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J

Joshua M. Stuart

University of California System

170H-index
578Paper Count
21.5WCitation Count
Published Papers 78
Publication Date
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Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
errCANCER CELL
IF44.5
err2025-02-01
err4
errOAAI
errEllrot, Kyle; Wong, Christopher K.; Yau, Christina; Castro, Mauro A. A.; Lee, Jordan A.; Karlberg, Brian J.; Grewal, Jasleen K.; Lagani, Vincenzo; Tercan, Bahar; Friedl, Verena; Hinoue, Toshinori; Uzunangelov, Vladislav; Westlake, Lindsay; Loinaz, Xavier; Felau, Ina; Wang, Peggy I.; Kemal, Anab; Caesar-Johnson, Samantha J.; Shmulevich, Ilya; Lazar, Alexander J.; Tsamardinos, Ioannis; Hoadley, Katherine A.; Robertson, A. Gordon; Knijnenburg, Theo A.; Benz, Christopher C.; Stuart, Joshua M.; Zenklusen, Jean C.; Cherniack, Andrew D.; Laird, Peter W.
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errSave
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer
errNPJ SYSTEMS BIOLOGY AND APPLICATIONS
IF3.5
err2025-01-10
err0
errOAAI
errMaulding, Nathan D.; Zou, Jun; Zhou, Wei; Metcalfe, Ciara; Stuart, Joshua M.; Ye, Xin; Hafner, Marc
errShare
errSave
Associating transcription factors to single-cell trajectories with DREAMIT
errGENOME BIOLOGY
IF9.4
err2024-08-14
err0
errOAAI
errMaulding, Nathan D.; Seninge, Lucas; Stuart, Joshua M.
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errSave
Single-cell signatures identify microenvironment factors in tumors associated with patient outcomes
errCELL REPORTS METHODS
IF4.5
err2024-06-01
err0
errOAAI
errXue, Yuanqing; Friedl, Verena; Ding, Hongxu; Wong, Christopher K.; Stuart, Joshua M.
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errSave
The manatee variational autoencoder model for predicting gene expression alterations caused by transcription factor perturbations
errSCIENTIFIC REPORTS
IF3.9
err2024-05-23
err1
errOAAI
errYang, Ying; Seninge, Lucas; Wang, Ziyuan; Oro, Anthony; Stuart, Joshua M.; Ding, Hongxu
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errSave
Pathway and network analysis of more than 2500 whole cancer genomes (vol 11, 729, 2020)
errNATURE COMMUNICATIONS
IF15.7
err2022-12-08
err0
errOAAI
errReyna, Matthew A.; Haan, David; Paczkowska, Marta; Verbeke, Lieven P. C.; Vazquez, Miguel; Kahraman, Abdullah; Pulido-Tamayo, Sergio; Barenboim, Jonathan; Wadi, Lina; Dhingra, Priyanka; Shrestha, Raunak; Getz, Gad; Lawrence, Michael S.; Pedersen, Jakob Skou; Rubin, Mark A.; Wheeler, David A.; Brunak, Sren; Izarzugaza, Jose M. G.; Khurana, Ekta; Marchal, Kathleen; von Mering, Christian; Sahinalp, S. Cenk; Valencia, Alfonso; Reimand, Jueri; Stuart, Joshua M.; Raphael, Benjamin J.
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errSave
A PAN-CANCER MULTI-OMIC IMMUNE SINGLE-CELL ATLAS FOR CANCER IMMUNOTHERAPY: FOCUS ON CD4+T CELLS
errJOURNAL FOR IMMUNOTHERAPY OF CANCER
IF10.6
err2022-11-07
err0
errOAAI
errMok, Lydia; Orlando, Andrea; Lehrer, Julian; Stuart, Joshua; Rudqvist, Nils-Petter; Vincent, Benjamin; Monette, Anne; Senbabaoglu, Yasin; Smith, Kellie; Thomas, Paul; Tschernia, Nicholas; Thorsson, Vesteinn; Zappasodi, Roberta; Jonsson, Vanessa
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errSave
Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity
errNATURE COMMUNICATIONS
IF15.7
err2022-09-15
err21
errOAAI
