kluwer Health

    Dr Barry Demchak

  18. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

    Article • F1000Research, October 2014, Faculty of 1000, Ltd.

    Dr Barry Demchak

  19. Biological Network Exploration with Cytoscape 3

    Article • Current Protocols in Bioinformatics, September 2014, Wiley

    Professor Gary D Bader, Dr Barry Demchak

  20. Cytoscape: the network visualization tool for GenomeSpace workflows

    Article • F1000Research, August 2014, Faculty of 1000, Ltd.

    Dr Barry Demchak

  21. The Cytoscape app article collection

    Article • F1000Research, July 2014, Faculty of 1000, Ltd.

    Professor Gary D Bader, Dr Alexander Pico, David Welker, Dr Barry Demchak

  22. Porting and using PanGIA for Cytoscape 3: challenges and solutions

    Article • F1000Research, July 2014, Faculty of 1000, Ltd.

    Dr Barry Demchak

  23. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

    Article • F1000Research, July 2014, F1000Research

    Dr Barry Demchak

  24. Cytoscape: the network visualization tool for GenomeSpace workflows

    Article • F1000Research, July 2014, F1000Research

    Mr. Michael Reich, Dr Barry Demchak

  25. NeXO Web: the NeXO ontology database and visualization platform

    Article • Nucleic Acids Research, November 2013, Oxford University Press (OUP)

    Dr Barry Demchak

  26. The anatomy of successful computational biology software

    Article • Nature Biotechnology, October 2013, Springer Science + Business Media

    Dr Barry Demchak

  27. Policy Driven Development: Flexible Policy Insertion for Large Scale Systems

    Article • July 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Barry Demchak