Dexter Pratt

19 papers Journal 16Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
CellMaster: Collaborative Cell Type Annotation in Single-Cell Analysis.
CoRR
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
2026 J jnl
scPilot: Large Language Model Reasoning Toward Automated Single-Cell Analysis and Discovery.
CoRR
Yiming Gao, Zhen Wang, Jefferson Chen, Mark Antkowiak, Mengzhou Hu, JungHo Kong, Dexter Pratt, Jieyuan Liu, Enze Ma, Zhiting Hu, Eric P. Xing
2026 J jnl
textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape.
Bioinform.
Favour James, Dexter Pratt, Christopher Churas, Augustin Luna
2025 J jnl
Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization.
Bioinform.
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
2024 — conf
ReguloGPT: Harnessing GPT for End-to-End Knowledge Graph Construction of Molecular Regulatory Pathways.
BHI
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
2024 — conf
Thought Graph: Generating Thought Process for Biological Reasoning.
WWW (Companion Volume)
Chi-Yang Hsu, Kyle Cox, Jiawei Xu, Zhen Tan, Tianhua Zhai, Mengzhou Hu, Dexter Pratt, Tianlong Chen, Ziniu Hu, Ying Ding
2024 J jnl
Thought Graph: Generating Thought Process for Biological Reasoning.
CoRR
Chi-Yang Hsu, Kyle Cox, Jiawei Xu, Zhen Tan, Tianhua Zhai, Mengzhou Hu, Dexter Pratt, Tianlong Chen, Ziniu Hu, Ying Ding
2023 J jnl
Evaluation of large language models for discovery of gene set function.
CoRR
Mengzhou Hu, Sahar Alkhairy, Ingoo Lee, Rudolf T. Pillich, Robin Bachelder, Trey Ideker, Dexter Pratt
2023 J jnl
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.
Bioinform.
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
2023 J jnl
Translating desktop success to the web in the cytoscape project.
Frontiers Bioinform.
Dexter Pratt, Rudolf T. Pillich, John H. Morris
2021 J jnl
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).
Bioinform.
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
2020 J jnl
Multiscale community detection in Cytoscape.
PLoS Comput. Biol.
Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker
2018 J jnl
ndexr - an R package to interface with the network data exchange.
Bioinform.
Florian Auer, Zaynab Hammoud, Alexandr Ishkin, Dexter Pratt, Trey Ideker, Frank Kramer
2017 J jnl
Network propagation in the cytoscape cyberinfrastructure.
PLoS Comput. Biol.
Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker
2014 J jnl
NeXO Web: the NeXO ontology database and visualization platform.
Nucleic Acids Res.
Janusz Dutkowski, Keiichiro Ono, Michael Kramer, Michael Yu, Dexter Pratt, Barry Demchak, Trey Ideker
2013 J jnl
Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data.
BMC Bioinform.
Natalie L. Catlett, Anthony J. Bargnesi, Stephen Ungerer, Toby Seagaran, William Ladd, Keith O. Elliston, Dexter Pratt
2012 J jnl
Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks.
BMC Syst. Biol.
Florian Martin, Ty M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch
2006 — conf
Computational Causal Reasoning Models of Mechanisms of Androgen Stimulation in Prostate Cancer.
EMBC
Dexter Pratt, William C. Hahn, Andrea Matthews, Phillip Febbo, Ranann Berger, Brian Duckworth, Josh Levy, Toby Segaran, Justin Sun, Bill Ladd, Keith O. Elliston
1990 J jnl
CYC: Toward Programs With Common Sense.
Commun. ACM
Douglas B. Lenat, Ramanathan V. Guha, Karen Pittman, Dexter Pratt, Mary Shepherd