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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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52/113 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
2024 Boruah N, Hoyos D, Moses R, Hausler R, Desai H, Le AN, Good M, Kelly G, Raghavakaimal A, Tayeb M, Narasimhamurthy M, Doucette A, Gabriel P, Feldman MJ, Park J, ... ... Greenbaum BD, et al. Distinct genomic and immunologic tumor evolution in germline driven breast cancers. Biorxiv : the Preprint Server For Biology. PMID 38617260 DOI: 10.1101/2024.04.03.588009  0.349
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  0.351
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  0.436
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  0.441
2020 Parikh AR, Rajurkar M, Van Seventer EE, Gemma AJ, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Hong TS, Wo JY, Corcoran RB, Solovyov A, Greenbaum B, Szabolcs A, Tai EC, et al. Phase II study of lamivudine in p53 mutant metastatic colorectal cancer (mCRC). Journal of Clinical Oncology. 38: 149-149. DOI: 10.1200/Jco.2020.38.4_Suppl.149  0.3
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  0.45
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  0.422
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  0.435
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  0.427
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  0.497
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  0.402
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  0.301
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  0.425
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  0.305
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  0.506
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  0.437
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  0.406
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  0.406
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  0.568
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  0.317
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  0.512
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  0.31
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  0.34
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  0.461
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  0.309
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  0.441
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  0.497
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  0.322
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  0.495
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  0.718
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
Low-probability matches (unlikely to be authored by this person)
2017 Lavin Y, Kobayashi S, Leader A, Amir ED, Elefant N, Bigenwald C, Remark R, Sweeney R, Becker CD, Levine JH, Meinhof K, Chow A, Kim-Shulze S, Wolf A, Medaglia C, ... ... Greenbaum BD, et al. Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses. Cell. 169: 750-765.e17. PMID 28475900 DOI: 10.1016/J.Cell.2017.04.014  0.297
2018 Abbate F, Badal B, Mendelson K, Aydin IT, Serasinghe MN, Iqbal R, Mohammed J, Solovyov A, Greenbaum BD, Chipuk JE, Celebi JT. FBXW7 regulates a mitochondrial transcription program by modulating MITF. Pigment Cell & Melanoma Research. PMID 29665239 DOI: 10.1111/Pcmr.12704  0.296
