Publications

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.

Chowell D, Morris GTL*, Grigg MC*, Weber KJ, Samstein MR, Makarov V, Fengshen K, Sviatoslav MK, Requena D, Riaz N, Greenbaum B, Carroll J, Garon E, Hyman DM, Zehir A, Solit D, Berger M, Zhou R, Rizvi NA*, Chan TA*. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science 359:582-587.

Abbate F, Badal B, Mendelson K, Aydin IT, Serasinghe MN, Iqbal R, Mohammed J, Solovyov AGreenbaum BD, Chipuk JE, Celebi JT. FBXW7 regulates a mitochondrial transcription program by modulating MITF. Pigment Cell Melanoma Research – in press.

Guccione E, Marazzi I, Greenbaum BD, Low D. Chromatin dependencies in cancer and inflammation. Nature Reviews Molecular Cell Biology 19:245-261.

2017:

Łuksza M, Riaz N, Makarov V, Balachandran VP, Hellman MD, Solovyov A, Rizvi NA, Merghoub T, Levine AJ, Chan TA, Wolchok JD, Greenbaum BD. A neoantigen fitness model predicts tumor response to checkpoint blockade immunotherapy. Nature 551:517-520.

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, Zhang J, Loo J, Saglimbeni J, Abu-Akeel M, Zappasodi R, Riaz N, Smoragiewicz M, Kelley ZL, Basturk O, Austrailian Pancreatic Genome Initiative, Gönen M, Levine AJ, Allen PJ, Fearon DT, Merad M, Gnjatic S, Iacobuzio-Donahue CA, Wolchok JD, DeMatteo RP, Chan TA, Greenbaum BD, Merghoub T*, Leach SD*. Neoantigen quality and an immunogenic hotspot define long term pancreatic cancer survivors. Nature 551:512-516.

Greenbaum B, Vabret N. Minority report: targeting emerging viruses before their emergence. Gene Therapy 10.1038/gt.2017.93

Greenbaum B, Pargellis AN. Self-replicators emerge from a self-organizing prebiotic computer world. Artificial Life 23:318-342.                     

Johnson KEE, Song T, Greenbaum B, Ghedin E. Getting the flu: 5 key facts about influenza virus evolution. PLoS Pathogens 13:e1006450.

Chatenay D, Cocco S, Greenbaum B, Monasson R, Netter P. Evolutionary constraints on coding sequences at the nucleotidic level: a statistical physics approach. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts 329-367.

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, Li H, Rytlewski JA, Emerson RO, Solovyov AGreenbaum BD, Sanders C, Vignali M, Beasley MB, Flores R, Gnjatic S, Pe’er D, Rahman A, Amit I, Merad M. Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell 169:750–765.

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, Raskin L, Phelps R, Bhardwaj N, Bernstein E, Ting DT, Brunner G, Schadt EE, Greenbaum BD*, Celebi JT*. Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation. JCI Insight 2:e9210.

Leonard AS, 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 91:e00171-17.

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, Basler CF, Mulder LC, García-Sastre A, Fernandez-Sesma A. Dengue virus NS2B protein targets cGAS for degradation and prevents mitochondrial DNA sensing during infection. Nature Microbiology 2:17037.

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.

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, Silverman L, Reddy EP, Papaemmanuil E, Parekh S, Greenbaum BD, Leslie CS, Kharas MG, Papapetrou EP. Stage-specific human induced pluripotent stem cells map the progression of myeloid transformation to transplantable leukemia. Cell Stem Cell 20:315-328.

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*, Deshpande V*, Ting DT*. Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer. JCI Insight 2:e91078.

Vabret N, Bhardwaj N, Greenbaum BD. Sequence-specific sensing of nucleic acids. Trends in Immunology 38:53-65.

2016:

Lehmann J, Libchaber A, Greenbaum BD. Fundamental amino acid mass distributions and entropy costs in proteomes. Journal of Theoretical Biology 410:119-124.

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, Belkaid Y, Grigg ME, Merad M. Host-protozoan interactions protect from mucosal infections through activation of the inflammasome. Cell 167:444-456.

Pargelis A, Greenbaum B. Digital replicators emerge from a self-organizing prebiotic world. Proceedings of the Artificial Life Conference 2016 60-67.

Levine AJ, Ting DT, Greenbaum BD. p53 and the defenses against genome instability caused by transposons and repetitive elements. BioEssays  38:508-513.

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 99: 723-734.

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.

Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs D, Sachs DH, Hamilton J, Leon PE, Chawdury A, Tripathi S, Melegari C, Campisi L, Hai R, Metreveli G, Gamarnik AV, García-Sastre A, Greenbaum B, Simon V, Fernandez-Sesma A, Krogan NJ, Mulder LC, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I. Targeting viral proteostasis limits influenza virus, HIV, and dengue virus infection. Immunity 44:46-58.

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, Peiris JS, Cowling BJ, Ghedin E. Quantifying influenza virus diversity and transmission in humans. Nature Genetics 48:195-200.

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 112:15154:15159.

Greenbaum BD, Ghedin E. Viral evolution: beyond drift and shift. Current Opinion in Microbiology 26:109-115.

Bonfante G, El-Aqqad M, Greenbaum B, Hoyrup M. Immune systems in computer virology. Conference on Computability in Europe 2015 127-136.

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:e02464-14.

2014:

Greenbaum BD, Kumar P, Libchaber A. Using first passage statistics to extract environmentally dependent amino acid correlations. PLoS One 9:e101665.

Wagh K, Bhatia A, Greenbaum BD, Bhanot G. Bird to human transmission biases and vaccine escape mutants in H5N1 infections. PLoS One 9:e100754.

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 111:5054-5059.

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 88:1209-1227.

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 7:969-978.

Greenbaum B, Kumar P, Libchaber A. Amino acid distributions and the effect of optimal growth temperature. arXiv 1309.4761.

2012:

Levine AJ, Greenbaum B. The maintenance of epigenetic states by p53: the guardian of the epigenome. Oncotarget 3:1503-1504.

Greenbaum BD, Li OT, Poon LL, Levine AJ, Rabadán R. Viral reassortment as an information exchange between viral segments. Proceedings of the National Academy of Sciences 109:3341-3346.

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 85:3893-3904.

Greenbaum B, Trifonov V, Khiabanian H, Levine A, Rabadán R. The emergence of 2009 H1N1 pandemic influenza. Influenza Vaccines for the Future 95-111.

2010:

Solovyov A, Greenbaum B, Palacios G, Lipkin WI, Rabadán R. Host dependent evolutionary patterns and the origin of 2009 H1N1 pandemic influenza. PLoS Currents Influenza.

2009:

Greenbaum BD, Rabadán 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.

Trifonov V, Khiabanian H, Greenbaum B, Rabadán R. The origin of the recent swine influenza A (H1N1) virus infecting humans. Eurosurveillance 14:1.

2008:

Greenbaum BD, Levine AJ, Bhanot G, Rabadán R. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathogens 4:e1000079.

2007:

Greenbaum BD, Habib S, Shizume K, Sundaram B. Semiclassics of the chaotic quantum-classical transition. Physical Review E 76: 046215.

Greenbaum BD, Shizume K, Sundaram B. Conditions for the quantum-to-classical transition: trajectories versus phase-space distributions. Physical Review E 76: 036213.

2005:

Greenbaum BD, Habib S, Shizume K, Sundaram B. The semiclassical regime of the chaotic quantum-classical transition. Chaos 15:033302.

Habib S, Bhattacharya T, Greenbaum BD, Jacobs K, Shizume K, Sundaram B. Chaos and quantum mechanics. Annals of the New York Academy of Sciences 1045:308-332.

2003:

Pattanayak AK, Sundaram B, Greenbaum BD. Parameter scaling in the decoherent quantum-classical transition for chaotic systems. Physical Review Letters 90:014103.