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 (Pacific Symposium on Biocomputing, 2005)

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; et al. (Nucleic Acids Res., 2006)

structureViz: linking Cytoscape and UCSF Chimera. - John H. Morris; Conrad C. Huang; Patricia C. Babbitt; Thomas E. Ferrin (Bioinform., 2007)

GLay: community structure analysis of biological networks. - Gang Su; Allan Kuchinsky; John H. Morris; David J. States; Fan Meng (Bioinform., 2010)

Protein network prediction and topological analysis in Leishmania major 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)

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)

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)

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; et al. (Nat., 2012)

enhancedGraphics: a Cytoscape app for enhanced node graphics. - John H. Morris; Allan Kuchinsky; Thomas E. Ferrin; Alexander R. Pico (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)

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; et al. (F1000Research, 2014)

The Structure-Function Linkage Database. - Eyal Akiva; Shoshana D. Brown; Daniel E. Almonacid; Alan E. Barber II; Ashley F. Custer; Michael A. Hicks 002; Conrad C. Huang; Florian Lauck; Susan T. Mashiyama; Elaine C. Meng; David Mischel; John H. Morris; et al. (Nucleic Acids Res., 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)

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)

CyAnimator: Simple Animations of Cytoscape Networks. - John H. Morris; Vijay Dhameliya; Steven Federowicz; Alexander R. Pico; Thomas E. Ferrin (F1000Research, 2015)

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)

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 002; 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)

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. - Damian Szklarczyk; John H. Morris; Helen Cook; Michael Kuhn 004; Stefan Wyder; Milan Simonovic; Alberto Santos; Nadezhda T. Doncheva; Alexander Roth 001; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 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 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; et al. (F1000Research, 2018)

Copycat Layout: Network layout alignment via Cytoscape Automation. - Brett Settle; David Otasek; John H. Morris; Barry Demchak (F1000Research, 2018)

aMatReader: Importing adjacency matrices via Cytoscape Automation. - Brett Settle; David Otasek; John H. Morris; Barry Demchak (F1000Research, 2018)

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)

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)

Visualize omics data on networks with Omics Visualizer, a Cytoscape App. - Marc Legeay; Nadezhda T. Doncheva; John H. Morris; Lars Juhl Jensen (F1000Research, 2020)

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)

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; et al. (AI Mag., 2022)

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; et al. (CoRR, 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; et al. (Bioinform., 2023)

Translating desktop success to the web in the cytoscape project. - Dexter Pratt; Rudolf T. Pillich; John H. Morris (Frontiers Bioinform., 2023)

clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape. - Maija Utriainen; John H. Morris (BMC Bioinform., 2023)