2020 Chang LW, Iqbal R, Badal B, Bernstein D, Mendelson K, Solovyov A, Friedlander P, Phelps R, Goodheart H, Desman G, Greenbaum BD, Celebi JT. Genomic analysis of metastatic melanoma in an adult with giant congenital melanocytic nevus. Pigment Cell & Melanoma Research. PMID 32096295 DOI: 10.1111/Pcmr.12872  0.296
2009 Trifonov V, Khiabanian H, Greenbaum B, Rabadan R. The origin of the recent swine influenza A(H1N1) virus infecting humans Eurosurveillance. 14: 19193. DOI: 10.2807/Ese.14.17.19193-En  0.295
2017 Marazzi I, Greenbaum BD, Low DHP, Guccione E. Chromatin dependencies in cancer and inflammation. Nature Reviews. Molecular Cell Biology. PMID 29184195 DOI: 10.1038/Nrm.2017.113  0.294
2019 Funt SA, Solovyov A, Faltas BM, Iyer G, Boyd ME, Cipolla CK, Regazzi AM, Teo MY, Lee C, Al-Ahmadie H, Rosenberg JE, Greenbaum B, Bajorin DF. Muscle invasive bladder cancer (MIBC) demonstrates neoadjuvant cisplatin-based chemotherapy (NAC) related changes in molecular subtype and immune infiltration. Journal of Clinical Oncology. 37: 443-443. DOI: 10.1200/Jco.2019.37.7_Suppl.443  0.288
2019 Orfanelli T, Roudko V, Bozkus CC, Greenbaum B, Blank S, Bhardwaj N. Shared tumor antigens in uterine cancers with microsatellite instability: Putative targets for immunotherapeutic approaches Gynecologic Oncology. 154: 91. DOI: 10.1016/J.Ygyno.2019.04.214  0.283
2014 Wagh K, Bhatia A, Greenbaum BD, Bhanot G. Bird to human transmission biases and vaccine escape mutants in H5N1 infections. Plos One. 9: e100754. PMID 24988306 DOI: 10.1371/Journal.Pone.0100754  0.282
2019 Sobel Leonard A, Weissman DB, Greenbaum B, Ghedin E, Koelle K. Correction for Sobel Leonard et al., "Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus". Journal of Virology. 93. PMID 31409730 DOI: 10.1128/Jvi.00936-19  0.282
2017 Aguirre S, Luthra P, Sanchez-Aparicio MT, Maestre AM, Patel J, Lamothe F, Fredericks AC, Tripathi S, Zhu T, Pintado-Silva J, Webb LG, Bernal-Rubio D, Solovyov A, Greenbaum B, Simon V, et al. Dengue virus NS2B protein targets cGAS for degradation and prevents mitochondrial DNA sensing during infection. Nature Microbiology. 2: 17037. PMID 28346446 DOI: 10.1038/Nmicrobiol.2017.37  0.277
2019 Poon LLM, Song T, Wentworth DE, Holmes EC, Greenbaum BD, Peiris JSM, Cowling BJ, Ghedin E. Reply to 'Reconciling disparate estimates of viral genetic diversity during human influenza infections'. Nature Genetics. PMID 31406345 DOI: 10.1038/S41588-019-0486-8  0.272
2020 Vabret N, Britton GJ, Gruber C, Hegde S, Kim J, Kuksin M, Levantovsky R, Malle L, Moreira A, Park MD, Pia L, Risson E, Saffern M, Salomé B, Esai Selvan M, ... ... Greenbaum B, et al. Immunology of COVID-19: Current State of the Science. Immunity. PMID 32505227 DOI: 10.1016/J.Immuni.2020.05.002  0.267
2015 Fernandez MV, Miller E, Krammer F, Gopal R, Greenbaum BD, Bhardwaj N. Ion efflux and influenza infection trigger NLRP3 inflammasome signaling in human dendritic cells. Journal of Leukocyte Biology. PMID 26574023 DOI: 10.1189/Jlb.3A0614-313Rrr  0.266
2023 Sun S, Hong J, You E, Tsanov KM, Chacon-Barahona J, Gioacchino AD, Hoyos D, Li H, Jiang H, Ly H, Marhon S, Murali R, Chanda P, Karacay A, Vabret N, ... ... Greenbaum BD, et al. Cancer cells co-evolve with retrotransposons to mitigate viral mimicry. Biorxiv : the Preprint Server For Biology. PMID 37292765 DOI: 10.1101/2023.05.19.541456  0.262
