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Author Details

Joshua M Stuart
University of California at Santa Cruz
2000
105
49
PMIDPaper TitleJournal TitlePublished Year
36697832Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.Nature2023
36697832Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.Nature2023
35079083Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression.Sci Rep2022
36109521Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity.Nat Commun2022
35079083Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression.Sci Rep2022
36109521Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity.Nat Commun2022
32286548Clinical and genomic characterization of Low PSA Secretors: a unique subset of metastatic castration resistant prostate cancer.Prostate Cancer Prostatic Dis2021
32286548Clinical and genomic characterization of Low PSA Secretors: a unique subset of metastatic castration resistant prostate cancer.Prostate Cancer Prostatic Dis2021
33861732Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.PLoS Comput Biol2021
33626341Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.Cell Rep2021
34146471A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.Cell Syst2021
34764310Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures.Nat Commun2021
34584103VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics.Nat Commun2021
33626341Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.Cell Rep2021
33861732Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.PLoS Comput Biol2021
34764310Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures.Nat Commun2021
34584103VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics.Nat Commun2021
34146471A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.Cell Syst2021
32424106Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance.Proc Natl Acad Sci U S A2020
31797609Using Transcriptional Signatures to Find Cancer Drivers with LURE.Pac Symp Biocomput2020
32424106Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance.Proc Natl Acad Sci U S A2020
32097025Exploring Integrative Analysis Using the BioMedical Evidence Graph.JCO Clin Cancer Inform2020
33490923Prioritizing transcriptional factors in gene regulatory networks with PageRank.iScience2020
32736587A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population.Breast Cancer Res2020
32624423Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer.Urol Oncol2020
32727885Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer.Clin Cancer Res2020
33490923Prioritizing transcriptional factors in gene regulatory networks with PageRank.iScience2020
32097025Exploring Integrative Analysis Using the BioMedical Evidence Graph.JCO Clin Cancer Inform2020
31797609Using Transcriptional Signatures to Find Cancer Drivers with LURE.Pac Symp Biocomput2020
32736587A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population.Breast Cancer Res2020
32624423Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer.Urol Oncol2020
32727885Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer.Clin Cancer Res2020
30557523Reply to A. Dalla Volta et al.J Clin Oncol2019
31653878Biological process activity transformation of single cell gene expression for cross-species alignment.Nat Commun2019
30557523Reply to A. Dalla Volta et al.J Clin Oncol2019
31506093Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.Genome Biol2019
30864317PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction.Pac Symp Biocomput2019
30804427MEK-ERK signaling is a therapeutic target in metastatic castration resistant prostate cancer.Prostate Cancer Prostatic Dis2019
31653878Biological process activity transformation of single cell gene expression for cross-species alignment.Nat Commun2019
31506093Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.Genome Biol2019
30864317PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction.Pac Symp Biocomput2019
30804427MEK-ERK signaling is a therapeutic target in metastatic castration resistant prostate cancer.Prostate Cancer Prostatic Dis2019
29625048Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.Cell2018
30400818Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.Genome Biol2018
30253747Valection: design optimization for validation and verification studies.BMC Bioinformatics2018
30340047Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.Cell2018
30096302Comprehensive Characterization of Cancer Driver Genes and Mutations.Cell2018
29898407Integrated Molecular Characterization of Testicular Germ Cell Tumors.Cell Rep2018
30033370Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.Cell2018
29985747Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study.J Clin Oncol2018
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Collaborators

Christopher K Wong
University of California
Co-authored papers 15
David Haussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 14
Kyle Ellrott
Oregon Health & Science University
Co-authored papers 14
Jiaoti Huang
Duke University School of Medicine
Co-authored papers 13
Adam A Margolin
Icahn School of Medicine
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Evan O Paull
Columbia University Irving Medical Center
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Artem Sokolov
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Yulia Newton
University of California, Santa Cruz Genomics Institute
Co-authored papers 11
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University of California san francisco
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University of California los angeles
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Rogel Cancer Center, University of Michigan ann arbor
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Rahul Aggarwal
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Felix Y Feng
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Adam Foye
University of California San Francisco
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Andrew D Cherniack
Dana-Farber Cancer Institute
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Peter W Laird
Van Andel Institute
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Martin E Gleave
University of British Columbia
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Tomasz M Beer
OHSU Knight Cancer Institute, Oregon Health & Science University
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Matthew B Rettig
David Geffen School of Medicine, University of California los angeles
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Theodore C Goldstein
Bakar Computational Health Sciences Institute, University of California san francisco
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Rehan Akbani
The University of Texas MD Anderson Cancer Center
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Daniel E Carlin
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Sam Ng
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Release 1.2