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ORCIDJohn Scotter Morris
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- affiliation: University of California, San Francisco, USA
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2020 – today
- 2023
[j22]John H. Morris, Karthik Soman
, Rabia E. Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C. Meng, Conrad C. Huang, Gabriel Cerono, Gundolf Schenk, Angela Rizk-Jackson, Adil Harroud, Lauren M. Sanders, Sylvain V. Costes, Krish Bharat, Arjun Chakraborty, Alexander R. Pico, Taline Mardirossian, Michael J. Keiser, Alice Tang, Josef Hardi, Yongmei Shi, Mark A. Musen, Sharat Israni, Sui Huang, Peter W. Rose, Charlotte A. Nelson, Sergio E. Baranzini:
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Bioinform. 39(2) (2023)- [j21]Maija Utriainen, John H. Morris:
clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape. BMC Bioinform. 24(1): 134 (2023) - [j20]Dexter Pratt, Rudolf T. Pillich, John H. Morris:
Translating desktop success to the web in the cytoscape project. Frontiers Bioinform. 3 (2023) - [i9]Karthik Soman, Peter W. Rose, John H. Morris, Rabia E. Akbas, Brett Smith, Braian Peetoom, Catalina Villouta-Reyes, Gabriel Cerono, Yongmei Shi, Angela Rizk-Jackson, Sharat Israni, Charlotte A. Nelson, Sui Huang, Sergio E. Baranzini:
Biomedical knowledge graph-enhanced prompt generation for large language models. CoRR abs/2311.17330 (2023) - 2022
- [j19]Sergio E. Baranzini, Katy Börner, John H. Morris, Charlotte A. Nelson, Karthik Soman, Erica Schleimer, Michael J. Keiser, Mark A. Musen, Roger Pearce, Tahsin Reza, Brett Smith, Bruce William Herr II, Boris Oskotsky, Angela Rizk-Jackson, Katherine P. Rankin, Stephan J. Sanders, Riley Bove, Peter W. Rose, Sharat Israni, Sui Huang:
A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology. AI Mag. 43(1): 46-58 (2022) - 2021
- [j18]Eliot Ragueneau, Anjali Shrivastava, John H. Morris, Noemi del-Toro, Henning Hermjakob, Pablo Porras:
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis. Bioinform. 37(20): 3684-3685 (2021) - 2020
- [i8]Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen:
Visualize omics data on networks with Omics Visualizer, a Cytoscape App. F1000Research 9: 157 (2020)
2010 – 2019
- 2019
- [j17]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 Juhl Jensen, Christian von Mering:
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47(Database-Issue): D607-D613 (2019) - [j16]G. Elisabeta Marai, Bruno Pinaud, Katja Bühler, Alexander Lex, John H. Morris:
Ten simple rules to create biological network figures for communication. PLoS Comput. Biol. 15(9) (2019) - 2018
- [i7]Barry Demchak, David Otasek, Alexander R. Pico, Gary D. Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H. Morris, William J. R. Longabaugh, Christian Tannus Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, Trey Ideker:
The Cytoscape Automation app article collection. F1000Research 7: 800 (2018) - [i6]Brett Settle, David Otasek, John H. Morris, Barry Demchak:
Copycat Layout: Network layout alignment via Cytoscape Automation. F1000Research 7: 822 (2018) - [i5]Brett Settle, David Otasek, John H. Morris, Barry Demchak:
aMatReader: Importing adjacency matrices via Cytoscape Automation. F1000Research 7: 823 (2018) - 2017
- [j15]Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt:
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017: bax006 (2017) - [j14]Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt:
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017: bax045 (2017) - [j13]Damian Szklarczyk, John H. Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T. Doncheva, Alexander Roth, Peer Bork, Lars Juhl Jensen, Christian von Mering:
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 45(Database-Issue): D362-D368 (2017) - [j12]Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow:
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput. Biol. 13(2) (2017) - 2016
