Author

B. D. Greenbaum

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 5 Evolutionary Biology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 6 Organism:human· 6 Approach:statistical model· 5 Assay:bulk RNA-seq· 4 Research Focus:differential expression· 3 Assay:whole-genome sequencing· 3 Research Focus:cancer & tumor microenvironment· 2 Research Focus:drug response / drug discovery· 2

Frequent Co-Authors

A. Solovyov· 3 shared D. Hoyos· 2 shared D. T. Ting· 2 shared N. Vabret· 2 shared S. Sun· 2 shared A. Chow· 1 shared A. D. Gioacchino· 1 shared A. Di Gioacchino· 1 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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3 shared papersCancer Biology

A. Solovyov

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Deciphering the code of viral-host adaptation through maximum entropy models

A. Di Gioacchino, B. D. Greenbaum, R. Monasson, S. Cocco

This paper introduces a method to decode host and viral family fingerprints in nucleotide usage, showing it outperforms deep learning for classification and enables manipulation of nucleotide composition in viral sequences.

bioRxiv · Oct 28, 2023 · PreprintEvolutionary Biology

Interferon response and epigenetic modulation by SMARCA4 mutations drive ovarian tumor immunogenicity

M. N. Brodeur, H. Dopeso, Y. Zhu, A. L. F. Longhini, A. Gazzo, S. Sun, R. Koche, R. Qu, P.-J. Hamard, Y. Bykov, H. Green, K. B. Chiappinelli, M. A. Ozsoy, T. Basili, R. Gardner, , D. Zamarin

This study shows that SMARCA4 mutations in ovarian cancer increase immunogenicity through interferon response and epigenetic changes, enhancing T cell and NK cell activity in the tumor microenvironment.

bioRxiv · Aug 8, 2023 · PreprintCancer Biology

Cancer cells co-evolve with retrotransposons to mitigate viral mimicry

S. Sun, J. Hong, E. You, K. M. Tsanov, J. Chacon-Barahona, A. D. Gioacchino, D. Hoyos, H. Li, H. Jiang, H. Ly, S. A. Marhon, R. Murali, P. Chanda, A. Karacay, N. Vabret, , B. D. Greenbaum

This study shows pancreatic tumors co-evolve with retrotransposons to modulate immune responses by regulating viral mimicry through SINEs and L1 retrotransposition.

bioRxiv · May 19, 2023 · PreprintCancer Biology

Mechanism-guided quantification of LINE-1 reveals p53 regulation of both retrotransposition and transcription

A. Solovyov, J. M. Behr, D. Hoyos, E. M. Banks, A. W. Drong, J. Z. Zhong, E. Garcia-Rivera, W. McKerrow, C. Chu, D. M. Zaller, M. Fromer, B. D. Greenbaum

This study quantifies LINE-1 retrotransposition and expression in cancer, showing TP53 mutations enable retrotransposition by disinhibiting L1 expression and enabling reintegration.

bioRxiv · May 11, 2023 · PreprintCancer Biology

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer

D. Memon, H. Rizvi, G. Fromm, J. Lihm, A. J. Schoenfeld, J. L. Sauter, J. Luo, A. Chow, U. K. Bhanot, C. McCarthy, D. Ye, C. M. Vanderbilt, C. Liu, M. Abu-Akeel, A. J. Plodkowski, , M. D. Hellmann

This study characterizes clinical and molecular features of acquired resistance to PD-(L)1 blockade in NSCLC, identifying persistent inflammation and dysfunctional IFN signaling as key features.

bioRxiv · Jul 21, 2021Cancer Biology

Discovery Of UFO Proteins: Human-Virus Chimeric Proteins Generated During Influenza Virus Infection

Y. Ma, M. Angel, G. Wang, J. S. Y. Ho, N. Zhao, J. Noel, N. Moshkina, J. Gibbs, J. Wei, B. Rosenberg, J. Johnson, M. Chang, Z. Peralta, N. Krogan, C. Benner, , I. Marazzi

The paper identifies host-virus chimeric proteins, called UFOs, generated during influenza virus infection through the translation of viral 5UTRs using host transcripts.

bioRxiv · Apr 8, 2019 · PreprintMicrobiology

Global Cancer Transcriptome Quantifies Repeat Element Polarization Between Immunotherapy Responsive and T cell Suppressive Classes

A. Solovyov, N. Vabret, K. S. Arora, A. Snyder, S. A. Funt, D. F. Bajorin, J. E. Rosenberg, N. Bhardwaj, D. T. Ting, B. D. Greenbaum

The paper quantifies repeat element polarization in cancer transcriptomes to identify biomarkers for immunotherapy response and tumor microenvironment immunosuppression.

bioRxiv · Jun 4, 2017Cancer Biology