Scooter Morris, PhD

Title(s)Professional Researcher, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address600 16th Street, #N453E
San Francisco CA 94158
ORCID ORCID Icon0000-0003-0290-7979 Additional info
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    Collapse Biography 
    Collapse Education and Training
    UC IrvineB.S.1977Biology
    UC IrvineB.A.1977Physics
    UC IrvineB.S.1977Information and Computer Science
    UC San FranciscoPh.D.1990Graduate Division (Medical Information Science)
    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 Research 
    Collapse Research Activities and Funding
    Human Cell Atlas Integration with the Cytoscape Ecosystem for Analysis of scRNASeq Data
    Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation 2018-183120Mar 1, 2018 - Feb 28, 2019
    Role: Principal Investigator
    National Resource for Network Biology (NRNB)
    NIH P41GM103504Sep 13, 2010 - Apr 30, 2025
    Role: Principal Investigator on a UCSF Contract with UCSD as part of NRNB
    Resource for Biocomputing Visualization and Informatics
    NIH/NIGMS P41GM103311Jul 15, 1997 - May 31, 2018
    Role: Co-Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

    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. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. UCSF ChimeraX: Tools for structure building and analysis. Protein Sci. 2023 11; 32(11):e4792. Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE. PMID: 37774136; PMCID: PMC10588335.
      View in: PubMed   Mentions: 52     Fields:    Translation:Cells
    2. clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape. BMC Bioinformatics. 2023 Apr 05; 24(1):134. Utriainen M, Morris JH. PMID: 37020209; PMCID: PMC10074866.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    3. Translating desktop success to the web in the cytoscape project. Front Bioinform. 2023; 3:1125949. Pratt D, Pillich RT, Morris JH. PMID: 37035036; PMCID: PMC10076771.
      View in: PubMed   Mentions:
    4. The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Bioinformatics. 2023 02 03; 39(2). Morris JH, Soman K, Akbas RE, Zhou X, Smith B, Meng EC, Huang CC, Cerono G, Schenk G, Rizk-Jackson A, Harroud A, Sanders L, Costes SV, Bharat K, Chakraborty A, Pico AR, Mardirossian T, Keiser M, Tang A, Hardi J, Shi Y, Musen M, Israni S, Huang S, Rose PW, Nelson CA, Baranzini SE. PMID: 36759942; PMCID: PMC9940622.
      View in: PubMed   Mentions: 12     Fields:    
    5. Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. J Proteome Res. 2023 02 03; 22(2):637-646. Doncheva NT, Morris JH, Holze H, Kirsch R, Nastou KC, Cuesta-Astroz Y, Rattei T, Szklarczyk D, von Mering C, Jensen LJ. PMID: 36512705; PMCID: PMC9904289.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    6. U-CIE [/juː 'siː/]: Color encoding of high-dimensional data. Protein Sci. 2022 09; 31(9):e4388. Koutrouli M, Morris JH, Jensen LJ. PMID: 36040253; PMCID: PMC9387205.
      View in: PubMed   Mentions:    Fields:    
    7. IntAct App: a Cytoscape application for molecular interaction network visualization and analysis. Bioinformatics. 2021 Oct 25; 37(20):3684-3685. Ragueneau E, Shrivastava A, Morris JH, Del-Toro N, Hermjakob H, Porras P. PMID: 33961020; PMCID: PMC8545338.
      View in: PubMed   Mentions: 16     Fields:    
    8. Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue. Sci Rep. 2021 06 24; 11(1):13289. Qu J, Fourman S, Fitzgerald M, Liu M, Nair S, Oses-Prieto J, Burlingame A, Morris JH, Davidson WS, Tso P, Bhargava A. PMID: 34168225; PMCID: PMC8225859.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    9. scNetViz: from single cells to networks using Cytoscape. F1000Res. 2021; 10. Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH. PMID: 34912541; PMCID: PMC8593621.