2020 Bozkus CC, Roudko V, Orfanelli T, Blank S, Greenbaum B, Bhardwaj N. Abstract 5587: Characterization of shared immunogenic frameshift mutations in microsatellite unstable cancers to guide the design of off-the-shelf immunotherapies Immunology. DOI: 10.1158/1538-7445.Am2020-5587  0.262
2017 Chowell D, Morris LGT, Grigg CM, Weber JK, Samstein RM, Makarov V, Kuo F, Kendall SM, Requena D, Riaz N, Greenbaum B, Carroll J, Garon E, Hyman DM, Zehir A, et al. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science (New York, N.Y.). PMID 29217585 DOI: 10.1126/Science.Aao4572  0.259
2017 Kotini AG, Chang CJ, Chow A, Yuan H, Ho TC, Wang T, Vora S, Solovyov A, Husser C, Olszewska M, Teruya-Feldstein J, Perumal D, Klimek VM, Spyridonidis A, Rampal RK, ... ... Greenbaum BD, et al. Stage-Specific Human Induced Pluripotent Stem Cells Map the Progression of Myeloid Transformation to Transplantable Leukemia. Cell Stem Cell. PMID 28215825 DOI: 10.1016/J.Stem.2017.01.009  0.252
2017 Greenbaum BD, Vabret N. Minority report: targeting emerging viruses before their emergence. Gene Therapy. 24: 755-756. PMID 29188795 DOI: 10.1038/Gt.2017.93  0.25
2024 Hosseini A, Lindholm HT, Chen R, Mehdipour P, Marhon SA, Ishak CA, Moore PC, Classon M, Di Gioacchino A, Greenbaum B, De Carvalho DD. Retroelement decay by the exonuclease XRN1 is a viral mimicry dependency in cancer. Cell Reports. 43: 113684. PMID 38261511 DOI: 10.1016/j.celrep.2024.113684  0.248
2019 Maura F, Rustad EH, Yellapantula V, Łuksza M, Hoyos D, Maclachlan KH, Diamond BT, Greenbaum BD, Morgan G, Lesokhin A, Papaemmanuil E, Landgren O. Role of AID in the temporal pattern of acquisition of driver mutations in multiple myeloma. Leukemia. PMID 31836853 DOI: 10.1038/S41375-019-0689-0  0.241
2021 Di Gioacchino A, Šulc P, Komarova AV, Greenbaum BD, Monasson R, Cocco S. The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2. Molecular Biology and Evolution. PMID 33555346 DOI: 10.1093/molbev/msab036  0.241
2022 Porter RL, Sun S, Flores MN, Berzolla E, You E, Phillips IE, Kc N, Desai N, Tai EC, Szabolcs A, Lang ER, Pankaj A, Raabe MJ, Thapar V, Xu KH, ... ... Greenbaum BD, et al. Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotype. The Journal of Clinical Investigation. PMID 35708912 DOI: 10.1172/JCI155931  0.241
2020 Di Gioacchino A, Sulc P, Komarova AV, Greenbaum BD, Monasson R, Cocco S. The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2. Ssrn. 3611280. PMID 32714120 DOI: 10.2139/ssrn.3611280  0.239
2017 Badal B, Solovyov A, Di Cecilia S, Chan JM, Chang LW, Iqbal R, Aydin IT, Rajan GS, Chen C, Abbate F, Arora KS, Tanne A, Gruber SB, Johnson TM, Fullen DR, ... ... Greenbaum BD, et al. Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation. Jci Insight. 2. PMID 28469092 DOI: 10.1172/Jci.Insight.92102  0.238
2020 di Gioacchino A, Šulc P, Komarova AV, Greenbaum BD, Monasson R, Cocco S. The heterogeneous landscape and early evolution of pathogen-associated CpG and UpA dinucleotides in SARS-CoV-2. Biorxiv : the Preprint Server For Biology. PMID 32511407 DOI: 10.1101/2020.05.06.074039  0.225
2023 Brodeur MN, Dopeso H, Zhu Y, Longhini ALF, Gazzo A, Sun S, Koche R, Qu R, Hamard PJ, Bykov Y, Green H, Chiappinelli KB, Ozsoy MA, Basili T, Gardner R, ... ... Greenbaum B, et al. Interferon response and epigenetic modulation by mutations drive ovarian tumor immunogenicity. Biorxiv : the Preprint Server For Biology. PMID 37609261 DOI: 10.1101/2023.08.08.552544  0.223
