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    Scooter Morris, PhD

    TitleProgrammer Analyst
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address600 16th St
    San Francisco CA 94158
    Phone415-514-4406
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      Collapse Biography 
      Collapse Education and Training
      UC IrvineB.S.Biology1977
      UC IrvineB.A.Physics1977
      UC IrvineB.S.Information and Computer Science1977
      UC San FranciscoPh.D.Graduate Division (Medical Information Science)1990
      Collapse Awards and Honors
      ACM/SIGCHI2005Lifetime Service Award

      Collapse Overview 
      Collapse Overview
      My major interests are in the visualization of diverse biological data in ways that can communicate important properties about underlying properties. The major vehicle for that visualization has been Cytoscape, an open source platform for integration and visualization of biological data -- particularly biological data that can be mapped onto networks of various different kinds. Some examples of our work in this area include:

      structureViz, which provides a linkage between the network view commonly used for visualization of pathways, protein-protein interaction networks, or protein similarity networks and the structural view commonly used by structural biologists to manipulate, analyze, and compare macromolecular structures. structureViz is a plugin for Cytoscape and is available from the Cytoscape web site or through the plugin manager.
      clusterMaker, which unifies a number of different clustering techniques commonly used by biologists for segregating proteins into groups, performing expression profiling, and more recently epistatic mini-array profiles (EMAPs). clusterMaker provides the algorithms as well as familiar visualizations for the cluster results. clusterMaker is a Cytoscape plugin, allowing the nodes and edges in a Cytoscape network to interact with the visualizations provided by clusterMaker. clusterMaker is a plugin for Cytoscape and is available from the Cytoscape web site or through the plugin manager.
      chemViz, extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks. chemViz is a plugin for Cytoscape and is available from the Cytoscape web site or through the plugin manager.

      In addition to the plugins mentioned above, I participate in the ongoing development of Cytoscape as a member of the core development team, contributing a number of plugins and extensions to Cytoscape to improve the general functionality as well as usability.


      Collapse ORNG Applications 
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      Collapse Awarded Grants

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov; 9(11):2539-54. PMID: 25275790; PMCID: PMC4332878.
      2. Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinformatics. 2015 Jan 1; 31(1):134-6. PMID: 25212755; PMCID: PMC4271147 [Available on 01/01/16].
      3. Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with cytoscape 3. Curr Protoc Bioinformatics. 2014; 47:8.13.1-8.13.24. PMID: 25199793; PMCID: PMC4174321.
      4. Doncheva NT, Klein K, Morris JH, Wybrow M, Domingues FS, Albrecht M. Integrative visual analysis of protein sequence mutations. BMC Proc. 2014; 8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S2. PMID: 25237389; PMCID: PMC4155609.
      5. Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. The Cytoscape app article collection. F1000Res. 2014; 3:138. PMID: 25580224; PMCID: PMC4288400.
      6. Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. setsApp: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149. PMID: 25352980; PMCID: PMC4207244.
      7. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147. PMID: 25285206; PMCID: PMC4176421.
      8. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Enhancing UCSF Chimera through web services. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W478-84. PMID: 24861624; PMCID: PMC4086125.
      9. Akiva E, Brown S, Almonacid DE, Barber AE, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. PMID: 24271399; PMCID: PMC3965090.
      10. Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FC, Hieter P, Guthrie C, Kaplan CD, Krogan NJ. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 2013 Aug 15; 154(4):775-88. PMID: 23932120; PMCID: PMC3932829.
      11. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2012 Jan 19; 481(7381):365-70. PMID: 22190034; PMCID: PMC3310911.
      12. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics. 2011; 12:436. PMID: 22070249; PMCID: PMC3262844.
      13. Su G, Kuchinsky A, Morris JH, States DJ, Meng F. GLay: community structure analysis of biological networks. Bioinformatics. 2010 Dec 15; 26(24):3135-7. PMID: 21123224; PMCID: PMC2995124.
      14. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 1; 27(3):326-33. PMID: 21118823; PMCID: PMC3031030.
      15. Flórez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C. Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. BMC Bioinformatics. 2010; 11:484. PMID: 20875130; PMCID: PMC2956735.
      16. Morris JH, Meng EC, Ferrin TE. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics. 2010 Aug; 9(8):1703-15. PMID: 20525940; PMCID: PMC2938059.
      17. Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J. Partitioning biological data with transitivity clustering. Nat Methods. 2010 Jun; 7(6):419-20. PMID: 20508635.
        View in: PubMed
      18. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009; 4(2):e4345. PMID: 19190775; PMCID: PMC2631154.
      19. Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1; 23(17):2345-7. PMID: 17623706.
        View in: PubMed
      20. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 2006 Feb 28; 45(8):2545-55. PMID: 16489747.
        View in: PubMed
      21. Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D642-8. PMID: 16381950; PMCID: PMC1347459.
      22. Ferrin TE, Huang CC, Greenblatt DM, Stryke D, Giacomini KM, Morris JH. Enhancing data sharing in collaborative research projects with DASH. Pac Symp Biocomput. 2005; 260-71. PMID: 15759632.
        View in: PubMed
      23. Jewett DL, Martin WM, Sininger YS, Gardi JN, Morris JH, Williston JS, Randolph MG, Chimento TC, Shah D. The 3-channel Lissajous' trajectory of the auditory brain-stem response. Electroencephalogr Clin Neurophysiol. 1987 Sep; 68(5):323-414. PMID: 2441974.
        View in: PubMed
      24. Jewett DL, Walden CA, Chimento TC, Morris JH. Effects of acute nerve compression on conduction of impulse trains of increasing frequency. J Neurol Sci. 1985 Feb; 67(2):187-99. PMID: 3981219.
        View in: PubMed
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