      View in: PubMed   Mentions:    Fields:    
    10. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 2021 01; 30(1):70-82. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. PMID: 32881101; PMCID: PMC7737788.
      View in: PubMed   Mentions: 2271     Fields:    
    11. Ten simple rules to create biological network figures for communication. PLoS Comput Biol. 2019 09; 15(9):e1007244. Marai GE, Pinaud B, Bühler K, Lex A, Morris JH. PMID: 31557157; PMCID: PMC6762067.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    12. Cytoscape Automation: empowering workflow-based network analysis. Genome Biol. 2019 09 02; 20(1):185. Otasek D, Morris JH, Bouças J, Pico AR, Demchak B. PMID: 31477170; PMCID: PMC6717989.
      View in: PubMed   Mentions: 479     Fields:    
    13. Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data. F1000Res. 2019; 8. Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH. PMID: 31508207; PMCID: PMC6720041.
      View in: PubMed   Mentions: 36     Fields:    
    14. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 01 08; 47(D1):D607-D613. Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. PMID: 30476243; PMCID: PMC6323986.
      View in: PubMed   Mentions: 6984     Fields:    Translation:HumansAnimals
    15. Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. J Proteome Res. 2019 02 01; 18(2):623-632. Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. PMID: 30450911; PMCID: PMC6800166.
      View in: PubMed   Mentions: 733     Fields:    
    16. aMatReader: Importing adjacency matrices via Cytoscape Automation. F1000Res. 2018; 7:823. Settle B, Otasek D, Morris JH, Demchak B. PMID: 30026937; PMCID: PMC6039939.
      View in: PubMed   Mentions: 3     Fields:    
    17. Copycat Layout: Network layout alignment via Cytoscape Automation. F1000Res. 2018; 7:822. Settle B, Otasek D, Morris JH, Demchak B. PMID: 30026936; PMCID: PMC6039917.
      View in: PubMed   Mentions: 1     Fields:    
    18. The Cytoscape Automation app article collection. F1000Res. 2018; 7:800. Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. PMID: 29983926; PMCID: PMC6013757.
      View in: PubMed   Mentions: 10     Fields:    
    19. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 2018 01 29; 7. Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. PMID: 29377793; PMCID: PMC5788505.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    20. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018 01; 27(1):14-25. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. PMID: 28710774; PMCID: PMC5734306.
      View in: PubMed   Mentions: 1833     Fields:    Translation:Cells
    21. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 04; 26(4):677-699. Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. PMID: 28054422; PMCID: PMC5368075.
      View in: PubMed   Mentions: 4     Fields:    
    22. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 01 01; 2017(1). Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. PMID: 28365730; PMCID: PMC5467563.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    23. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. PMID: 28605775; PMCID: PMC5467548.
      View in: PubMed   Mentions: 2     Fields:    
    24. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11; 17(1):458. Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. PMID: 27835946; PMCID: PMC5106842.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    25. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017 01 04; 45(D1):D362-D368. Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C. PMID: 27924014; PMCID: PMC5210637.
      View in: PubMed   Mentions: 3358     Fields:    Translation:Cells
    26. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482. Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. PMID: 26937268.
      View in: PubMed   Mentions: 6     Fields:    
    27. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov; 9(11):2539-54. Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. PMID: 25275790; PMCID: PMC4332878.
      View in: PubMed   Mentions: 85     Fields:    
    28. cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinformatics. 2015 Jan 01; 31(1):134-6. Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. PMID: 25212755; PMCID: PMC4271147.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    29. Biological network exploration with Cytoscape 3. Curr Protoc Bioinformatics. 2014 Sep 08; 47:8.13.1-24. Su G, Morris JH, Demchak B, Bader GD. PMID: 25199793; PMCID: PMC4174321.
      View in: PubMed   Mentions: 425     Fields:    Translation:HumansCells
    30. Integrative visual analysis of protein sequence mutations. BMC Proc. 2014; 8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S2. Doncheva NT, Klein K, Morris JH, Wybrow M, Domingues FS, Albrecht M. PMID: 25237389; PMCID: PMC4155609.
