John H. Morris

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 16

Top Topics

Protein Sequences

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Top Venues

Nucleic Acids Res.

Publications

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)
Maija Utriainen, John H. Morris
clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape. BMC Bioinform. 24 (1) (2023)
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 (2023)
Dexter Pratt, Rudolf T. Pillich, John H. Morris
Translating desktop success to the web in the cytoscape project. Frontiers Bioinform. 3 (2023)
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) (2021)
Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen
Visualize omics data on networks with Omics Visualizer, a Cytoscape App. F1000Research 9 (2020)
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) (2019)
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)
Brett Settle, David Otasek, John H. Morris, Barry Demchak
Copycat Layout: Network layout alignment via Cytoscape Automation. F1000Research 7 (2018)
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 (2018)
Brett Settle, David Otasek, John H. Morris, Barry Demchak
aMatReader: Importing adjacency matrices via Cytoscape Automation. F1000Research 7 (2018)
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)
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 (2017)
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 (2017)
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) (2017)
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 (2016)
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) (2015)
John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin
CyAnimator: Simple Animations of Cytoscape Networks. F1000Research 4 (2015)
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) (2014)
John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin
setsApp: Set operations for Cytoscape Nodes and Edges. F1000Research 3 (2014)
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 (2014)
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) (2014)
John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico
enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Research 3 (2014)
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) (2012)
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) (2011)
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 (2011)
Gang Su, Allan Kuchinsky, John H. Morris, David J. States, Fan Meng
GLay: community structure analysis of biological networks. Bioinform. 26 (24) (2010)
Andrés F. Flórez, Daeui Park, Jong Bhak, Byoung-Chul Kim, Allan Kuchinsky, John H. Morris, Jairo Espinosa, Carlos Muskus
as a tool for drug target selection. BMC Bioinform. 11 (2010)
John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin
structureViz: linking Cytoscape and UCSF Chimera. Bioinform. 23 (17) (2007)
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) (2006)
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)