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Journal Articles
- 2023
[j10]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:
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinform. 39(3) (2023)- [j9]Dexter Pratt, Rudolf T. Pillich, John H. Morris:
Translating desktop success to the web in the cytoscape project. Frontiers Bioinform. 3 (2023) - 2021
- [j8]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:
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). Bioinform. 36(24): 5712-5718 (2021) - 2020
- [j7]Akshat Singhal, Song Cao, Christopher Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker:
Multiscale community detection in Cytoscape. PLoS Comput. Biol. 16(10) (2020) - 2018
- [j6]Florian Auer, Zaynab Hammoud, Alexandr Ishkin, Dexter Pratt, Trey Ideker, Frank Kramer:
ndexr - an R package to interface with the network data exchange. Bioinform. 34(4): 716-717 (2018) - 2017
- [j5]Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker:
Network propagation in the cytoscape cyberinfrastructure. PLoS Comput. Biol. 13(10) (2017) - 2014
- [j4]Janusz Dutkowski, Keiichiro Ono, Michael Kramer, Michael Yu, Dexter Pratt, Barry Demchak, Trey Ideker:
NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 42(Database-Issue): 1269-1274 (2014) - 2013
- [j3]Natalie L. Catlett, Anthony J. Bargnesi, Stephen Ungerer, Toby Seagaran, William Ladd, Keith O. Elliston, Dexter Pratt:
Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. BMC Bioinform. 14: 340 (2013) - 2012
- [j2]Florian Martin, Ty M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch:
Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. BMC Syst. Biol. 6: 54 (2012) - 1990
- [j1]Douglas B. Lenat, Ramanathan V. Guha, Karen Pittman, Dexter Pratt, Mary Shepherd:
CYC: Toward Programs With Common Sense. Commun. ACM 33(8): 30-49 (1990)
Conference and Workshop Papers
- 2024
- [c2]Chi-Yang Hsu, Kyle Cox, Jiawei Xu, Zhen Tan, Tianhua Zhai, Mengzhou Hu, Dexter Pratt, Tianlong Chen, Ziniu Hu, Ying Ding:
Thought Graph: Generating Thought Process for Biological Reasoning. WWW (Companion Volume) 2024: 537-540 - 2006
- [c1]Dexter Pratt, William C. Hahn, Andrea Matthews, Phillip Febbo, Ranann Berger, Brian Duckworth, Josh Levy, Toby Segaran, Justin Sun, Bill Ladd, Keith O. Elliston:
Computational Causal Reasoning Models of Mechanisms of Androgen Stimulation in Prostate Cancer. EMBC 2006: 38
Informal and Other Publications
- 2024
- [i2]Chi-Yang Hsu, Kyle Cox, Jiawei Xu, Zhen Tan, Tianhua Zhai, Mengzhou Hu, Dexter Pratt, Tianlong Chen, Ziniu Hu, Ying Ding:
Thought Graph: Generating Thought Process for Biological Reasoning. CoRR abs/2403.07144 (2024) - 2023
- [i1]Mengzhou Hu, Sahar Alkhairy, Ingoo Lee, Rudolf T. Pillich, Robin Bachelder, Trey Ideker, Dexter Pratt:
Evaluation of large language models for discovery of gene set function. CoRR abs/2309.04019 (2023)
Coauthor Index
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