      View in: PubMed   Mentions: 6  
    31. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. PMID: 25285206; PMCID: PMC4176421.
      View in: PubMed   Mentions: 25     Fields:    
    32. setsApp: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149. Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. PMID: 25352980; PMCID: PMC4207244.
      View in: PubMed   Mentions: 7     Fields:    
    33. The Cytoscape app article collection. F1000Res. 2014; 3:138. 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. PMID: 25580224; PMCID: PMC4288400.
      View in: PubMed   Mentions: 7     Fields:    
    34. Enhancing UCSF Chimera through web services. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W478-84. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. PMID: 24861624; PMCID: PMC4086125.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    35. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. 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. PMID: 24271399; PMCID: PMC3965090.
      View in: PubMed   Mentions: 127     Fields:    
    36. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 2013 Aug 15; 154(4):775-88. 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. PMID: 23932120; PMCID: PMC3932829.
      View in: PubMed   Mentions: 89     Fields:    Translation:AnimalsCells
    37. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. 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. PMID: 22190034; PMCID: PMC3310911.
      View in: PubMed   Mentions: 412     Fields:    Translation:HumansCells
    38. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics. 2011 Nov 09; 12:436. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. PMID: 22070249; PMCID: PMC3262844.
      View in: PubMed   Mentions: 275     Fields:    Translation:Animals
    39. GLay: community structure analysis of biological networks. Bioinformatics. 2010 Dec 15; 26(24):3135-7. Su G, Kuchinsky A, Morris JH, States DJ, Meng F. PMID: 21123224; PMCID: PMC2995124.
      View in: PubMed   Mentions: 126     Fields:    
    40. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 01; 27(3):326-33. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. PMID: 21118823; PMCID: PMC3031030.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    41. Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. BMC Bioinformatics. 2010 Sep 27; 11:484. Flórez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C. PMID: 20875130; PMCID: PMC2956735.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimals
    42. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics. 2010 Aug; 9(8):1703-15. Morris JH, Meng EC, Ferrin TE. PMID: 20525940; PMCID: PMC2938059.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    43. Partitioning biological data with transitivity clustering. Nat Methods. 2010 Jun; 7(6):419-20. Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J. PMID: 20508635.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimals
    44. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009; 4(2):e4345. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. PMID: 19190775; PMCID: PMC2631154.
      View in: PubMed   Mentions: 238     Fields:    Translation:HumansCells
    45. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 01; 23(17):2345-7. Morris JH, Huang CC, Babbitt PC, Ferrin TE. PMID: 17623706.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    46. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. PMID: 17947979; PMCID: PMC3685583.
      View in: PubMed   Mentions: 1245     Fields:    
    47. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 2006 Feb 28; 45(8):2545-55. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. PMID: 16489747.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansAnimals
    48. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D642-8. 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. PMID: 16381950; PMCID: PMC1347459.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    49. Enhancing data sharing in collaborative research projects with DASH. Pac Symp Biocomput. 2005; 260-71. Ferrin TE, Huang CC, Greenblatt DM, Stryke D, Giacomini KM, Morris JH. PMID: 15759632.
      View in: PubMed   Mentions:    Fields:    
    50. The 3-channel Lissajous' trajectory of the auditory brain-stem response. Electroencephalogr Clin Neurophysiol. 1987 Sep; 68(5):323-414. Jewett DL, Martin WM, Sininger YS, Gardi JN, Morris JH, Williston JS, Randolph MG, Chimento TC, Shah D. PMID: 2441974.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    51. Effects of acute nerve compression on conduction of impulse trains of increasing frequency. J Neurol Sci. 1985 Feb; 67(2):187-99. Jewett DL, Walden CA, Chimento TC, Morris JH. PMID: 3981219.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
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