Publications by authors named "Kyle Ellrott"

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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

April 2020

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Robust software development practices improve citations of RNA-seq tools.
Sanskruti Sharma, Ecem Ilgun, Tuna Okcu, Vladyslav Ostash, Vitalina Bashynska, Kyle Ellrott

bioRxiv· September 2025

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A decentralized future for the open-science databases.
Gaurav Sharma, Viorel Munteanu, Nika Mansouri Ghiasi, Jineta Banerjee, Susheel Varma, Kyle Ellrott

ArXiv· September 2025

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Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles.
Bhavneet Bhinder, Verena Friedl, Sunantha Sethuraman, Davide Risso, Kami E Chiotti, Kyle P Ellrott

Sci Rep· July 2025

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Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods.
Bahar Tercan, Victor H Apolonio, Vinicius S Chagas, Christopher K Wong, Jordan A Lee, Kyle Ellrott

STAR Protoc· June 2025

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Protocol for obtaining cancer type and subtype predictions using subSCOPE.
Jasleen K Grewal, A Gordon Robertson, Kyle Ellrott, Christopher K Wong, Jordan A Lee

STAR Protoc· June 2025

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Aggregating multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal.
Raphael Kirchgaessner, Kaya Keutler, Layaa Sivakumar, Xubo Song, Kyle Ellrott

bioRxiv· May 2025

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Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.
Adriana Salcedo, Maxime Tarabichi, Alex Buchanan, Shadrielle M G Espiritu, Hongjiu Zhang, Kyle Ellrott

Nat Biotechnol· April 2025

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Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.
Kyle Ellrott, Christopher K Wong, Christina Yau, Mauro A A Castro, Jordan A Lee

Cancer Cell· February 2025

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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, Kyle Ellrott

Genome Biol· December 2024

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The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution.
Alexander Kanitz, Matthew H McLoughlin, Liam Beckman, , Venkat S Malladi, Kyle Ellrott

Comput Sci Eng· June 2024

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recountmethylation enables flexible analysis of public blood DNA methylation array data.
Sean K Maden, Brian Walsh, Kyle Ellrott, Kasper D Hansen, Reid F Thompson

Bioinform Adv· February 2023

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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, Kyle Ellrott

Cell Genom· January 2022

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GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Heidi L Rehm, Angela J H Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Kyle P Ellrott

Cell Genom· November 2021

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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, Kyle Ellrott

Cell Syst· August 2021

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Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Kyle Ellrott

Nat Commun· November 2020

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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Kyle Ellrott

Nat Commun· September 2020

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neoepiscope improves neoepitope prediction with multivariant phasing.
Mary A Wood, Austin Nguyen, Adam J Struck, Kyle Ellrott, Abhinav Nellore

Bioinformatics· February 2020

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Exploring Integrative Analysis Using the BioMedical Evidence Graph.
Adam Struck, Brian Walsh, Alexander Buchanan, Jordan A Lee, Ryan Spangler, Kyle Ellrott

JCO Clin Cancer Inform· February 2020

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A community effort to create standards for evaluating tumor subclonal reconstruction.
Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, Amit G Deshwar, Matei David, Kyle Ellrott

Nat Biotechnol· January 2020

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Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.
Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter

Genome Biol· September 2019

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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
Anna Y Lee, Adam D Ewing, Kyle Ellrott, Yin Hu, Kathleen E Houlahan

Genome Biol· November 2018

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Valection: design optimization for validation and verification studies.
Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P'ng, Kyle Ellrott

BMC Bioinformatics· September 2018

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Population-level distribution and putative immunogenicity of cancer neoepitopes.
Mary A Wood, Mayur Paralkar, Mihir P Paralkar, Austin Nguyen, Adam J Struck, Kyle Ellrott

BMC Cancer· April 2018

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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.
Kyle Ellrott, Matthew H Bailey, Gordon Saksena, Kyle R Covington, Cyriac Kandoth

Cell Syst· March 2018

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