Research Activities

My major interests are in the visualization of diverse biological data in ways that can communicate important properties about underlying biological processes and relationships. 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.

Recent Awards

• ACM/SIGCHI Lifetime Service Award for service to the field of Human Computer Interaction.

Selected Publications

1. Giovanni Scardoni, Gabriele Tosadori, John Morris, Sakshi Pratap, Carlo Laudanna, Alice Han. Computational Methods for Signal Transduction: A Network Approach. Cellular Signal Transduction in Toxicology and Pharmacology: Data Collection, Analysis, and Interpretation. Pages 201-237, John Wiley & Sons, Inc. 2019.
2. J Javier Diaz-Mejia, Elaine C Meng, Alexander R Pico, Sonya A MacParland, Troy Ketela, Trevor J Pugh, Gary D Bader, John H Morris. Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data. F1000Research 8
3. Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork, Lars J Jensen, Christian von Mering, STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D607–D613,
4. NT Doncheva, JH Morris, J Gorodkin, LJ Jensen. Cytoscape stringApp: Network analysis and visualization of proteomics data. Journal of proteome research 18 (2), 623-632 https://doi.org/10.1093/nar/gky1131
5. 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. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 2018 Jan 29;7. pii: e31097. doi: 10.7554/ eLife.31097. PubMed PMID: 29377793; PubMed Central PMCID: 29377793
6. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018 Jan;27(1):14-25. doi: 10.1002/pro.3235. Epub 2017 Sep 6. PubMed PMID: 28710774;
7. Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol. 2017 Feb 10;13(2):e1005284. doi: 10.1371/journal.pcbi.1005284. eCollection 2017 Feb. PubMed PMID: 28187133; PubMed Central PMCID: PMC5302317.
8. 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. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 Apr;26(4):677-699. doi: 10.1002/pro.3112. Epub 2017 Mar 8. PubMed PMID: 28054422; PubMed Central PMCID: PMC5368075.
9. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018 Jan;27(1):14-25. doi: 10.1002/pro.3235. Epub 2017 Sep 6. PubMed PMID: 28710774; PubMed Central PMCID: PMC5734306.
10. 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. The Cytoscape Automation app article collection. F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. PubMed PMID: 29983926; PubMed Central PMCID: PMC6013757.
11. Settle B, Otasek D, Morris JH, Demchak B. aMatReader: Importing adjacency matrices via Cytoscape Automation. Version 2. F1000Res. 2018 Jun 21 [revised 2018 Jan 1];7. pii: ISCB Comm J-823. doi: 10.12688/f1000research.15146.2. eCollection 2018. PubMed PMID: 30026937; PubMed Central PMCID: PMC6039939.2.
12. Settle B, Otasek D, Morris JH, Demchak B. Copycat Layout: Network layout alignment via Cytoscape Automation. Version 2. F1000Res. 2018 Jun 21 [revised 2018 Jan 1];7. pii: ISCB Comm J-822. doi: 10.12688/f1000research.15144.2. eCollection 2018. PubMed PMID: 30026936; PubMed Central PMCID: PMC6039917.2.
13. 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. "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible." Nucleic Acids Research. 2017 Jan 4;45(D1):D362-D368
14. 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." Nature Protocols. 2014 Nov;9(11):2539-54
15. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. "Enhancing UCSF Chimera through web services." Nucleic Acids Research. 2014, doi: 10.1093/nar/gku377
16. Akiva E1, Brown S, Almonacid DE, Barber AE 2nd, 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. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.
17. Braberg H, Jin H, Moehle EA, Chan Y,; Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FCP, Hieter P, Guthrie C, Kaplan CD, Krogan NJ. "From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II" Cell. 2013, doi:10.1016/j.cell.2013.07.033
18. 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. 2011, 481(7381):365-70.
19. 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 (9 November 2011).
20. 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.
21. 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. Epub 2010 Nov 29.
22. 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 Sep 27;11:484.
23. 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. Epub 2010 Jun 4. PMID: 20525940
24. 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
25. Atkinson HJ, Morris JH, Ferrin TE, Babbitt TC. " Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies" PLoS ONE. 2009;4(2). PMID: 19190775
26. Morris JH, Huang CC, Babbitt PC, Ferrin TE. "structureViz: linking Cytoscape and UCSF Chimera." Bioinformatics. 2007 Sep 1;23(17):2345-7. Epub 2007 Jul 10. PMID: 17623706
27. 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. "Integration of biological networks and gene expression data using Cytoscape." Nat Protoc. 2007;2(10):2366-82. PMID: 17947979
28. 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
29. 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
30. Rowley T, Morris J, Watt J, Fritz A. "Implementing SVG in a Web Browser: Past, Present, and Future of Mozilla SVG" Paper to be given at SVGOpen 2005, Enschede, Netherlands, August 15-18, 2005.
31. 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
32. "Genentech, Inc.: Adding Value to Research and Development" A chapter in The Internet Strategy Handbook: Lessons From the New Frontier. Edited by Mary J. Cronin. Harvard Business School Press, Boston, MA, 1996 ISBN 0-87584-631-9
33. F.A. Miller, J.L. Chow, T. Oberzeir, J.H. Morris. "A Client-Server Architecture for Biomedical Laboratory Automation", LRA, 4, 315-321 (1992)
34. Huang CC, Klein TE, Morris JH III, Ferrin TE, Langridge R. "Application of the macromolecular workbench to the study of collagen." Proceedings of 24th Hawaii International Conference on System Sciences, Biotechnology Computing, (1991).
35. Y.S. Sininger, J.N. Gardi, J.H. Morris, W.H. Martin, and D.L. Jewett. "The 3-channel Lissajous' trajectory of the auditory brain-stem response. VII. Planar segments in humans" Electroencephalography and Clinical Neurophysiology, 68, 368-379 (1987)
36. W.H. Martin, D.L. Jewett, J.H. Morris, J.S. Williston, and J.N. Gardi. "The 3-channel Lissajous' trajectory of the auditory brain-stem response. II. Methodology" Electroencephalography and Clinical Neurophysiology, 68, 327-332 (1987)
37. D.L. Jewett, C.A. Walden, T.C. Chimento, and J.H. Morris. "Effects of Acute Nerve Compression on Conduction of Impulse Trains of Increasing Frequency" Journal of the Neurological Science, 67, 187-199 (1985).
38. D.J. Nickolai, C.J. Lammel, B.A. Byford, J.H. Morris, E.B. Kaplan, W.K. Hadley, and G.F. Brooks. "Effects of storage temperature and pH on stability of 11 beta-lactanus in MIC trays." Journal of Clinical Microbiology, 21, 366-370 (1985)

