Publications by authors named "Jason Greenbaum"

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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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Peptide-driven identification of TCRs reveals dynamics and phenotypes of CD4 T cells in tuberculosis.
Rashmi Tippalagama, Raphael Trevizani, Leila Y Chihab, Ashu Chawla, Kai Fung, Jason Greenbaum

J Immunol· November 2025

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Enrichment of a CD4 CD8 NK-like cytotoxic Vδ1/3 T cell subset in tuberculosis disease.
Kendall Kearns, Rashmi Tippalagama, Ashu Chawla, Jason Greenbaum, Aruna Dharshan De Silva

bioRxiv· November 2025

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NetMHCpan-4.2: improved prediction of CD8+ epitopes by use of transfer learning and structural features.
Jonas Birkelund Nilsson, Jason Greenbaum, Bjoern Peters, Morten Nielsen

Front Immunol· August 2025

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Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis.
Rashmi Tippalagama, Raphael Trevizani, Leila Y Chihab, Ashu Chawla, Kai Fung, Jason Greenbaum

bioRxiv· May 2025

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Comparative performance analysis of neoepitope prediction algorithms in head and neck cancer.
Leila Y Chihab, Julie G Burel, Aaron M Miller, Luise Westernberg, Brandee Brown, Jason Greenbaum

Front Immunol· March 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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The Immune Epitope Database (IEDB): 2024 update.
Randi Vita, Nina Blazeska, Daniel Marrama, , Sebastian Duesing, Jason Greenbaum

Nucleic Acids Res· January 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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A functional identification platform reveals frequent, spontaneous neoantigen-specific T cell responses in patients with cancer.
Aaron M Miller, Zeynep Koşaloğlu-Yalçın, Luise Westernberg, Leslie Montero, Milad Bahmanof, Jason Greenbaum

Sci Transl Med· February 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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Transcriptomes and metabolism define mouse and human MAIT cell populations.
Shilpi Chandra, Gabriel Ascui, Thomas Riffelmacher, Ashu Chawla, Ciro Ramírez-Suástegui, Jason Greenbaum

Sci Immunol· November 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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IEDB-3D 2.0: Structural data analysis within the Immune Epitope Database.
Marcus Mendes, Jarjapu Mahita, Nina Blazeska, Jason Greenbaum, Brendan Ha

Protein Sci· April 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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Predicting the Success of Fmoc-Based Peptide Synthesis.
Ilanit Gutman, Ron Gutman, John Sidney, Leila Chihab, Michele Mishto, Jason Greenbaum

ACS Omega· July 2022

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