John H Morris

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint structureViz: linking Cytoscape and UCSF Chimera
    John H Morris
    Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
    Bioinformatics 23:2345-7. 2007
  2. pmc clusterMaker: a multi-algorithm clustering plugin for Cytoscape
    John H Morris
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    BMC Bioinformatics 12:436. 2011
  3. pmc Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection
    Andrés F Flórez
    Programa de Estudio y Control de Enfermedades Tropicales PECET, Universidad de Antioquia, Calle 62 No 52 59, Lab 632, Medellin, Colombia
    BMC Bioinformatics 11:484. 2010
  4. pmc Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
    Leonard Apeltsin
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
    Bioinformatics 27:326-33. 2011
  5. pmc Computational tools for the interactive exploration of proteomic and structural data
    John H Morris
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
    Mol Cell Proteomics 9:1703-15. 2010
  6. pmc Enhancing UCSF Chimera through web services
    Conrad C Huang
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA
    Nucleic Acids Res 42:W478-84. 2014
  7. pmc The Structure-Function Linkage Database
    Eyal Akiva
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Santiago 8370146, Chile, Nodality, Inc, South San Francisco, CA 94080, USA, Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, MA 02215, USA, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA, Center for Bioinformatics ZBH, University of Hamburg, Hamburg 20146, Germany, Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA, UC Berkeley UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158 and Berkeley, CA 94720, USA and California Institute for Quantitative Biosciences, University of California, San Francisco, Canada
    Nucleic Acids Res 42:D521-30. 2014
  8. ncbi request reprint Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database
    Scott C H Pegg
    Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143 2250, USA
    Biochemistry 45:2545-55. 2006
  9. pmc Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions
    John H Morris
    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
    Nat Protoc 9:2539-54. 2014
  10. pmc From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II
    Hannes Braberg
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 154:775-88. 2013

Collaborators

Detail Information

Publications14

  1. ncbi request reprint structureViz: linking Cytoscape and UCSF Chimera
    John H Morris
    Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
    Bioinformatics 23:2345-7. 2007
    ..This interface uses a tree-based paradigm to allow users to select and affect the display of models, chains and residues, mostly through the use of context menus...
  2. pmc clusterMaker: a multi-algorithm clustering plugin for Cytoscape
    John H Morris
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
    BMC Bioinformatics 12:436. 2011
    ....
  3. pmc Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection
    Andrés F Flórez
    Programa de Estudio y Control de Enfermedades Tropicales PECET, Universidad de Antioquia, Calle 62 No 52 59, Lab 632, Medellin, Colombia
    BMC Bioinformatics 11:484. 2010
    ..We have taken a computational approach to the detection of new drug targets, which may become an effective strategy for the discovery of new drugs for this tropical disease...
  4. pmc Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
    Leonard Apeltsin
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
    Bioinformatics 27:326-33. 2011
    ..We investigate an important aspect of network construction used in analyzing protein superfamilies and present a heuristic approach for improving the performance of several algorithms...
  5. pmc Computational tools for the interactive exploration of proteomic and structural data
    John H Morris
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
    Mol Cell Proteomics 9:1703-15. 2010
    ..We briefly describe several relevant tools, and then, using three scenarios, we present in depth two tools for the integrated exploration of proteomics and structural data...
  6. pmc Enhancing UCSF Chimera through web services
    Conrad C Huang
    Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94143, USA
    Nucleic Acids Res 42:W478-84. 2014
    ..Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList. ..
  7. pmc The Structure-Function Linkage Database
    Eyal Akiva
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biologicas, Santiago 8370146, Chile, Nodality, Inc, South San Francisco, CA 94080, USA, Department of Electrical and Computer Engineering, College of Engineering, Boston University, Boston, MA 02215, USA, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA, Center for Bioinformatics ZBH, University of Hamburg, Hamburg 20146, Germany, Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA, UC Berkeley UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158 and Berkeley, CA 94720, USA and California Institute for Quantitative Biosciences, University of California, San Francisco, Canada
    Nucleic Acids Res 42:D521-30. 2014
    ..The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity. ..
  8. ncbi request reprint Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database
    Scott C H Pegg
    Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143 2250, USA
    Biochemistry 45:2545-55. 2006
    ..The SFLD is freely accessible at http://sfld.rbvi.ucsf.edu...
  9. pmc Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions
    John H Morris
    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
    Nat Protoc 9:2539-54. 2014
    ..Similarly, the network analysis and visualization protocol in Cytoscape takes 2-4 h to complete with the provided sample data, but we recommend taking days or even weeks to explore one's data and find the right questions. ..
  10. pmc From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II
    Hannes Braberg
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 154:775-88. 2013
    ..The pE-MAP approach provides a powerful strategy to understand other multifunctional machines at amino acid resolution...
  11. pmc The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse
    Alex S Nord
    University of California San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 34:D642-8. 2006
    ....
  12. pmc Using sequence similarity networks for visualization of relationships across diverse protein superfamilies
    Holly J Atkinson
    Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 4:e4345. 2009
    ..As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships...
  13. pmc cddApp: a Cytoscape app for accessing the NCBI conserved domain database
    John H Morris
    Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 31:134-6. 2015
    ..Together, these three apps provide powerful tools to annotate nodes with CDD domain and site information and visualize that information in both network and structural contexts...
  14. pmc Global landscape of HIV-human protein complexes
    Stefanie Jäger
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
    Nature 481:365-70. 2012
    ..This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection...