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Benjamin D. Greenbaum, Ph.D. - Publications

Affiliations: 
2006 Physics Columbia University, New York, NY 
 2020- Computational Oncology Memorial Sloan Kettering Cancer, New York, NY, United States 
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50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Boeke JD, Burns KH, Chiappinelli KB, Classon M, Coffin JM, DeCarvalho DD, Dukes JD, Greenbaum B, Kassiotis G, Knutson SK, Levine AJ, Nath A, Papa S, Rios D, Sedivy J, et al. Proceedings of the inaugural Dark Genome Symposium: November 2022. Mobile Dna. 14: 18. PMID 37990347 DOI: 10.1186/s13100-023-00306-5  0.352
2022 Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, ... ... Greenbaum BD, et al. Author Correction: Fundamental immune-oncogenicity trade-offs define driver mutation fitness. Nature. PMID 35641605 DOI: 10.1038/s41586-022-04879-8  0.431
2022 Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamundi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, ... ... Greenbaum BD, et al. Fundamental immune-oncogenicity trade-offs define driver mutation fitness. Nature. PMID 35545680 DOI: 10.1038/s41586-022-04696-z  0.464
2022 Hoyos D, Greenbaum B, Levine AJ. The genotypes and phenotypes of missense mutations in the proline domain of the p53 protein. Cell Death and Differentiation. 29: 938-945. PMID 35383292 DOI: 10.1038/s41418-022-00980-7  0.417
2020 Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, ... ... Greenbaum BD, et al. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell. PMID 32559462 DOI: 10.1016/J.Cell.2020.05.035  0.437
2020 Roudko V, Greenbaum B, Bhardwaj N. Computational Prediction and Validation of Tumor-Associated Neoantigens. Frontiers in Immunology. 11: 27. PMID 32117226 DOI: 10.3389/Fimmu.2020.00027  0.44
2020 Porter RL, Szabolcs A, Desai N, Thapar V, Mohan R, Solovyov A, Pepin D, Liu J, Greenbaum B, Ting DT. Abstract A66: Repeatome profiling in high-grade serous ovarian cancer reveals abundant repeat noncoding RNA expression Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Ovca19-A66  0.449
2019 Perumal D, Imai N, Laganà A, Finnigan J, Melnekoff D, Leshchenko VV, Solovyov A, Madduri D, Chari A, Cho HJ, Dudley JT, Brody JD, Jagannath S, Greenbaum B, Gnjatic S, et al. Mutation-derived Neoantigen-specific T-cell Responses in Multiple Myeloma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 31857430 DOI: 10.1158/1078-0432.Ccr-19-2309  0.42
2019 Nogalski MT, Solovyov A, Kulkarni AS, Desai N, Oberstein A, Levine AJ, Ting DT, Shenk T, Greenbaum BD. A tumor-specific endogenous repetitive element is induced by herpesviruses. Nature Communications. 10: 90. PMID 30626867 DOI: 10.1038/S41467-018-07944-X  0.544
2019 Luksza M, Leung JP, Solovyov A, Redmond D, Merad M, Gnjatic S, Iacubuzio-Donohue C, DeMatteo RP, Chan TA, Wolchock J, Leach SD, Greenbaum BD, Merghoub T, Balachandran VP. Abstract IA34: Mapping immune recognition of non-self neoantigens in human pancreatic cancer Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-Ia34  0.434
2019 Luksza M, Solovyov A, Vabret N, Balachandran V, Riaz N, Makarov V, Hellmann MD, Snyder A, Funt S, Remark R, Merad M, Gnjatic S, Bajorin DF, Rosenberg J, Leach S, ... ... Greenbaum BD, et al. Abstract IA31: Measuring the emergence of non-self in tumors Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-Ia31  0.447
2018 Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sánchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, ... ... Greenbaum B, et al. Influenza virus infection causes global RNAPII termination defects. Nature Structural & Molecular Biology. PMID 30177761 DOI: 10.1038/S41594-018-0124-7  0.428
2018 Kyi C, Roudko V, Sabado R, Saenger YM, Loging W, Mandeli J, Donovan M, Lehrer D, Posner MR, Misiukiewicz K, Greenbaum B, Salazar AM, Friedlander P, Bhardwaj N. Therapeutic Immune Modulation Against Solid Cancers with Intratumoral Poly-ICLC: A Pilot Trial. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 29950349 DOI: 10.1158/1078-0432.Ccr-17-1866  0.312
2018 Solovyov A, Vabret N, Arora KS, Snyder A, Funt SA, Bajorin DF, Rosenberg JE, Bhardwaj N, Ting DT, Greenbaum BD. Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes. Cell Reports. 23: 512-521. PMID 29642008 DOI: 10.1016/J.Celrep.2018.03.042  0.45
2017 Balachandran VP, Łuksza M, Zhao JN, Makarov V, Moral JA, Remark R, Herbst B, Askan G, Bhanot U, Senbabaoglu Y, Wells DK, Cary CIO, Grbovic-Huezo O, Attiyeh M, Medina B, ... ... Greenbaum BD, et al. Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer. Nature. PMID 29132146 DOI: 10.1038/Nature24462  0.496
2017 Łuksza M, Riaz N, Makarov V, Balachandran VP, Hellmann MD, Solovyov A, Rizvi NA, Merghoub T, Levine AJ, Chan TA, Wolchok JD, Greenbaum BD. A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy. Nature. PMID 29132144 DOI: 10.1038/Nature24473  0.524
2017 Johnson KEE, Song T, Greenbaum B, Ghedin E. Getting the flu: 5 key facts about influenza virus evolution. Plos Pathogens. 13: e1006450. PMID 28837690 DOI: 10.1371/Journal.Ppat.1006450  0.403
2017 Sobel Leonard A, Weissman D, Greenbaum B, Ghedin E, Koelle K. Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus. Journal of Virology. PMID 28468874 DOI: 10.1128/Jvi.00171-17  0.302
2017 Desai N, Sajed D, Arora KS, Solovyov A, Rajurkar M, Bledsoe JR, Sil S, Amri R, Tai E, MacKenzie OC, Mino-Kenudson M, Aryee MJ, Ferrone CR, Berger DL, Rivera MN, ... Greenbaum BD, et al. Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer. Jci Insight. 2: e91078. PMID 28194445 DOI: 10.1172/Jci.Insight.91078  0.424
2017 Greenbaum BD. Innate immune driven evolution via immunostimulatory RNA: Viruses that mimic hosts, tumors that mimic viruses Current Opinion in Systems Biology. 1: 137-142. DOI: 10.1016/J.Coisb.2016.12.008  0.463
2016 Vabret N, Bhardwaj N, Greenbaum BD. Sequence-Specific Sensing of Nucleic Acids. Trends in Immunology. PMID 27856145 DOI: 10.1016/J.It.2016.10.006  0.306
2016 Chudnovskiy A, Mortha A, Kana V, Kennard A, Ramirez JD, Rahman A, Remark R, Mogno I, Ng R, Gnjatic S, Amir ED, Solovyov A, Greenbaum B, Clemente J, Faith J, et al. Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome. Cell. 167: 444-456.e14. PMID 27716507 DOI: 10.1016/J.Cell.2016.08.076  0.306
2016 Lehmann J, Libchaber A, Greenbaum BD. Fundamental amino acid mass distributions and entropy costs in proteomes. Journal of Theoretical Biology. PMID 27544420 DOI: 10.1016/J.Jtbi.2016.08.011  0.51
2016 Levine AJ, Ting DT, Greenbaum BD. P53 and the defenses against genome instability caused by transposons and repetitive elements. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 27172878 DOI: 10.1002/Bies.201600031  0.505
2016 Kumar N, Bera BC, Greenbaum BD, Bhatia S, Sood R, Selvaraj P, Anand T, Tripathi BN, Virmani N. Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses. Plos One. 11: e0154376. PMID 27119730 DOI: 10.1371/Journal.Pone.0154376  0.438
2016 Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs DH, Hamilton J, Leon PE, Chawdury A, Tripathi S, ... ... Greenbaum B, et al. Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection. Immunity. 44: 46-58. PMID 26789921 DOI: 10.1016/J.Immuni.2015.12.017  0.407
2016 Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, et al. Quantifying influenza virus diversity and transmission in humans. Nature Genetics. PMID 26727660 DOI: 10.1038/Ng.3479  0.407
2016 Tanne A, Muniz L, Ting D, Levine A, Bhardwaj N, Greenbaum B. Abstract A077: Unraveling predicted immunomodulatory effects of novel cancer-associated noncoding RNAs Cancer Immunology Research. 4. DOI: 10.1158/2326-6074.Cricimteatiaacr15-A077  0.578
2016 Solovyov A, Tanne A, Muniz L, Cocco S, Monasson R, Levine A, Ting DT, Bhardwaj N, Greenbaum B. Abstract A087: Quantifying the landscape of immunostimulatory tumoral RNA Cancer Immunology Research. 4. DOI: 10.1158/2326-6066.Imm2016-A087  0.544
2016 Solovyov A, Tanne A, Ting D, Levine A, Bhardwaj N, Greenbaum B. Abstract 531: The landscape of immunostimulatory RNA transcription Cancer Research. 76: 531-531. DOI: 10.1158/1538-7445.Am2016-531  0.569
2016 Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs D, Hamilton J, Leon PE, Chawdury A, Tripathi S, ... ... Greenbaum B, et al. Corrections to Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection. (Immunity 44, 46-58, January 19, 2016) Immunity. 44: 438. DOI: 10.1016/J.Immuni.2016.01.016  0.318
2015 Tanne A, Muniz LR, Puzio-Kuter A, Leonova KI, Gudkov AV, Ting DT, Monasson R, Cocco S, Levine AJ, Bhardwaj N, Greenbaum BD. Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 26575629 DOI: 10.1073/Pnas.1517584112  0.511
