Publications by authors named "Benjamin D Greenbaum"

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Repeats mimic pathogen-associated patterns across a vast evolutionary landscape.
Petr Šulc, Andrea Di Gioacchino, Alexander Solovyov, Siyu Sun, Stephen Martis, Benjamin D Greenbaum

Cell Genom· December 2025

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Neoantigenic properties of TP53 variants influence cancer risk in individuals with Li-Fraumeni syndrome.
Emilie Montellier, Olivier Manches, Jonathan Gaucher, Claire Freycon, David Hoyos, Benjamin D Greenbaum

EBioMedicine· December 2025

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T cell epitope mapping reveals immunodominance of evolutionarily conserved regions within SARS-CoV-2 proteome.
Cansu Cimen Bozkus, Matthew Brown, Leandra Velazquez, Marcus Thomas, Eric A Wilson, Benjamin D Greenbaum

iScience· August 2025

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Restoration of the Tumor Suppressor Function of Y220C-Mutant p53 by Rezatapopt, a Small-Molecule Reactivator.
Anna M Puzio-Kuter, Lizhong Xu, Mary Kate McBrayer, Romyr Dominique, Hongju H Li, Benjamin D Greenbaum

Cancer Discov· June 2025

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Mis-splicing-derived neoantigens and cognate TCRs in splicing factor mutant leukemias.
Won Jun Kim, Edie I Crosse, Emma De Neef, Inaki Etxeberria, Erich Y Sabio, Benjamin D Greenbaum

Cell· June 2025

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Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models.
Andrea Di Gioacchino, Ivan Lecce, Benjamin D Greenbaum, Rémi Monasson, Simona Cocco

Mol Biol Evol· June 2025

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LINE-1 ORF1p Mimics Viral Innate Immune Evasion Mechanisms in Pancreatic Ductal Adenocarcinoma.
Eunae You, Bidish K Patel, Alexandra S Rojas, Siyu Sun, Patrick Danaher, Benjamin D Greenbaum

Cancer Discov· May 2025

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T cell epitope mapping reveals immunodominance of evolutionarily conserved regions within SARS-CoV-2 proteome.
Cansu Cimen Bozkus, Matthew Brown, Leandra Velazquez, Marcus Thomas, Eric A Wilson, Benjamin D Greenbaum

bioRxiv· April 2025

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Chronic Viral Mimicry Induction following p53 Loss Promotes Immune Evasion.
Charles A Ishak, Sajid A Marhon, Naïri Tchrakian, Anjelica Hodgson, Helen Loo Yau, Benjamin D Greenbaum

Cancer Discov· April 2025

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An inflammatory biomarker signature of response to CAR-T cell therapy in non-Hodgkin lymphoma.
Sandeep S Raj, Teng Fei, Shalev Fried, Andrew Ip, Joshua A Fein, Benjamin D Greenbaum

Nat Med· April 2025

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Terminal differentiation and persistence of effector regulatory T cells essential for preventing intestinal inflammation.
Stanislav Dikiy, Aazam P Ghelani, Andrew G Levine, Stephen Martis, Paolo Giovanelli, Benjamin D Greenbaum

Nat Immunol· March 2025

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RNA neoantigen vaccines prime long-lived CD8 T cells in pancreatic cancer.
Zachary Sethna, Pablo Guasp, Charlotte Reiche, Martina Milighetti, Nicholas Ceglia, Benjamin D Greenbaum

Nature· March 2025

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Author Correction: Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency.
Alexander Solovyov, Julie M Behr, David Hoyos, Eric Banks, Alexander W Drong, Benjamin D Greenbaum

Nat Commun· March 2025

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Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency.
Alexander Solovyov, Julie M Behr, David Hoyos, Eric Banks, Alexander W Drong, Benjamin D Greenbaum

Nat Commun· February 2025

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Disruption of cellular plasticity by repeat RNAs in human pancreatic cancer.
Eunae You, Patrick Danaher, Chenyue Lu, Siyu Sun, Luli Zou, Benjamin D Greenbaum

Cell· December 2024

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Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms.
Siyu Sun, Eunae You, Jungeui Hong, David Hoyos, Isabella Del Priore, Benjamin D Greenbaum

Immunity· December 2024

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Distinct genomic and immunologic tumor evolution in germline -driven breast cancers.
Nabamita Boruah, David Hoyos, Renyta Moses, Ryan Hausler, Heena Desai, Benjamin D Greenbaum

bioRxiv· April 2024

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Structures, functions and adaptations of the human LINE-1 ORF2 protein.
Eric T Baldwin, Trevor van Eeuwen, David Hoyos, Arthur Zalevsky, Egor P Tchesnokov, Benjamin D Greenbaum

Nature· February 2024

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Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer.
Danish Memon, Adam J Schoenfeld, Darwin Ye, George Fromm, Hira Rizvi, Benjamin D Greenbaum

Cancer Cell· February 2024

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Trade-offs inside the black box of neoantigen prediction.
Ning Yao, Benjamin D Greenbaum

Immunity· November 2023

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Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector.
Nicholas Ceglia, Zachary Sethna, Samuel S Freeman, Florian Uhlitz, Viktoria Bojilova, Benjamin D Greenbaum

Nat Commun· July 2023

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Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse.
Susan DeWolf, Yuval Elhanati, Katherine Nichols, Nicholas R Waters, Chi L Nguyen, Benjamin D Greenbaum

Sci Transl Med· July 2023

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Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer.
Luis A Rojas, Zachary Sethna, Kevin C Soares, Cristina Olcese, Nan Pang, Benjamin D Greenbaum

Nature· June 2023

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Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer.
Arvind Ravi, Matthew D Hellmann, Monica B Arniella, Mark Holton, Samuel S Freeman, Benjamin D Greenbaum

Nat Genet· May 2023

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Cancer cells co-evolve with retrotransposons to mitigate viral mimicry.
Siyu Sun, Jungeui Hong, Eunae You, Kaloyan M Tsanov, Jonathan Chacon-Barahona, Benjamin D Greenbaum

bioRxiv· May 2023

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