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Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets

Summary Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer’s underlying biology, bringing hope …

Kyle Ellrott, Christopher K. Wong, Christina Yau, Mauro A. A. Castro, Jordan A. Lee, Brian J. Karlberg, Jasleen K. Grewal, Vincenzo Lagani, Bahar Tercan, Verena Friedl, Toshinori Hinoue, Vladislav Uzunangelov, Lindsay Westlake, Xavier Loinaz, Ina Felau, Peggy I. Wang, Anab Kemal, Samantha J. Caesar-Johnson, Ilya Shmulevich, Alexander J. Lazar, Ioannis Tsamardinos, Katherine A. Hoadley, A. Gordon Robertson, Theo A. Knijnenburg, Christopher C. Benz, Joshua M. Stuart, Jean C. Zenklusen, Andrew D. Cherniack, Peter W. Laird

SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation for improved cancer subtype predictions

Brian Karlberg, Raphael Kirchgaessner, Jordan Lee, Matthew Peterkort, Liam Beckman, Jeremy Goecks, Kyle Ellrott

The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution

Alexander Kanitz, Matthew H. McLoughlin, Liam Beckman, Venkat S. Malladi, Kyle Ellrott

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Michael C Schatz, Anthony A Philippakis, Enis Afgan, Eric Banks, Vincent J Carey, Robert J Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L Grossman, others

recountmethylation enables flexible analysis of public blood DNA methylation array data

Sean K Maden, Brian Walsh, Kyle Ellrott, Kasper D Hansen, Reid Thompson, Abhinav Nellore

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

Allison Creason, David Haan, Kristen Dang, Kami E Chiotti, Matthew Inkman, Andrew Lamb, Thomas Yu, Yin Hu, Thea C Norman, Alex Buchanan, others

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L Rehm, Angela JH Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Lawrence J Babb, Maxmillian P Barkley, Michael Baudis, Michael JS Beauvais, Tim Beck, others

A community effort to create standards for evaluating tumor subclonal reconstruction

Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, Amit G Deshwar, Matei David, Nathan M Wilson, Stefan Dentro, Jeff A Wintersinger, Lydia Y Liu, Minjeong Ko, others

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

Alex H Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, Kilannin Krysiak, Jordi Deu-Pons, Ryan P Duren, Jianjiong Gao, Julie McMurry, others

Butler enables rapid cloud-based analysis of thousands of human genomes

Sergei Yakneen, Sebastian M Waszak, Michael Gertz, Jan O Korbel