Dexter Pratt

According to our database, Dexter Pratt authored at least 18 papers between 1990 and 2026.

Collaborative distances:

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

2026

CellMaster: Collaborative Cell Type Annotation in Single-Cell Analysis.

Zhen Wang, Yiming Gao, Jieyuan Liu, Enze Ma, Jefferson Chen, Mark Antkowiak, Mengzhou Hu, JungHo Kong, Dexter Pratt, Zhiting Hu, Wei Wang, Trey Ideker, Eric P. Xing

CoRR, February, 2026

scPilot: Large Language Model Reasoning Toward Automated Single-Cell Analysis and Discovery.

Yiming Gao, Zhen Wang, Jefferson Chen, Mark Antkowiak, Mengzhou Hu, JungHo Kong, Dexter Pratt, Jieyuan Liu, Enze Ma, Zhiting Hu, Eric P. Xing

CoRR, February, 2026

textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape.

Favour James, Dexter Pratt, Christopher Churas, Augustin Luna

Bioinform., 2026

2025

Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization.

Joanna Lenkiewicz, Christopher Churas, Mengzhou Hu, Gege Qian, Mayank Jain, Maxwell Adam Levinson, Sadnan Al Manir, Yue Qin, Dylan Fong, Keiichiro Ono, Jing Chen, Chengzhan Gao, Dexter Pratt, Jillian Parker, Timothy W. Clark, Trey Ideker, Leah V. Schaffer

Bioinform., 2025

2024

Thought Graph: Generating Thought Process for Biological Reasoning.

Chi-Yang Hsu, Kyle Cox, Jiawei Xu, Zhen Tan, Tianhua Zhai, Mengzhou Hu, Dexter Pratt, Tianlong Chen, Ziniu Hu, Ying Ding

Proceedings of the Companion Proceedings of the ACM on Web Conference 2024, 2024

ReguloGPT: Harnessing GPT for End-to-End Knowledge Graph Construction of Molecular Regulatory Pathways.

Xidong Wu, Sumin Jo, Yiming Zeng, Arun Das, Tinghe Zhang, Parth Patel, Yuanjing Wei, Lei Li, Shou-Jiang Gao, Jianqiu Zhang, Dexter Pratt, Yu-Chiao Chiu, Yufei Huang

Proceedings of the IEEE EMBS International Conference on Biomedical and Health Informatics, 2024

2023

Translating desktop success to the web in the cytoscape project.

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

Frontiers Bioinform., May, 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., March, 2023

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

2021

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, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper

Bioinform., 2021

2020

Multiscale community detection in Cytoscape.

Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker

PLoS Comput. Biol., 2020

2018

ndexr - an R package to interface with the network data exchange.

Florian Auer, Zaynab Hammoud, Alexandr Ishkin, Dexter Pratt, Trey Ideker, Frank Kramer

Bioinform., 2018

2017

Network propagation in the cytoscape cyberinfrastructure.

Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker

PLoS Comput. Biol., 2017

2014

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

2013

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

2012

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks.

Florian Martin, Ty M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch

BMC Syst. Biol., 2012

2006

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

Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

1990

CYC: Toward Programs With Common Sense.

Douglas B. Lenat, Ramanathan V. Guha, Karen Pittman, Dexter Pratt, Mary Shepherd

Commun. ACM, 1990