2017 Greenbaum B, Pargellis AN. Self-Replicators Emerge from a Self-Organizing Prebiotic Computer World Artificial Life. 23: 318-342. PMID 28786722 DOI: 10.1162/Artl_A_00234  0.219
2016 Pargellis A, Greenbaum B. Digital Replicators Emerge from a Self-Organizing Prebiotic World Artificial Life. 60-67. DOI: 10.7551/978-0-262-33936-0-Ch016  0.213
2018 Germain RN, Greenbaum BD, Hoffmann A, Miller-Jensen K, Mora T, Walczak AM, Segal E, Vogl T, Klompus S, Peled-Liviatan S, Weinberger A, Smale ST, Tsang JS. What Can Immunologists Learn from Systems Approaches Trends in Immunology. 39: 163-166. PMID 29477635 DOI: 10.1016/J.It.2018.01.002  0.21
2022 Łuksza M, Sethna ZM, Rojas LA, Lihm J, Bravi B, Elhanati Y, Soares K, Amisaki M, Dobrin A, Hoyos D, Guasp P, Zebboudj A, Yu R, Chandra AK, Waters T, ... ... Greenbaum BD, et al. Neoantigen quality predicts immunoediting in survivors of pancreatic cancer. Nature. PMID 35589842 DOI: 10.1038/s41586-022-04735-9  0.208
2021 Lu SX, De Neef E, Thomas JD, Sabio E, Rousseau B, Gigoux M, Knorr DA, Greenbaum B, Elhanati Y, Hogg SJ, Chow A, Ghosh A, Xie A, Zamarin D, Cui D, et al. Pharmacologic modulation of RNA splicing enhances anti-tumor immunity. Cell. PMID 34171309 DOI: 10.1016/j.cell.2021.05.038  0.204
2021 Ho JS, Di Tullio F, Schwarz M, Low D, Incarnato D, Gay F, Tabaglio T, Zhang J, Wollmann H, Chen L, An O, Chan THM, Hall Hickman A, Zheng S, Roudko V, ... ... Greenbaum BD, et al. HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness. Elife. 10. PMID 34075878 DOI: 10.7554/eLife.59654  0.186
2022 Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, ... ... Greenbaum BD, et al. Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discovery. PMID 35320348 DOI: 10.1158/2159-8290.CD-21-1117  0.186
2020 Roudko V, Bozkus CC, Orfanelli T, McClain CB, Carr C, O'Donnell T, Chakraborty L, Samstein R, Huang KL, Blank SV, Greenbaum B, Bhardwaj N. Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors. Cell. PMID 33259803 DOI: 10.1016/j.cell.2020.11.004  0.176
2023 Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, ... ... Greenbaum BD, et al. Structures, functions, and adaptations of the human LINE-1 ORF2 protein. Nature. PMID 38096902 DOI: 10.1038/s41586-023-06947-z  0.175
2023 Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, ... ... Greenbaum BD, et al. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nature Genetics. PMID 37024582 DOI: 10.1038/s41588-023-01355-5  0.167
2020 Desai N, Neyaz A, Szabolcs A, Shih AR, Chen JH, Thapar V, Nieman LT, Solovyov A, Mehta A, Lieb DJ, Kulkarni AS, Jaicks C, Xu KH, Raabe MJ, Pinto CJ, ... ... Greenbaum BD, et al. Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection. Nature Communications. 11: 6319. PMID 33298930 DOI: 10.1038/s41467-020-20139-7  0.167
2020 Cable J, Greenbaum B, Pe'er D, Bollard CM, Bruni S, Griffin ME, Allison JP, Wu CJ, Subudhi SK, Mardis ER, Brentjens R, Sosman JA, Cemerski S, Zavitsanou AM, Proia T, et al. Frontiers in cancer immunotherapy-a symposium report. Annals of the New York Academy of Sciences. PMID 33184911 DOI: 10.1111/nyas.14526  0.167
2022 Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, ... ... Greenbaum BD, et al. Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. Iscience. 25: 104599. PMID 35789859 DOI: 10.1016/j.isci.2022.104599  0.166
2023 Ceglia N, Sethna Z, Freeman SS, Uhlitz F, Bojilova V, Rusk N, Burman B, Chow A, Salehi S, Kabeer F, Aparicio S, Greenbaum BD, Shah SP, McPherson A. Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector. Nature Communications. 14: 4400. PMID 37474509 DOI: 10.1038/s41467-023-39985-2  0.164
