Publications by authors named "Jacob Pfeil"

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Pairwise ratio transformation of gene expression data leads to improved checkpoint response prediction in lung cancer patients.
Jacob Pfeil, Liqian Ma, Hin Ching Lo, Tolga Turan, R Tyler McLaughlin

BMC Bioinformatics· December 2025

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A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer.
Mike Mason, Óscar Lapuente-Santana, Anni S Halkola, Wenyu Wang, Raghvendra Mall, Jacob Pfeil

J Transl Med· February 2024

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Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors.
Lauren M Sanders, Rahul Chandra, Navid Zebarjadi, Holly C Beale, A Geoffrey Lyle, Jacob Pfeil

Commun Biol· December 2022

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ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy.
Arjun A Rao, Ada A Madejska, Jacob Pfeil, Benedict Paten, Sofie R Salama

Front Immunol· April 2021

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The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets.
Holly C Beale, Jacquelyn M Roger, Matthew A Cattle, Liam T McKay, Drew K A Thompson, Jacob Pfeil

Gigascience· March 2021

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Identification of a differentiation stall in epithelial mesenchymal transition in histone H3-mutant diffuse midline glioma.
Lauren M Sanders, Allison Cheney, Lucas Seninge, Anouk van den Bout, Marissa Chen, Jacob Pfeil

Gigascience· December 2020

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Complete Response to PD-1 Inhibition in an Adolescent With Relapsed Clear Cell Adenocarcinoma of the Cervix Predicted by Neoepitope Burden and APOBEC Signature.
Anya Levinson, Alex G Lee, Henry J Martell, Marcus R Breese, Charles Zaloudek, Jacob Pfeil

JCO Precis Oncol· November 2020

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Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures.
Jacob Pfeil, Lauren M Sanders, Ioannis Anastopoulos, A Geoffrey Lyle, Alana S Weinstein

PLoS Comput Biol· April 2020

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Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.
Jo Lynne Rokita, Komal S Rathi, Maria F Cardenas, Kristen A Upton, Joy Jayaseelan, Jacob Pfeil

Cell Rep· November 2019

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Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor.
Lauren M Sanders, Arun Rangaswami, Isabel Bjork, Du Linh Lam, Holly C Beale, Jacob Pfeil

Cold Spring Harb Mol Case Stud· October 2019

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Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer.
Olena M Vaske, Isabel Bjork, Sofie R Salama, Holly Beale, Avanthi Tayi Shah, Jacob Pfeil

JAMA Netw Open· October 2019

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Barriers to accessing public cancer genomic data.
Katrina Learned, Ann Durbin, Robert Currie, Ellen Towle Kephart, Holly C Beale, Jacob Pfeil

Sci Data· June 2019

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A Novel Histone Crosstalk Pathway Important for Regulation of UV-Induced DNA Damage Repair in .
Anna L Boudoures, Jacob J Pfeil, Elizabeth M Steenkiste, Rachel A Hoffman, Elizabeth A Bailey

Genetics· July 2017

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Toil enables reproducible, open source, big biomedical data analyses.
John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Jacob Pfeil

Nat Biotechnol· April 2017

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RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.
Jerome Bouquet, Jennifer L Gardy, Scott Brown, Jacob Pfeil, Ruth R Miller

Clin Infect Dis· February 2017

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Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014.
Charles Y Chiu, Vanessa Bres, Guixia Yu, David Krysztof, Samia N Naccache, Jacob Pfeil

Emerg Infect Dis· August 2015

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Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.
Wilson Leung, Christopher D Shaffer, Laura K Reed, Sheryl T Smith, William Barshop, Jacob J Pfeil

G3 (Bethesda)· March 2015

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