errWestbrook, Thomas C.; Guan, Xiangnan; Rodansky, Eva; Flores, Diana; Liu, Chia Jen; Udager, Aaron M.; Patel, Radhika A.; Haffner, Michael C.; Hu, Ya-Mei; Sun, Duanchen; Beer, Tomasz M.; Foye, Adam; Aggarwal, Rahul; Quigley, David A.; Youngren, Jack F.; Ryan, Charles J.; Gleave, Martin; Wang, Yuzhuo; Huang, Jiaoti; Coleman, Ilsa; Morrissey, Colm; Nelson, Peter S.; Evans, Christopher P.; Lara, Primo; Reiter, Robert E.; Witte, Owen; Rettig, Matthew; Wong, Christopher K.; Weinstein, Alana S.; Uzunangelov, Vlado; Stuart, Josh M.; Thomas, George, V; Feng, Felix Y.; Small, Eric J.; Yates, Joel A.; Xia, Zheng; Alumkal, Joshi J.
errShare
errSave
Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression
errSCIENTIFIC REPORTS
IF3.9
err2022-01-25
err6
errOAAI
errMaulding, Nathan D.; Seiler, Spencer; Pearson, Alexander; Kreusser, Nicholas; Stuart, Joshua M.
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errSave
Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
errNATURE COMMUNICATIONS
IF15.7
err2021-11-11
err5
errOAAI
errDing, Hongxu; Anastopoulos, Ioannis; Bailey, Andrew D.; Stuart, Joshua; Paten, Benedict
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errSave
VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics
errNATURE COMMUNICATIONS
IF15.7
err2021-09-28
err39
errOAAI
errSeninge, Lucas; Anastopoulos, Ioannis; Ding, Hongxu; Stuart, Joshua
errShare
errSave
Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease
errDEVELOPMENTAL CELL
IF8.7
err2021-02-01
err61
errOAAI
errKathiriya, Irfan S.; Rao, Kavitha S.; Iacono, Giovanni; Devine, W. Patrick; Blair, Andrew P.; Hota, Swetansu K.; Lai, Michael H.; Garay, Bayardo, I; Thomas, Reuben; Gong, Henry Z.; Wasson, Lauren K.; Goyal, Piyush; Sukonnik, Tatyana; Hu, Kevin M.; Akgun, Gunes A.; Bernard, Laure D.; Akerberg, Brynn N.; Gu, Fei; Li, Kai; Speir, Matthew L.; Haeussler, Maximilian; Pu, William T.; Stuart, Joshua M.; Seidman, Christine E.; Seidman, J. G.; Heyn, Holger; Bruneau, Benoit G.
errShare
errSave
Exploring Integrative Analysis Using the BioMedical Evidence Graph
errJCO CLINICAL CANCER INFORMATICS
IF2.8
err2020-11-01
err3
errOAAI
errStruck, Adam; Walsh, Brian; Buchanan, Alexander; Lee, Jordan A.; Spangler, Ryan; Stuart, Joshua M.; Ellrott, Kyle
errShare
errSave
Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer
errCLINICAL CANCER RESEARCH
IF10.2
err2020-09-01
err12
errOAAI
errGuan, Xiangnan; Sun, Duanchen; Lu, Eric; Urrutia, Joshua A.; Reiter, Robert Evan; Rettig, Matthew; Evans, Christopher P.; Lara, Primo, Jr.; Gleave, Martin; Beer, Tomasz M.; Thomas, George, V; Huang, Jiaoti; Aggarwal, Rahul R.; Quigley, David A.; Foye, Adam; Chen, William S.; Youngren, Jack; Weinstein, Alana S.; Stuart, Joshua M.; Feng, Felix Y.; Small, Eric J.; Xia, Zheng; Alumkal, Joshi J.
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errSave
Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2020-05-18
err94
errOAAI
errAlumkal, Joshi J.; Sun, Duanchen; Lu, Eric; Beer, Tomasz M.; Thomas, George V.; Latour, Emile; Aggarwal, Rahul; Cetnar, Jeremy; Ryan, Charles J.; Tabatabaei, Shaadi; Bailey, Shawna; Turina, Claire B.; Quigley, David A.; Guan, Xiangnan; Foye, Adam; Youngren, Jack F.; Urrutia, Joshua; Huang, Jiaoti; Weinstein, Alana S.; Friedl, Verena; Rettig, Matthew; Reiter, Robert E.; Spratt, Daniel E.; Gleave, Martin; Evans, Christopher P.; Stuart, Joshua M.; Chen, Yiyi; Feng, Felix Y.; Small, Eric J.; Witte, Owen N.; Xia, Zheng
