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 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
  7. 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
  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. doi request reprint 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 California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA
    Cell 154:775-88. 2013
  10. 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

Collaborators

Detail Information

Publications10

  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 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
    ....
  7. 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...
  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. doi request reprint 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 California Institute for Quantitative Biosciences, QB3, 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. ..
  10. 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...