2015 Greenbaum BD, Ghedin E. Viral evolution: beyond drift and shift. Current Opinion in Microbiology. 26: 109-15. PMID 26189048 DOI: 10.1016/J.Mib.2015.06.015  0.311
2015 Rogers MB, Song T, Sebra R, Greenbaum BD, Hamelin ME, Fitch A, Twaddle A, Cui L, Holmes EC, Boivin G, Ghedin E. Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection. Mbio. 6. PMID 25852163 DOI: 10.1128/Mbio.02464-14  0.341
2015 Tanne AJ, Muniz LR, Ting DT, Solovyov AV, Levine A, Greenbaum B, Bhardwaj N. Unraveling predicted immunomodulatory effects of novel cancer-associated non-coding RNAs Journal For Immunotherapy of Cancer. 3: P396. DOI: 10.1186/2051-1426-3-S2-P396  0.511
2014 Greenbaum BD, Kumar P, Libchaber A. Using first passage statistics to extract environmentally dependent amino acid correlations. Plos One. 9: e101665. PMID 25000191 DOI: 10.1371/Journal.Pone.0101665  0.516
2014 Greenbaum BD, Cocco S, Levine AJ, Monasson R. Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses. Proceedings of the National Academy of Sciences of the United States of America. 111: 5054-9. PMID 24639520 DOI: 10.1073/Pnas.1402285111  0.462
2014 Szpara ML, Gatherer D, Ochoa A, Greenbaum B, Dolan A, Bowden RJ, Enquist LW, Legendre M, Davison AJ. Evolution and diversity in human herpes simplex virus genomes. Journal of Virology. 88: 1209-27. PMID 24227835 DOI: 10.1128/Jvi.01987-13  0.312
2013 Chin AW, Greenbaum BD, Li OT, Webby RJ, Poon LL. A statistical strategy to identify recombinant viral ribonucleoprotein of avian, human, and swine influenza A viruses with elevated polymerase activity. Influenza and Other Respiratory Viruses. 7: 969-78. PMID 23634764 DOI: 10.1111/Irv.12117  0.31
2012 Levine AJ, Greenbaum B. The maintenance of epigenetic states by p53: the guardian of the epigenome. Oncotarget. 3: 1503-4. PMID 23237909 DOI: 10.18632/Oncotarget.780  0.449
2012 Greenbaum BD, Li OT, Poon LL, Levine AJ, Rabadan R. Viral reassortment as an information exchange between viral segments. Proceedings of the National Academy of Sciences of the United States of America. 109: 3341-6. PMID 22331898 DOI: 10.1073/Pnas.1113300109  0.442
2011 Jimenez-Baranda S, Greenbaum B, Manches O, Handler J, Rabadán R, Levine A, Bhardwaj N. Oligonucleotide motifs that disappear during the evolution of influenza virus in humans increase alpha interferon secretion by plasmacytoid dendritic cells. Journal of Virology. 85: 3893-904. PMID 21307198 DOI: 10.1128/Jvi.01908-10  0.498
2010 Solovyov A, Greenbaum B, Palacios G, Lipkin WI, Rabadan R. Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza. Plos Currents. 2: RRN1147. PMID 20126278 DOI: 10.1371/Currents.Rrn1147  0.323
2009 Greenbaum BD, Rabadan R, Levine AJ. Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. Plos One. 4: e5969. PMID 19536338 DOI: 10.1371/Journal.Pone.0005969  0.494
2008 Greenbaum BD, Levine AJ, Bhanot G, Rabadan R. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. Plos Pathogens. 4: e1000079. PMID 18535658 DOI: 10.1371/Journal.Ppat.1000079  0.496
2007 Greenbaum BD, Habib S, Shizume K, Sundaram B. Semiclassics of the chaotic quantum-classical transition. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 046215. PMID 17995090 DOI: 10.1103/Physreve.76.046215  0.719
2007 Greenbaum BD, Jacobs K, Sundaram B. Conditions for the quantum-to-classical transition: trajectories versus phase-space distributions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 036213. PMID 17930329 DOI: 10.1103/Physreve.76.036213  0.696
2005 Greenbaum BD, Habib S, Shizume K, Sundaram B. The semiclassical regime of the chaotic quantum-classical transition. Chaos (Woodbury, N.Y.). 15: 33302. PMID 16252988 DOI: 10.1063/1.1979227  0.717
2005 Habib S, Bhattacharya T, Greenbaum B, Jacobs K, Shizume K, Sundaram B. Chaos and quantum mechanics. Annals of the New York Academy of Sciences. 1045: 308-32. PMID 15980320 DOI: 10.1196/Annals.1350.026  0.732
2003 Pattanayak AK, Sundaram B, Greenbaum BD. Parameter scaling in the decoherent quantum-classical transition for chaotic systems. Physical Review Letters. 90: 014103. PMID 12570616 DOI: 10.1103/Physrevlett.90.014103  0.624
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