- [j11]Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow:
DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinform. 17: 458:1-458:13 (2016) - 2015
- [j10]John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin:
cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinform. 31(1): 134-136 (2015) - [i4]John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin:
CyAnimator: Simple Animations of Cytoscape Networks. F1000Research 4: 482 (2015) - 2014
- [j9]Eyal Akiva, Shoshana D. Brown, Daniel E. Almonacid, Alan E. Barber II, Ashley F. Custer, Michael A. Hicks, Conrad C. Huang, Florian Lauck, Susan T. Mashiyama, Elaine C. Meng, David Mischel, John H. Morris, Sunil Ojha, Alexandra M. Schnoes, Doug Stryke, Jeffrey M. Yunes, Thomas E. Ferrin, Gemma L. Holliday, Patricia C. Babbitt:
The Structure-Function Linkage Database. Nucleic Acids Res. 42(Database-Issue): 521-530 (2014) - [j8]Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin:
Enhancing UCSF Chimera through web services. Nucleic Acids Res. 42(Webserver-Issue): 478-484 (2014) - [i3]Alexander R. Pico, Gary D. Bader, Barry Demchak, Oriol Guitart Pla, Timothy Hull, William J. R. Longabaugh, Christian Tannus Lopes, Samad Lotia, Piet Molenaar, Jason Montojo, John H. Morris, Keiichiro Ono, Benno Schwikowski, David Welker, Trey Ideker:
The Cytoscape app article collection. F1000Research 3: 138 (2014) - [i2]John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico:
enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Research 3: 147 (2014) - [i1]John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin:
setsApp: Set operations for Cytoscape Nodes and Edges. F1000Research 3: 149 (2014) - 2012
- [j7]Stefanie Jäger, Peter Cimermancic, Natali Gulbahce, Jeffrey R. Johnson, Kathryn E. McGovern, Starlynn C. Clarke, Michael Shales, Gaelle Mercenne, Lars Pache, Kathy Li, Hilda Hernandez, Gwendolyn M. Jang, Shoshannah L. Roth, Eyal Akiva, John Marlett, Melanie Stephens, Iván D'Orso, Jason Fernandes, Marie E. Fahey, Cathal Mahon, Anthony J. O'Donoghue, Aleksandar Todorovic, John H. Morris, David A. Maltby, Tom Alber, Gerard Cagney, Frederic D. Bushman, John A. Young, Sumit K. Chanda, Wesley I. Sundquist, Tanja Kortemme, Ryan D. Hernandez, Charles S. Craik, Alma Burlingame, Andrej Sali, Alan D. Frankel, Nevan J. Krogan:
Global landscape of HIV-human protein complexes. Nat. 481(7381): 365-370 (2012) - 2011
- [j6]Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin:
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinform. 27(3): 326-333 (2011) - [j5]John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin:
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. 12: 436 (2011) - 2010
- [j4]Gang Su, Allan Kuchinsky, John H. Morris, David J. States, Fan Meng:
GLay: community structure analysis of biological networks. Bioinform. 26(24): 3135-3137 (2010) - [j3]Andrés F. Flórez, Daeui Park, Jong Bhak, Byoung-Chul Kim, Allan Kuchinsky, John H. Morris, Jairo Espinosa, Carlos Muskus:
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. BMC Bioinform. 11: 484 (2010)
2000 – 2009
- 2007
- [j2]John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin:
structureViz: linking Cytoscape and UCSF Chimera. Bioinform. 23(17): 2345-2347 (2007) - 2006
- [j1]Alex S. Nord, Patricia J. Chang, Bruce R. Conklin, Antony V. Cox, Courtney A. Harper, Geoffrey G. Hicks, Conrad C. Huang, Susan J. Johns, Michiko Kawamoto, Songyan Liu, Elaine C. Meng, John H. Morris, Janet Rossant, Patricia Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug Stryke, Harald von Melchner, Wolfgang Wurst, Ken-ichi Yamamura, Stephen G. Young, Patricia C. Babbitt, Thomas E. Ferrin:
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 34(Database-Issue): 642-648 (2006) - 2005
- [c1]Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris:
Enhancing Data Sharing in Collaborative Research Projects with DASH. Pacific Symposium on Biocomputing 2005
Coauthor Index
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