CYC: Toward Programs With Common Sense. - Douglas B. Lenat; Ramanathan V. Guha; Karen Pittman; Dexter Pratt; Mary Shepherd (Commun. ACM, 1990)

Computational Causal Reasoning Models of Mechanisms of Androgen Stimulation in Prostate Cancer. - Dexter Pratt; William C. Hahn; Andrea Matthews; Phillip Febbo; Ranann Berger; Brian Duckworth; Josh Levy; Toby Segaran; Justin Sun; Bill Ladd; Keith O. Elliston (EMBC, 2006)

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. - Florian Martin 002; Ty M. Thomson; Alain Sewer; David A. Drubin; Carole Mathis; Dirk Weisensee; Dexter Pratt; Julia Hoeng; Manuel C. Peitsch (BMC Syst. Biol., 2012)

Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. - Natalie L. Catlett; Anthony J. Bargnesi; Stephen Ungerer; Toby Seagaran; William Ladd; Keith O. Elliston; Dexter Pratt (BMC Bioinform., 2013)

NeXO Web: the NeXO ontology database and visualization platform. - Janusz Dutkowski; Keiichiro Ono; Michael Kramer; Michael Yu; Dexter Pratt; Barry Demchak; Trey Ideker (Nucleic Acids Res., 2014)

Network propagation in the cytoscape cyberinfrastructure. - Daniel E. Carlin; Barry Demchak; Dexter Pratt; Eric Sage; Trey Ideker (PLoS Comput. Biol., 2017)

ndexr - an R package to interface with the network data exchange. - Florian Auer; Zaynab Hammoud; Alexandr Ishkin; Dexter Pratt; Trey Ideker; Frank Kramer 001 (Bioinform., 2018)

Multiscale community detection in Cytoscape. - Akshat Singhal; Song Cao; Christopher Churas; Dexter Pratt; Santo Fortunato; Fan Zheng; Trey Ideker (PLoS Comput. Biol., 2020)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Vasundra Touré; Steven Vercruysse; Marcio Luis Acencio; Ruth C. Lovering; Sandra E. Orchard; Glyn Bradley; Cristina Casals-Casas; Claudine Chaouiya; Noemi del-Toro; Åsmund Flobak; Pascale Gaudet; Henning Hermjakob; et al. (Bioinform., 2021)

Evaluation of large language models for discovery of gene set function. - Mengzhou Hu; Sahar Alkhairy; Ingoo Lee; Rudolf T. Pillich; Robin Bachelder; Trey Ideker; Dexter Pratt (CoRR, 2023)

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. - Rudolf T. Pillich; Jing Chen; Christopher Churas; Dylan Fong; Benjamin M. Gyori; Trey Ideker; Klas Karis; Sophie N. Liu; Keiichiro Ono; Alexander R. Pico; Dexter Pratt (Bioinform., 2023)

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

ReguloGPT: Harnessing GPT for End-to-End Knowledge Graph Construction of Molecular Regulatory Pathways. - Xidong Wu; Sumin Jo; Yiming Zeng 014; Arun Das 001; Tinghe Zhang; Parth Patel; Yuanjing Wei; Lei Li; Shou-Jiang Gao; Jianqiu Zhang 002; Dexter Pratt; Yu-Chiao Chiu; et al. (BHI, 2024)

Thought Graph: Generating Thought Process for Biological Reasoning. - Chi-Yang Hsu; Kyle Cox; Jiawei Xu 006; Zhen Tan 001; Tianhua Zhai; Mengzhou Hu; Dexter Pratt; Tianlong Chen 001; Ziniu Hu; Ying Ding 001 (WWW (Companion Volume), 2024)