errShare
errSave
Clinical and genomic characterization of Low PSA Secretors: a unique subset of metastatic castration resistant prostate cancer
errPROSTATE CANCER AND PROSTATIC DISEASES
IF5.8
err2020-04-14
err17
PREAI
errAggarwal, Rahul; Romero, Gustavo Rubio; Friedl, Verena; Weinstein, Alana; Foye, Adam; Huang Jiaoti; Feng, Felix; Stuart, Joshua M.; Small, Eric J.
errShare
errSave
Pathway and network analysis of more than 2500 whole cancer genomes
errNATURE COMMUNICATIONS
IF15.7
err2020-02-05
err77
errOAAI
errReyna, Matthew A.; Haan, David; Paczkowska, Marta; Verbeke, Lieven P. C.; Vazquez, Miguel; Kahraman, Abdullah; Pulido-Tamayo, Sergio; Barenboim, Jonathan; Wadi, Lina; Dhingra, Priyanka; Shrestha, Raunak; Getz, Gad; Lawrence, Michael S.; Pedersen, Jakob Skou; Rubin, Mark A.; Wheeler, David A.; Brunak, Soren; Izarzugaza, Jose M. G.; Khurana, Ekta; Marchal, Kathleen; von Mering, Christian; Sahinalp, S. Cenk; Valencia, Alfonso; Reimand, Juri; Stuart, Joshua M.; Raphael, Benjamin J.
errShare
errSave
A community effort to create standards for evaluating tumor subclonal reconstruction
errNATURE BIOTECHNOLOGY
IF41.7
err2020-01-09
err53
errOAAI
errSalcedo, Adriana; Tarabichi, Maxime; Espiritu, Shadrielle Melijah G.; Deshwar, Amit G.; David, Matei; Wilson, Nathan M.; Dentro, Stefan; Wintersinger, Jeff A.; Liu, Lydia Y.; Ko, Minjeong; Sivanandan, Srinivasan; Zhang, Hongjiu; Zhu, Kaiyi; Ou Yang, Tai-Hsien; Chilton, John M.; Buchanan, Alex; Lalansingh, Christopher M.; P'ng, Christine; Anghel, Catalina V.; Umar, Imaad; Lo, Bryan; Zou, William; Simpson, Jared T.; Stuart, Joshua M.; Anastassiou, Dimitris; Guan, Yuanfang; Ewing, Adam D.; Ellrott, Kyle; Wedge, David C.; Morris, Quaid; Van Loo, Peter; Boutros, Paul C.; Jha, Alokkumar; Huang, Tanxiao; Yang, Tsun-Po; Peifer, Martin; Sahinalp, Cenk; Malikic, Salem; Vazquez-Garcia, Ignacio; Mustonen, Ville; Yang, Hsih-Te; Lee, Ken-Ray; Ji, Yuan; Sengupta, Subhajit; Rudewicz, Justine; Nikolski, Macha; Schaeverbeke, Quentin; Yuan, Ke; Markowetz, Florian; Macintyre, Geoff; Cmero, Marek; Chaudhary, Belal; Leshchiner, Ignaty; Livitz, Dimitri; Getz, Gad; Loher, Phillipe; Yu, Kaixian; Wang, Wenyi; Zhu, Hongtu
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errSave
Biological process activity transformation of single cell gene expression for cross-species alignment
errNATURE COMMUNICATIONS
IF15.7
err2019-10-25
err26
errOAAI
errDing, Hongxu; Blair, Andrew; Yang, Ying; Stuart, Joshua M.
errShare
errSave
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
errGENOME BIOLOGY
IF9.4
err2019-09-10
err17
errOAAI
errEllrott, Kyle; Buchanan, Alex; Creason, Allison; Mason, Michael; Schaffter, Thomas; Hoff, Bruce; Eddy, James; Chilton, John M.; Yu, Thomas; Stuart, Joshua M.; Saez-Rodriguez, Julio; Stolovitzky, Gustavo; Boutros, Paul C.; Guinney, Justin
errShare
errSave

Research Directions

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Co-authors
Cooperation Journals
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Gad Getz
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Gordon B. Mills
H-index: 231 · Papers: 3.5K
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Matthew Meyerson
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C
Chris Sander
H-index: 191 · Papers: 849
S
Steven J.M. Jones
H-index: 189 · Papers: 1.3K
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