Invited Lectures and Seminars

• "DASH and other tools" Presentation given at the NCRR Booth at the Biophysical Society Meeting in Long Beach, CA February, 2005.
• "Database Concepts" Lecture given to UCSF graduate course in bioinformatics on January 30, 2003
• "Life Sciences at Genentech" Plenary talk given at Life Sciences Day at Oracle World in San Francisco, CA on November 13, 2002.
• "Genentech's IT Infrastructure: Evolutionary Response to the Life Science Technology Revolution" Presented at 21st Century Life Science Technology Revolution, a symposium sponsored by the Whitehead Institute and HP in Cambridge, MA on June 11, 2002.
• "The Computational Impact of Genomics on Biotechnology R&D" Presented at SuperComputing 2001 in Denver, CO on November 13, 2001
• "XML at Genentech -- Not yet?" Presented at the XML Workshop at the 9th World Wide Web Conference in Amsterdam, Netherlands on May 15, 200.
• "Genentech's IT Infrastructure." Presented at Bioinformatics in the Post-Genomic Era, a symposium sponsored by Genentech and Compaq Computer in South San Francisco, CA on April 14, 2000.
• "HCI and the Web" Position Paper for the HCI and the Web Workshop at CHI'96, Vancouver, British Columbia, Canada on April 14, 1996
• "Biotechnology and the Internet: the Genentech Experience..." A presentation at the Biotechnology Industry Association meeting, May, 1995
• "Scientific Computing at Genentech", Presented at The Biotech Meeting at Laguna Nigel, 1988.

Personal Information

My wife, Suzanne, and I have been married since 1981 and have two great kids, and a very friendly yellow lab named "Missy". Suzanne has a doctorate in clinical pharmacy (Pharm.D.) from UCSF, and is currently employed in the anti-coagulation clinic at Kaiser in South San Francisco. Before going back to pharmacy after raising Ben & Sarah, she spent 5 years teaching science at Alma Heights Christian Academy and coaching volleyball (she even let me help, sometimes). She now enjoys long walks with Missy and swimming with me.

Ben graduated from UC Irvine with a degree in Information and Computer Science (with honors!) and is now working at Lockheed Martin in San Jose as a Systems Engineer. He is currently part of Lockheed's Engineering Leadership Development Program (ELDP), and is in the master's program at Santa Clara University. After dating since high school, he and his girlfriend, Jaime, were married in January, 2010.

Sarah graduated Magna Cum Laude from Westmont College in Montecito, California with a degree in English. She is currently an intern at IMPACT, an organization that organizes and supports cross-cultural short-term missions trips. Sarah has developed a talent for the written word that neither her Mother nor I possess, and we are continually amazed by her. Her poem about lap swimming has a special place in my heart (yes, that is me swimming in the background).

As for me, amongst other things, I enjoy photography, snow skiing, sailing, and swimming. I swim the Alcatraz Invitational each year (no, I don't wear a wet suit) and most weekends in the summer you can find me at least one day swimming off Pacifica State Beach (Linda Mar Beach) "for fun". Just look for my funky yellow hood! This year, Suzanne finished her second Alcatraz swim with me, and did great! When I'm not traveling, I also join 5 others for a brisk 11.5 mile relay swim across Lake Tahoe. Whenever I get the chance (which is all too rare), we run away for some sailing, which is my definition of true relaxation.