2022 Lyudovyk O, Kim JY, Qualls D, Hwee MA, Lin YH, Boutemine SR, Elhanati Y, Solovyov A, Douglas M, Chen E, Babady NE, Ramanathan L, Vedantam P, Bandlamudi C, Gouma S, ... ... Greenbaum B, et al. Impaired humoral immunity is associated with prolonged COVID-19 despite robust CD8 T cell responses. Cancer Cell. PMID 35679859 DOI: 10.1016/j.ccell.2022.05.013  0.163
2021 Roudko V, Cimen Bozkus C, Greenbaum B, Lucas A, Samstein R, Bhardwaj N. Lynch Syndrome and MSI-H Cancers: From Mechanisms to "Off-The-Shelf" Cancer Vaccines. Frontiers in Immunology. 12: 757804. PMID 34630437 DOI: 10.3389/fimmu.2021.757804  0.158
2023 Wang G, Lyudovyk O, Kim JY, Lin YH, Elhanati Y, Mathew D, Wherry EJ, Herati RS, Greenplate AR, Greenbaum B, Vardhana SA, Huang AC. High-throughput interrogation of immune responses using the Human Immune Profiling Pipeline. Star Protocols. 4: 102289. PMID 37159385 DOI: 10.1016/j.xpro.2023.102289  0.158
2021 Di Gioacchino A, Legendre R, Rahou Y, Najburg V, Charneau P, Greenbaum BD, Tangy F, van der Werf S, Cocco S, Komarova AV. sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. Rna (New York, N.Y.). PMID 34937774 DOI: 10.1261/rna.078969.121  0.157
2020 Desai N, Neyaz A, Szabolcs A, Shih AR, Chen JH, Thapar V, Nieman LT, Solovyov A, Mehta A, Lieb DJ, Kulkarni AS, Jaicks C, Pinto CJ, Juric D, Chebib I, ... ... Greenbaum BD, et al. Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection. Medrxiv : the Preprint Server For Health Sciences. PMID 32766600 DOI: 10.1101/2020.07.30.20165241  0.154
2021 Bravi B, Balachandran VP, Greenbaum BD, Walczak AM, Mora T, Monasson R, Cocco S. Probing T-cell response by sequence-based probabilistic modeling. Plos Computational Biology. 17: e1009297. PMID 34473697 DOI: 10.1371/journal.pcbi.1009297  0.153
2021 Parikh AR, Szabolcs A, Allen JN, Clark JW, Wo JY, Raabe M, Thel H, Hoyos D, Mehta A, Arshad S, Lieb DJ, Drapek LC, Blaszkowsky LS, Giantonio BJ, Weekes CD, ... ... Greenbaum BD, et al. Radiation therapy enhances immunotherapy response in microsatellite stable colorectal and pancreatic adenocarcinoma in a phase II trial. Nature Cancer. 2: 1124-1135. PMID 35122060 DOI: 10.1038/s43018-021-00269-7  0.153
2022 Lee CY, Shah MK, Hoyos D, Solovyov A, Douglas M, Taur Y, Maslak P, Babady NE, Greenbaum B, Kamboj M, Vardhana SA. Prolonged SARS-CoV-2 Infection in Patients with Lymphoid Malignancies. Cancer Discovery. 12: 62-73. PMID 34753749 DOI: 10.1158/2159-8290.CD-21-1033  0.143
2023 Knorr K, Rahman J, Erickson C, Wang E, Monetti M, Li Z, Ortiz-Pacheco J, Jones A, Lu SX, Stanley RF, Baez M, Fox N, Castro C, Marino AE, Jiang C, ... ... Greenbaum B, et al. Systematic evaluation of AML-associated antigens identifies anti-U5 SNRNP200 therapeutic antibodies for the treatment of acute myeloid leukemia. Nature Cancer. PMID 37872381 DOI: 10.1038/s43018-023-00656-2  0.141
2023 Sarfaty M, Golkaram M, Funt SA, Al-Ahmadie H, Kaplan S, Song F, Regazzi A, Makarov V, Kuo F, Ostrovnaya I, Seshan V, Zhao C, Greenbaum B, Liu L, Rosenberg JE, et al. Novel Genetic Subtypes of Urothelial Carcinoma With Differential Outcomes on Immune Checkpoint Blockade. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. JCO2202144. PMID 36927002 DOI: 10.1200/JCO.22.02144  0.135
