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Author Details

Trey Ideker (CM4AI)
University of California San Diego
0000-0002-1708-8454
1996
465
108
Contact PI, tools, machine learning, cancer genomics
PMIDPaper TitleJournal TitlePublished Year
37731657Evaluation of large language models for discovery of gene set function.ArXiv2024
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
37577681Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS.bioRxiv2023
37790547Evaluation of large language models for discovery of gene set function.Res Sq2023
37786690Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation.bioRxiv2023
37553760GABA Regulates Electrical Activity and Tumor Initiation in Melanoma.Cancer Discov2023
36653526Mapping the common gene networks that underlie related diseases.Nat Protoc2023
36882166NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.Bioinformatics2023
37169829Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation.Sci Rep2023
37228113Hierarchical association of COPD to principal genetic components of biological systems.PLoS One2023
37527041Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks.Cell Rep2023
37220749A multi-scale map of protein assemblies in the DNA damage response.Cell Syst2023
37527041Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks.Cell Rep2023
37553760GABA Regulates Electrical Activity and Tumor Initiation in Melanoma.Cancer Discov2023
37790547Evaluation of large language models for discovery of gene set function.Res Sq2023
37786690Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation.bioRxiv2023
37577681Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS.bioRxiv2023
37220749A multi-scale map of protein assemblies in the DNA damage response.Cell Syst2023
37169829Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation.Sci Rep2023
37228113Hierarchical association of COPD to principal genetic components of biological systems.PLoS One2023
36653526Mapping the common gene networks that underlie related diseases.Nat Protoc2023
34992246Deep distributed computing to reconstruct extremely large lineage trees.Nat Biotechnol2022
35726002Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging.J Intern Med2022
36379252On the illusion of auxotrophy: met15ο yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w.J Biol Chem2022
35534633Understudied proteins: opportunities and challenges for functional proteomics.Nat Methods2022
35534555An open invitation to the Understudied Proteins Initiative.Nat Biotechnol2022
36534452Epigenetic aging is associated with aberrant neural oscillatory dynamics serving visuospatial processing in people with HIV.Aging (Albany NY)2022
34992246Deep distributed computing to reconstruct extremely large lineage trees.Nat Biotechnol2022
35149760Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance.Commun Biol2022
35534633Understudied proteins: opportunities and challenges for functional proteomics.Nat Methods2022
35726002Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging.J Intern Med2022
35534555An open invitation to the Understudied Proteins Initiative.Nat Biotechnol2022
36534452Epigenetic aging is associated with aberrant neural oscillatory dynamics serving visuospatial processing in people with HIV.Aging (Albany NY)2022
36379252On the illusion of auxotrophy: met15ο yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w.J Biol Chem2022
35149760Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance.Commun Biol2022
33413539HiDeF: identifying persistent structures in multiscale 'omics data.Genome Biol2021
34223192Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients.Nat Cancer2021
34162224Unveiling Complexity and Multipotentiality of Early Heart Fields.Circ Res2021
33930332Functional landscape of SARS-CoV-2 cellular restriction.Mol Cell2021
34139169Mapping the multiscale structure of biological systems.Cell Syst2021
33822880Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging.Cereb Cortex2021
33441978Author Correction: A census of pathway maps in cancer systems biology.Nat Rev Cancer2021
33413539HiDeF: identifying persistent structures in multiscale 'omics data.Genome Biol2021
33398071Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences.Nat Commun2021
34911780Uncovering Tumorigenesis Circuitry with Combinatorial CRISPR.Cancer Res2021
34556855Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.Nat Microbiol2021
34819669A multi-scale map of cell structure fusing protein images and interactions.Nature2021
34591642A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.Science2021
34591613Interpretation of cancer mutations using a multiscale map of protein systems.Science2021
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Collaborators

Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 25
Jason F Kreisberg
University of California San Diego
Co-authored papers 25
Dexter Pratt (CM4AI)
UC San Diego
Co-authored papers 20
Katherine Licon
University of California San Diego
Co-authored papers 19
Keiichiro Ono
university of california san diego
Co-authored papers 19
Roded Sharan
Tel Aviv University
Co-authored papers 16
John Paul Shen
The University of Texas MD Anderson Cancer Center
Co-authored papers 15
Sourav Bandyopadhyay
University of California San Francisco
Co-authored papers 14
Hannah Carter
University of California San Diego
Co-authored papers 13
Matan Hofree
Broad Institute of Harvard and MIT
Co-authored papers 13
Andrew M Gross
Illumina Inc.
Co-authored papers 13
Michael Ku Yu
University of California San Diego
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Fan Zheng
University of California San Diego
Co-authored papers 12
Tina Wang
Harvard University
Co-authored papers 11
Jianzhu Ma
Purdue University
Co-authored papers 11
Rohith Srivas
Amgen Inc.
Co-authored papers 11
Janusz Dutkowski
Data4Cure Inc.
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Philipp A Jaeger
University of California
Co-authored papers 10
Samson H Fong
University of California San Diego
Co-authored papers 10
Barry Demchak
University of California
Co-authored papers 10
Haico van Attikum
Leiden University Medical Center
Co-authored papers 9
Sumit K Chanda
The Scripps Research Institute
Co-authored papers 9
Justin K Huang
The University of Texas MD Anderson Cancer Center
Co-authored papers 9
Ryan Kelley
Stanford University School of Medicine
Co-authored papers 8
Danielle L Swaney
J. David Gladstone Institutes
Co-authored papers 8
Anne-Ruxandra Carvunis
University of Pittsburgh School of Medicine.
Co-authored papers 8
Daniel E Carlin
University of California San Diego
Co-authored papers 8
Christopher Churas (CM4AI)
University of California San Diego
Co-authored papers 8
Leroy Hood
Center for Phenomic Health, The Buck Institute for Research on Aging
Co-authored papers 8
Michael Smoot
University of California
Co-authored papers 8
Release 1.2