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Author Details

Dexter Pratt (CM4AI)
UC San Diego
0000-0002-1471-9513
2006
79
34
Tools, software development
PMIDPaper TitleJournal TitlePublished Year
37731657Evaluation of large language models for discovery of gene set function.ArXiv2024
36882166NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.Bioinformatics2023
37790547Evaluation of large language models for discovery of gene set function.Res Sq2023
37220749A multi-scale map of protein assemblies in the DNA damage response.Cell Syst2023
37035036Translating desktop success to the web in the cytoscape project.Front Bioinform2023
36653526Mapping the common gene networks that underlie related diseases.Nat Protoc2023
35337019A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins.Viruses2022
34992246Deep distributed computing to reconstruct extremely large lineage trees.Nat Biotechnol2022
32637990The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics2021
33930332Functional landscape of SARS-CoV-2 cellular restriction.Mol Cell2021
34591613Interpretation of cancer mutations using a multiscale map of protein systems.Science2021
34556855Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.Nat Microbiol2021
34580671A BioID-derived proximity interactome for SARS-CoV-2 proteins.bioRxiv2021
34570431NDEx: Accessing Network Models and Streamlining Network Biology Workflows.Curr Protoc2021
33413539HiDeF: identifying persistent structures in multiscale 'omics data.Genome Biol2021
32587977Identifying persistent structures in multiscale 'omics data.bioRxiv2020
31951200Dynamic post-translational modification profiling of <i>Mycobacterium tuberculosis</i>-infected primary macrophages.Elife2020
33024967Functional Landscape of SARS-CoV-2 Cellular Restriction.bioRxiv2020
33095781Multiscale community detection in Cytoscape.PLoS Comput Biol2020
30878356DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.Cell Syst2019
29087446ndexr-an R package to interface with the network data exchange.Bioinformatics2018
28815022Modeling of RAS complexes supports roles in cancer for less studied partners.BMC Biophys2017
28150243NDEx: A Community Resource for Sharing and Publishing of Biological Networks.Methods Mol Biol2017
29023449Network propagation in the cytoscape cyberinfrastructure.PLoS Comput Biol2017
29092941NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.Cancer Res2017
26594663NDEx, the Network Data Exchange.Cell Syst2015
24271398NeXO Web: the NeXO ontology database and visualization platform.Nucleic Acids Res2014
24266983Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data.BMC Bioinformatics2013
24151423On Crowd-verification of Biological Networks.Bioinform Biol Insights2013
22155224A network-based approach to quantifying the impact of biologically active substances.Drug Discov Today2012
22651900Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks.BMC Syst Biol2012
20604938Causal reasoning identifies mechanisms of sensitivity for a novel AKT kinase inhibitor, GSK690693.BMC Genomics2010
17946775Computational causal reasoning models of mechanisms of androgen stimulation in prostate cancer.Conf Proc IEEE Eng Med Biol Soc2006
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Collaborators

Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 20
Christopher Churas (CM4AI)
University of California San Diego
Co-authored papers 9
Keiichiro Ono
university of california san diego
Co-authored papers 8
Fan Zheng
University of California San Diego
Co-authored papers 7
Rudolf T Pillich
University of California San Diego
Co-authored papers 7
Laura Martin-Sancho
The Scripps Research Institute
Co-authored papers 5
Barry Demchak
University of California
Co-authored papers 5
Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 4
Jing Chen
University of Science and Technology of China
Co-authored papers 4
Michael Ku Yu
University of California San Diego
Co-authored papers 3
Lars Pache
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 3
Sumit K Chanda
The Scripps Research Institute
Co-authored papers 3
Danielle L Swaney
J. David Gladstone Institutes
Co-authored papers 3
Christopher Benner
Michigan State University College of Human Medicine
Co-authored papers 3
Sara Brin Rosenthal
Center for Computational Biology and Bioinformatics, University of California
Co-authored papers 3
Ariel Rodriguez-Frandsen
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 3
Vladimir Rynkov
University of California San Diego
Co-authored papers 3
Julia Hoeng
Vectura Fertin Pharma
Co-authored papers 3
Judd F Hultquist
Northwestern University Feinberg School of Medicine
Co-authored papers 3
Keith Elliston
tranSMART Foundation
Co-authored papers 3
Manuel C Peitsch
Philip Morris International Research Laboratories Pte. Ltd
Co-authored papers 3
Paul D De Jesus
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 3
Charles T Halfmann
South Dakota State University
Co-authored papers 2
Katherine Licon
University of California San Diego
Co-authored papers 2
Florian Martin
Co-authored papers 2
Andrea L Matthews
Co-authored papers 2
Jason F Kreisberg
University of California San Diego
Co-authored papers 2
Alain Sewer
Universitat Basel
Co-authored papers 2
Jisoo Park
University of California San Diego san francisco
Co-authored papers 2
Kyle J Roux
Sanford School of Medicine, University of South Dakota
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