John H. Morris

33 papers Misc 1Journal 32
YearRankTypeTitle / Venue / Authors
2024 J jnl
Biomedical knowledge graph-optimized prompt generation for large language models.
Bioinform.
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
2023 J jnl
Biomedical knowledge graph-enhanced prompt generation for large language models.
CoRR
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
2023 J jnl
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.
Bioinform.
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
2023 J jnl
Translating desktop success to the web in the cytoscape project.
Frontiers Bioinform.
Dexter Pratt, Rudolf T. Pillich, John H. Morris
2023 J jnl
clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape.
BMC Bioinform.
Maija Utriainen, John H. Morris
2022 J jnl
A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology.
AI Mag.
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
2021 J jnl
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis.
Bioinform.
Eliot Ragueneau, Anjali Shrivastava, John H. Morris, Noemi del-Toro, Henning Hermjakob, Pablo Porras
2020 J jnl
Visualize omics data on networks with Omics Visualizer, a Cytoscape App.
F1000Research
Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen
2019 J jnl
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Nucleic Acids Res.
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
2019 J jnl
Ten simple rules to create biological network figures for communication.
PLoS Comput. Biol.
G. Elisabeta Marai, Bruno Pinaud, Katja Bühler, Alexander Lex, John H. Morris
2018 J jnl
Copycat Layout: Network layout alignment via Cytoscape Automation.
F1000Research
Brett Settle, David Otasek, John H. Morris, Barry Demchak
2018 J jnl
The Cytoscape Automation app article collection.
F1000Research
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
2018 J jnl
aMatReader: Importing adjacency matrices via Cytoscape Automation.
F1000Research
Brett Settle, David Otasek, John H. Morris, Barry Demchak
2017 J jnl
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.
PLoS Comput. Biol.
Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow
2017 J jnl
Biocuration in the structure-function linkage database: the anatomy of a superfamily.
Database J. Biol. Databases Curation
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
2017 J jnl
Biocuration in the structure-function linkage database: the anatomy of a superfamily.
Database J. Biol. Databases Curation
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
2017 J jnl
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Nucleic Acids Res.
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
2016 J jnl
DASP3: identification of protein sequences belonging to functionally relevant groups.
BMC Bioinform.
Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow
2015 J jnl
CyAnimator: Simple Animations of Cytoscape Networks.
F1000Research
John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin
2015 J jnl
cddApp: a Cytoscape app for accessing the NCBI conserved domain database.
Bioinform.
John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin
2014 J jnl
Enhancing UCSF Chimera through web services.
Nucleic Acids Res.
Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin
2014 J jnl
The Cytoscape app article collection.
F1000Research
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
2014 J jnl
The Structure-Function Linkage Database.
Nucleic Acids Res.
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
2014 J jnl
enhancedGraphics: a Cytoscape app for enhanced node graphics.
F1000Research
John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico
2014 J jnl
setsApp: Set operations for Cytoscape Nodes and Edges.
F1000Research
John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin
2012 J jnl
Global landscape of HIV-human protein complexes.
Nat.
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
2011 J jnl
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
Bioinform.
Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin
2011 J jnl
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
BMC Bioinform.
John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
2010 J jnl
GLay: community structure analysis of biological networks.
Bioinform.
Gang Su, Allan Kuchinsky, John H. Morris, David J. States, Fan Meng
2010 J jnl
Protein network prediction and topological analysis in
BMC Bioinform.
Andrés F. Flórez, Daeui Park, Jong Bhak, Byoung-Chul Kim, Allan Kuchinsky, John H. Morris, Jairo Espinosa, Carlos Muskus
2007 J jnl
structureViz: linking Cytoscape and UCSF Chimera.
Bioinform.
John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin
2006 J jnl
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
Nucleic Acids Res.
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
2005 Misc conf
Enhancing Data Sharing in Collaborative Research Projects with DASH.
Pacific Symposium on Biocomputing
Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris