Publications by authors named "Jason A Greenbaum"

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Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals.
Alba Grifoni, Daniela Weiskopf, Sydney I Ramirez, Jose Mateus, Jennifer M Dan, Carolyn Rydyznski Moderbacher, Stephen A Rawlings, Aaron Sutherland, Lakshmanane Premkumar, Ramesh S Jadi

June 2020

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Symptomatic SARS-CoV-2 breakthrough infections broaden the repertoire of Spike-reactive CD4 T cells.
Emil Johansson, Yeji Lee, Vicente Fajardo-Rosas, Adam Abawi, Ashmitaa Logandha Ramamoorthy Premlal, Jason A Greenbaum

mBio· December 2025

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Putting computational models of immunity to the test-An invited challenge to predict B.pertussis vaccination responses.
Pramod Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Jason A Greenbaum

PLoS Comput Biol· March 2025

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Putting computational models of immunity to the test - an invited challenge to predict vaccination outcomes.
Pramod Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Jason A Greenbaum

bioRxiv· September 2024

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Next-generation IEDB tools: a platform for epitope prediction and analysis.
Zhen Yan, Kevin Kim, Haeuk Kim, Brendan Ha, Anaïs Gambiez, Jason A Greenbaum

Nucleic Acids Res· July 2024

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The receiver operating characteristic curve accurately assesses imbalanced datasets.
Eve Richardson, Raphael Trevizani, Jason A Greenbaum, Hannah Carter, Morten Nielsen

Patterns (N Y)· June 2024

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Intra-tumoral T cells in pediatric brain tumors display clonal expansion and effector properties.
Aditi Upadhye, Kevin E Meza Landeros, Ciro Ramírez-Suástegui, Benjamin J Schmiedel, Edwin Woo, Jason A Greenbaum

Nat Cancer· May 2024

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A multi-omics systems vaccinology resource to develop and test computational models of immunity.
Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Jason A Greenbaum

Cell Rep Methods· March 2024

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Late-rising CD4 T cells resolve mouse cytomegalovirus persistent replication in the salivary gland.
Simon Brunel, Gaelle Picarda, Ankan Gupta, Raima Ghosh, Bryan McDonald, Jason A Greenbaum

PLoS Pathog· January 2024

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PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.
Daniel Marrama, William D Chronister, Luise Westernberg, Randi Vita, Zeynep Koşaloğlu-Yalçın, Jason A Greenbaum

BMC Bioinformatics· December 2023

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Linked CD4+/CD8+ T cell neoantigen vaccination overcomes immune checkpoint blockade resistance and enables tumor regression.
Joseph S Dolina, Joey Lee, Spencer E Brightman, Sara McArdle, Samantha M Hall, Jason A Greenbaum

J Clin Invest· September 2023

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A systems vaccinology resource to develop and test computational models of immunity.
Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Jason A Greenbaum

bioRxiv· August 2023

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Linked CD4 /CD8 T cell neoantigen vaccination overcomes immune checkpoint blockade resistance and enables tumor regression.
Joseph S Dolina, Joey Lee, Spencer E Brightman, Sara McArdle, Samantha M Hall, Jason A Greenbaum

bioRxiv· May 2023

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Coronavirus Immunotherapeutic Consortium Database.
Jarjapu Mahita, Brendan Ha, Anais Gambiez, Sharon L Schendel, Haoyang Li, Jason A Greenbaum

Database (Oxford)· February 2023

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Tumor cells fail to present MHC-II-restricted epitopes derived from oncogenes to CD4+ T cells.
Spencer E Brightman, Martin S Naradikian, Rukman R Thota, Angelica Becker, Leslie Montero, Jason A Greenbaum

JCI Insight· January 2023

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Estimating tissue-specific peptide abundance from public RNA-Seq data.
Angela Frentzen, Jason A Greenbaum, Haeuk Kim, Bjoern Peters, Zeynep Koşaloğlu-Yalçın

Front Genet· January 2023

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Distinguishing cell-cell complexes from dual lineage cells using single-cell transcriptomics is not trivial.
Julie G Burel, Ashu Chawla, Jason A Greenbaum, Bjoern Peters

Cytometry A· July 2022

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A comprehensive analysis of the IEDB MHC class-I automated benchmark.
Raphael Trevizani, Zhen Yan, Jason A Greenbaum, Alessandro Sette, Morten Nielsen

Brief Bioinform· July 2022

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Developmentally distinct CD4 T lineages shape the CD8 T cell response to acute infection.
Joseph S Dolina, Joey Lee, Eugene L Moore, Jennifer L Hope, Donald T Gracias, Jason A Greenbaum

Proc Natl Acad Sci U S A· March 2022

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Towards the prediction of non-peptidic epitopes.
Paul F Zierep, Randi Vita, Nina Blazeska, Aurélien F A Moumbock, Jason A Greenbaum

PLoS Comput Biol· February 2022

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Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants.
Benjamin J Schmiedel, Cristian Gonzalez-Colin, Vicente Fajardo, Job Rocha, Ariel Madrigal, Jason A Greenbaum

Sci Immunol· February 2022

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TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors.
William D Chronister, Austin Crinklaw, Swapnil Mahajan, Randi Vita, Zeynep Koşaloğlu-Yalçın, Jason A Greenbaum

Front Immunol· September 2021

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Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases.
Alison Tarke, John Sidney, Conner K Kidd, Jennifer M Dan, Sydney I Ramirez, Jason A Greenbaum

bioRxiv· December 2020

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A behind-the-scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts.
Nima Salimi, Lindy Edwards, Gabriele Foos, Jason A Greenbaum, Sheridan Martini

Immunology· October 2020

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