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List of works by Joshua M Stuart

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

scientific article published on 3 October 2017

A community effort to create standards for evaluating tumor subclonal reconstruction

scientific article published on 09 January 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Biological process activity transformation of single cell gene expression for cross-species alignment

scientific article published on 25 October 2019

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

scientific article published in April 2018

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

scientific article published on 14 April 2020

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

scientific article published on 06 November 2018

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

scientific article published on 18 May 2015

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Comprehensive Characterization of Cancer Driver Genes and Mutations

scientific article published in April 2018

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Computational Identification of Tumor Anatomic Location Associated with Survival in 2 Large Cohorts of Human Primary Glioblastomas

scientific article published on 7 January 2016

Computational Integration of Homolog and Pathway Gene Module Expression Reveals General Stemness Signatures ⬇️

scientific article published on April 29, 2011

Dual-specificity phosphatases 2: surprising positive effect at the molecular level and a potential biomarker of diseases ⬇️

scientific article published on November 29, 2012

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

scientific article published in April 2018

Global optimization of somatic variant identification in cancer genomes with a global community challenge

scientific article

Inferring causal molecular networks: empirical assessment through a community-based effort

scientific article

Molecular Pathways: Extracting Medical Knowledge from High-Throughput Genomic Data ⬇️

scientific article published on February 21, 2013

ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES

scientific article published on January 2016

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

scientific article

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Pathway and network analysis of more than 2500 whole cancer genomes

scientific article published on 05 February 2020

PharmGKB: the Pharmacogenetics Knowledge Base ⬇️

scientific article published on January 1, 2002

Prophetic Granger Causality to infer gene regulatory networks.

scientific article

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

Toward better benchmarking: challenge-based methods assessment in cancer genomics

scientific article

Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

scientific article published on 11 November 2021

Whole-genome analysis informs breast cancer response to aromatase inhibition

scientific article

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

scientific article published on 2 February 2021

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