Scooter Morris, PhD
Professional Researcher
Pharmaceutical Chemistry
School of Pharmacy

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.

• U-CIE [/juː 'siː/]: Color encoding of high-dimensional data.
  Protein science : a publication of the Protein Society 2022 Koutrouli M, Morris JH, Jensen LJ
• IntAct App: a Cytoscape application for molecular interaction network visualization and analysis.
  Bioinformatics (Oxford, England) 2021 Ragueneau E, Shrivastava A, Morris JH, Del-Toro N, Hermjakob H, Porras P
• Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue.
  Scientific reports 2021 Qu J, Fourman S, Fitzgerald M, Liu M, Nair S, Oses-Prieto J, Burlingame A, Morris JH, Davidson WS, Tso P, Bhargava A
• scNetViz: from single cells to networks using Cytoscape.
  F1000Research 2021 Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH
• UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
  Protein science : a publication of the Protein Society 2020 Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE
• Ten simple rules to create biological network figures for communication.
  PLoS computational biology 2019 Marai GE, Pinaud B, Bühler K, Lex A, Morris JH
• Cytoscape Automation: empowering workflow-based network analysis.
  Genome biology 2019 Otasek D, Morris JH, Bouças J, Pico AR, Demchak B
• Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.
  F1000Research 2019 Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH
• STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
  Nucleic acids research 2019 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
• Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.
  Journal of proteome research 2018 Doncheva NT, Morris JH, Gorodkin J, Jensen LJ
• Copycat Layout: Network layout alignment via Cytoscape Automation.
  F1000Research 2018 Settle B, Otasek D, Morris JH, Demchak B
• aMatReader: Importing adjacency matrices via Cytoscape Automation.
  F1000Research 2018 Settle B, Otasek D, Morris JH, Demchak B
• The Cytoscape Automation app article collection.
  F1000Research 2018 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
• Prediction of enzymatic pathways by integrative pathway mapping.
  eLife 2018 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, …
• UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
  Protein science : a publication of the Protein Society 2017 Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE
• An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.
  Protein science : a publication of the Protein Society 2017 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
• Biocuration in the structure-function linkage database: the anatomy of a superfamily.
  Database : the journal of biological databases and curation 2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC
• Biocuration in the structure-function linkage database: the anatomy of a superfamily.
  Database : the journal of biological databases and curation 2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC
• DASP3: identification of protein sequences belonging to functionally relevant groups.
  BMC bioinformatics 2016 Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS
• The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
  Nucleic acids research 2016 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
• CyAnimator: Simple Animations of Cytoscape Networks.
  F1000Research 2015 Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE
• Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.
  Nature protocols 2014 Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR
• cddApp: a Cytoscape app for accessing the NCBI conserved domain database.
  Bioinformatics (Oxford, England) 2014 Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE
• Biological network exploration with Cytoscape 3.
  Current protocols in bioinformatics 2014 Su G, Morris JH, Demchak B, Bader GD
• Integrative visual analysis of protein sequence mutations.
  BMC proceedings 2014 Doncheva NT, Klein K, Morris JH, Wybrow M, Domingues FS, Albrecht M
• The Cytoscape app article collection.
  F1000Research 2014 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
• enhancedGraphics: a Cytoscape app for enhanced node graphics.
  F1000Research 2014 Morris JH, Kuchinsky A, Ferrin TE, Pico AR
• setsApp: Set operations for Cytoscape Nodes and Edges.
  F1000Research 2014 Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE
• Enhancing UCSF Chimera through web services.
  Nucleic acids research 2014 Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE
• The Structure-Function Linkage Database.
  Nucleic acids research 2013 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 …
• From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
  Cell 2013 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
• Global landscape of HIV-human protein complexes.
  Nature 2011 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…
• clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
  BMC bioinformatics 2011 Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE
• GLay: community structure analysis of biological networks.
  Bioinformatics (Oxford, England) 2010 Su G, Kuchinsky A, Morris JH, States DJ, Meng F
• Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
  Bioinformatics (Oxford, England) 2010 Apeltsin L, Morris JH, Babbitt PC, Ferrin TE
• Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection.
  BMC bioinformatics 2010 Flórez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C
• Computational tools for the interactive exploration of proteomic and structural data.
  Molecular & cellular proteomics : MCP 2010 Morris JH, Meng EC, Ferrin TE
• Partitioning biological data with transitivity clustering.
  Nature methods 2010 Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J
• Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
  PloS one 2009 Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC
• structureViz: linking Cytoscape and UCSF Chimera.
  Bioinformatics (Oxford, England) 2007 Morris JH, Huang CC, Babbitt PC, Ferrin TE
• Integration of biological networks and gene expression data using Cytoscape.
  Nature protocols 2007 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, …
• Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.
  Biochemistry 2006 Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC
• The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
  Nucleic acids research 2006 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, …
• Enhancing data sharing in collaborative research projects with DASH.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005 Ferrin TE, Huang CC, Greenblatt DM, Stryke D, Giacomini KM, Morris JH
• The 3-channel Lissajous' trajectory of the auditory brain-stem response.
  Electroencephalography and clinical neurophysiology 1987 Jewett DL, Martin WM, Sininger YS, Gardi JN, Morris JH, Williston JS, Randolph MG, Chimento TC, Shah D
• Effects of acute nerve compression on conduction of impulse trains of increasing frequency.
  Journal of the neurological sciences 1985 Jewett DL, Walden CA, Chimento TC, Morris JH