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All papers authored by Joshua Stuart

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2022 Nathan D. Maulding, Spencer Seiler, Alexander Pearson, Nicholas Kreusser, Joshua M. Stuart

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Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression

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2021 Hongxu Ding

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, Ioannis Anastopoulos

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, Andrew D. Bailey

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, Joshua Stuart

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, Benedict Paten

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Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

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Lucas Seninge, Ioannis Anastopoulos

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ORCID

, Joshua Stuart

ORCID

VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics

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Ioannis Anastopoulos, Lucas Seninge, Hongxu Ding, Joshua Stuart

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Patient Informed Domain Adaptation Improves Clinical Drug Response Prediction

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Vladislav Uzunangelov

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, Christopher K. Wong, Joshua M. Stuart

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Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge

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Jian Carrot-Zhang

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, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande

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, Jeffrey S. Damrauer

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, Tiago Chedraoui Silva, Christopher K. Wong

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, Hyo Young Choi

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, Ina Felau, A. Gordon Robertson

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, A. Gordon Robertson, Mauro A. A. Castro

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, Lisui Bao, Esther Rheinbay, Eric Minwei Liu and 70 other authors

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway

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2020 Lucas Seninge, Ioannis Anastopoulos, Hongxu Ding, Joshua Stuart

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Biological network-inspired interpretable variational autoencoder

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Matthew A. Reyna, Ken Chen, Mark P. Hamilton, Lieven P. C. Verbeke, Jaegil Kim, Jong K. Kim, Youngwook Kim, Sushant Kumar, Donghoon Lee, Shantao Li, Xiaotong Li, Ziao Lin, Eric Minwei Liu, Miguel Vazquez, William Meyerson and 1324 other authors

Pathway and network analysis of more than 2500 whole cancer genomes

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Irfan S. Kathiriya, Reuben Thomas, Lauren K. Wasson, Tatyana Sukonnik, Kavitha S. Rao, Giovanni Iacono, W. Patrick Devine, Andrew P. Blair, Swetansu K. Hota, Michael H. Lai, Bayardo I. Garay, Henry Z. Gong, Piyush Goyal, Kevin M. Hu, Gunes A. Akgun and 12 other authors

Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease

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Xiangnan Guan, Duanchen Sun, Eric Lu, Joshua A. Urrutia

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, Robert Evan Reiter, Matthew Rettig

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, Christopher P. Evans, Primo Lara, Martin Gleave, Tomasz M. Beer

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, George V. Thomas, Jiaoti Huang, Rahul R. Aggarwal, David A. Quigley, Adam Foye and 8 other authors

Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer

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Joshua Stuart

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Highly Accurate Cancer Phenotype Prediction with AKLIMATE, a Stacked Kernel Learner Integrating Multimodal Genomic Data and Pathway Knowledge

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Daniel H. Kwon, Li Zhang

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, David A. Quigley, Adam Foye, William S. Chen, Christopher K. Wong, Felix Y. Feng, Adina Bailey, Jiaoti Huang, Joshua M. Stuart

ORCID

, Verena Friedl, Alana S. Weinstein, Tomasz M. Beer, Joshi J. Alumkal, Matthew Rettig and 7 other authors

Down-regulation of ADRB2 expression is associated with small cell neuroendocrine prostate cancer and adverse clinical outcomes in castration-resistant prostate cancer

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Joshi J. Alumkal, Duanchen Sun

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, Eric Lu, Tomasz M. Beer, George V. Thomas, Emile Latour

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, Rahul Aggarwal, Jeremy Cetnar, Charles J. Ryan, Shaadi Tabatabaei, Shawna Bailey, Claire B. Turina, David A. Quigley, Xiangnan Guan, Adam Foye and 16 other authors

Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance

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Jian Carrot-Zhang, Nyasha Chambwe, Jeffrey S. Damrauer, Theo A. Knijnenburg, A. Gordon Robertson, Christina Yau, Wanding Zhou, Ashton C. Berger, Kuan-Lin Huang, Justin Y. Newberg, R. Jay Mashl, Alessandro Romanel, Rosalyn W. Sayaman, Francesca Demichelis, Ina Felau and 28 other authors

Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

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Rahul Aggarwal, Gustavo Rubio Romero, Verena Friedl

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, Alana Weinstein

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, Adam Foye, Jiaoti Huang, Felix Feng, Joshua M. Stuart

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, Eric J. Small

Clinical and genomic characterization of Low PSA Secretors: a unique subset of metastatic castration resistant prostate cancer

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Eric Jay Small, Alana Weinstein, George V. Thomas, Lawrence D. True, Rahul Raj Aggarwal, Verena Friedl, Adam Foye, Tomasz M. Beer, Matthew Rettig, Martin Gleave, Christopher P. Evans, Joshi J. Alumkal, Robert Evan Reiter, Primo Lara, Kim N. Chi and 4 other authors

Intermediate atypical carcinoma (IAC): A discrete subtype of metastatic castration-resistant prostate cancer (mCRPC) suggesting that treatment-associated small cell/neuroendocrine prostate cancer (t-SCNC) may evolve from mCRPC adenocarcinoma (adeno)—Results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).

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This paper was not found in any repository; the policy of its publisher is unknown or unclear.

Joshua Stuart

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Abstract P3-08-20: The normal breast Active transcriptome associated with future breast cancer risk is driven by a dysregulated adipocyte microenvironment

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This paper was not found in any repository; the policy of its publisher is unknown or unclear.

Joshua Stuart

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Pan-cancer analysis of whole genomes

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Adam Struck, Brian Walsh, Alexander Buchanan, Jordan A. Lee, Ryan Spangler, Joshua M. Stuart

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, Kyle Ellrott

Exploring Integrative Analysis Using the BioMedical Evidence Graph

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2019 David Haan, Ruikang Tao, Christopher K. Wong, Alana S. Weinstein, Verena Friedl, Ioannis N. Anastopoulos, Joshua M. Stuart

ORCID

Using Transcriptional Signatures to Find Cancer Drivers with LURE

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