2022 Gigoux M, Holmström MO, Zappasodi R, Park JJ, Pourpe S, Bozkus CC, Mangarin LMB, Redmond D, Verma S, Schad S, George MM, Venkatesh D, Ghosh A, Hoyos D, Molvi Z, ... ... Greenbaum B, et al. Calreticulin mutant myeloproliferative neoplasms induce MHC-I skewing, which can be overcome by an optimized peptide cancer vaccine. Science Translational Medicine. 14: eaba4380. PMID 35704596 DOI: 10.1126/scitranslmed.aba4380  0.135
2022 Hoyos D, Greenbaum BD. Perfecting antigen prediction. The Journal of Experimental Medicine. 219. PMID 35972475 DOI: 10.1084/jem.20220846  0.126
2024 Memon D, Schoenfeld AJ, Ye D, Fromm G, Rizvi H, Zhang X, Keddar MR, Mathew D, Yoo KJ, Qiu J, Lihm J, Miriyala J, Sauter JL, Luo J, Chow A, ... ... Greenbaum BD, et al. Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer. Cancer Cell. PMID 38215748 DOI: 10.1016/j.ccell.2023.12.013  0.125
2023 Rojas LA, Sethna Z, Soares KC, Olcese C, Pang N, Patterson E, Lihm J, Ceglia N, Guasp P, Chu A, Yu R, Chandra AK, Waters T, Ruan J, Amisaki M, ... ... Greenbaum BD, et al. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature. 1-7. PMID 37165196 DOI: 10.1038/s41586-023-06063-y  0.118
2023 Shahid S, Ceglia N, Le Luduec JB, McPherson A, Spitzer B, Kontopoulos T, Bojilova V, Panjwani MK, Roshal M, Shah S, Abdel-Wahab OI, Greenbaum BD, Hsu KC. Immune Escape after Allogeneic Hematopoietic Cell Transplantation in Pediatric Acute Myeloid Leukemia. Blood Advances. PMID 37327118 DOI: 10.1182/bloodadvances.2022009468  0.116
2020 Luo J, Rizvi H, Preeshagul IR, Egger JV, Hoyos D, Bandlamudi C, McCarthy CG, Falcon CJ, Schoenfeld AJ, Arbour KC, Chaft JE, Daly RM, Drilon A, Eng J, Iqbal A, ... ... Greenbaum BD, et al. COVID-19 in patients with lung cancer. Annals of Oncology : Official Journal of the European Society For Medical Oncology. PMID 32561401 DOI: 10.1016/J.Annonc.2020.06.007  0.109
2020 Chang LW, Badal B, Lu CJ, Solovyov A, Greenbaum BD, Celebi JT. An integrative approach identifies dysregulated long non-coding RNAs as microRNA decoys during nevus to melanoma transformation. Melanoma Research. PMID 32976222 DOI: 10.1097/CMR.0000000000000695  0.102
2021 Robilotti EV, Whiting K, Lucca A, Poon C, Guest R, McMillen T, Jani K, Solovyov A, Kelson S, Browne K, Freeswick S, Hohl TM, Korenstein D, Ruchnewitz D, Lässig M, ... ... Greenbaum B, et al. Clinical and Genomic Characterization of SARS CoV-2 infections in mRNA Vaccinated Health Care Personnel in New York City. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 34644393 DOI: 10.1093/cid/ciab886  0.101
2023 DeWolf S, Elhanati Y, Nichols K, Waters NR, Nguyen CL, Slingerland JB, Rodriguez N, Lyudovyk O, Giardina PA, Kousa AI, Andrlová H, Ceglia N, Fei T, Kappagantula R, Li Y, ... ... Greenbaum BD, et al. Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse. Science Translational Medicine. 15: eabq0476. PMID 37494469 DOI: 10.1126/scitranslmed.abq0476  0.098
2023 Yao N, Greenbaum BD. Trade-offs inside the black box of neoantigen prediction. Immunity. 56: 2466-2468. PMID 37967528 DOI: 10.1016/j.immuni.2023.10.011  0.086
2022 Schoenfeld AJ, Rizvi HA, Memon D, Shaverdian N, Bott MJ, Sauter JL, Tsai CJ, Lihm J, Hoyos D, Plodkowski AJ, Perez-Johnston R, Sawan P, Egger JV, Greenbaum BD, Rimner A, et al. Systemic and oligo-acquired resistance to PD-(L)1 blockade in lung cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 35767426 DOI: 10.1158/1078-0432.CCR-22-0657  0.062
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