John Scotter Morris

According to our database, John Scotter Morris authored at least 31 papers between 2005 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape.

Maija Utriainen, John H. Morris

BMC Bioinform., December, 2023

Translating desktop success to the web in the cytoscape project.

Dexter Pratt, Rudolf T. Pillich, John H. Morris

Frontiers Bioinform., May, 2023

The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.

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

Bioinform., February, 2023

Biomedical knowledge graph-enhanced prompt generation for large language models.

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

CoRR, 2023

2022

A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology.

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

AI Mag., 2022

2021

IntAct App: a Cytoscape application for molecular interaction network visualization and analysis.

Eliot Ragueneau, Anjali Shrivastava, John H. Morris, Noemi del-Toro, Henning Hermjakob, Pablo Porras

Bioinform., 2021

2020

Visualize omics data on networks with Omics Visualizer, a Cytoscape App.

Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen

F1000Research, 2020

2019

Ten simple rules to create biological network figures for communication.

G. Elisabeta Marai, Bruno Pinaud, Katja Bühler, Alexander Lex, John H. Morris

PLoS Comput. Biol., 2019

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

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

Nucleic Acids Res., 2019

2018

aMatReader: Importing adjacency matrices via Cytoscape Automation.

Brett Settle, David Otasek, John H. Morris, Barry Demchak

F1000Research, 2018

Copycat Layout: Network layout alignment via Cytoscape Automation.

Brett Settle, David Otasek, John H. Morris, Barry Demchak

F1000Research, 2018

The Cytoscape Automation app article collection.

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

F1000Research, 2018

2017

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow

PLoS Comput. Biol., 2017

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

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

Nucleic Acids Res., 2017

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

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

Database J. Biol. Databases Curation, 2017

2016

DASP3: identification of protein sequences belonging to functionally relevant groups.

Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow

BMC Bioinform., 2016

2015

CyAnimator: Simple Animations of Cytoscape Networks.

John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin

F1000Research, 2015

cddApp: a Cytoscape app for accessing the NCBI conserved domain database.

John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin

Bioinform., 2015

2014

Enhancing UCSF Chimera through web services.

Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin

Nucleic Acids Res., 2014

The Structure-Function Linkage Database.

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

Nucleic Acids Res., 2014

The Cytoscape app article collection.

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

F1000Research, 2014

setsApp: Set operations for Cytoscape Nodes and Edges.

John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin

F1000Research, 2014

enhancedGraphics: a Cytoscape app for enhanced node graphics.

John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico

F1000Research, 2014

2012

Global landscape of HIV-human protein complexes.

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

Nat., 2012

2011

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.

John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin

BMC Bioinform., 2011

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.

Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin

Bioinform., 2011

2010

Protein network prediction and topological analysis in <i>Leishmania major </i>as a tool for drug target selection.

Andrés F. Flórez, Daeui Park, Jong Bhak, Byoung-Chul Kim, Allan Kuchinsky, John H. Morris, Jairo Espinosa, Carlos Muskus

BMC Bioinform., 2010

GLay: community structure analysis of biological networks.

Gang Su, Allan Kuchinsky, John H. Morris, David J. States, Fan Meng

Bioinform., 2010

2007

structureViz: linking Cytoscape and UCSF Chimera.

John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin

Bioinform., 2007

2006

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.

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

Nucleic Acids Res., 2006

2005

Enhancing Data Sharing in Collaborative Research Projects with DASH.

Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris

Proceedings of the Biocomputing 2005, 2005