Publications by authors named "Benjamin Greenbaum"

55Publications

Computational Prediction and Validation of Tumor-Associated Neoantigens.

Front Immunol 2020 24;11:27. Epub 2020 Jan 24.

Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States.

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http://dx.doi.org/10.3389/fimmu.2020.00027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025577PMC
January 2020

Genomic analysis of metastatic melanoma in an adult with giant congenital melanocytic nevus.

Pigment Cell Melanoma Res 2020 07 10;33(4):633-636. Epub 2020 Mar 10.

Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York.

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http://dx.doi.org/10.1111/pcmr.12872DOI Listing
July 2020

Role of AID in the temporal pattern of acquisition of driver mutations in multiple myeloma.

Leukemia 2020 05 13;34(5):1476-1480. Epub 2019 Dec 13.

Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1038/s41375-019-0689-0DOI Listing
May 2020

Reply to 'Reconciling disparate estimates of viral genetic diversity during human influenza infections'.

Nat Genet 2019 09;51(9):1301-1303

Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.

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http://dx.doi.org/10.1038/s41588-019-0486-8DOI Listing
September 2019

A tumor-specific endogenous repetitive element is induced by herpesviruses.

Nat Commun 2019 01 9;10(1):90. Epub 2019 Jan 9.

Department of Medicine, Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.

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http://dx.doi.org/10.1038/s41467-018-07944-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327058PMC
January 2019

FBXW7 regulates a mitochondrial transcription program by modulating MITF.

Pigment Cell Melanoma Res 2018 09 29;31(5):636-640. Epub 2018 Apr 29.

Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York.

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http://dx.doi.org/10.1111/pcmr.12704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192859PMC
September 2018

Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes.

Cell Rep 2018 Apr;23(2):512-521

Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences and Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute at the Icahn School of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016853PMC
April 2018

Chromatin dependencies in cancer and inflammation.

Nat Rev Mol Cell Biol 2018 04 29;19(4):245-261. Epub 2017 Nov 29.

Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos Building #3-06, 138673 Singapore.

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http://www.nature.com/doifinder/10.1038/nrm.2017.113
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http://dx.doi.org/10.1038/nrm.2017.113DOI Listing
April 2018

Getting the flu: 5 key facts about influenza virus evolution.

PLoS Pathog 2017 08 24;13(8):e1006450. Epub 2017 Aug 24.

Center for Genomics & Systems Biology, Department of Biology, New York University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600439PMC
August 2017

Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses.

Cell 2017 05;169(4):750-765.e17

Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737939PMC
May 2017

Stage-Specific Human Induced Pluripotent Stem Cells Map the Progression of Myeloid Transformation to Transplantable Leukemia.

Cell Stem Cell 2017 03 16;20(3):315-328.e7. Epub 2017 Feb 16.

Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5337161PMC
March 2017

Sequence-Specific Sensing of Nucleic Acids.

Trends Immunol 2017 01 14;38(1):53-65. Epub 2016 Nov 14.

Tisch Cancer Institute, Departments of Medicine, Hematology, and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Departments of Oncological Sciences and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2016.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5205569PMC
January 2017

Fundamental amino acid mass distributions and entropy costs in proteomes.

J Theor Biol 2016 12 18;410:119-124. Epub 2016 Aug 18.

The Simons Center for Systems Biology, Institute for Advanced Study, 1 Einstein Dr, Princeton, NJ 08540, USA; Tisch Cancer Institute, Departments of Medicine, Division of Hematology and Medical Oncology, Oncological Sciences, and Pathology, Icahn School of Medicine at Mount Sinai, 1428 Madison Avenue, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.08.011DOI Listing
December 2016

Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome.

Cell 2016 Oct;167(2):444-456.e14

Department of Oncological Science, Icahn School of Medicine at Mount Sinai, 1475 Madison Avenue, New York, NY 10028, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1475 Madison Avenue, New York, NY 10028, USA; The Immunological Institute, Icahn School of Medicine at Mount Sinai, 1475 Madison Avenue, New York, NY 10028, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.08.076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129837PMC
October 2016

P53 and the defenses against genome instability caused by transposons and repetitive elements.

Bioessays 2016 06 13;38(6):508-13. Epub 2016 May 13.

Department of Medicine, Hematology, and Medical Oncology, and Pathology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031199PMC
http://dx.doi.org/10.1002/bies.201600031DOI Listing
June 2016

Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells.

Proc Natl Acad Sci U S A 2015 Dec 2;112(49):15154-9. Epub 2015 Nov 2.

Tisch Cancer Institute, Department of Medicine, Hematology, and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029; The Simons Center for Systems Biology, School of Natural Sciences, Institute for Advanced Study, Princeton, NJ 08540; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029

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http://dx.doi.org/10.1073/pnas.1517584112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679042PMC
December 2015

Ion efflux and influenza infection trigger NLRP3 inflammasome signaling in human dendritic cells.

J Leukoc Biol 2016 05 16;99(5):723-34. Epub 2015 Nov 16.

Division of Hematology and Oncology, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA

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http://dx.doi.org/10.1189/jlb.3A0614-313RRRDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831479PMC
May 2016

Viral evolution: beyond drift and shift.

Curr Opin Microbiol 2015 Aug 17;26:109-15. Epub 2015 Jul 17.

Center for Genomics & Systems Biology, Department of Biology, and Global Institute of Public Health, New York University, 100 Washington Place, 1009 Silver Center, New York, NY 10003, United States.

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http://dx.doi.org/10.1016/j.mib.2015.06.015DOI Listing
August 2015

Using first passage statistics to extract environmentally dependent amino acid correlations.

PLoS One 2014 7;9(7):e101665. Epub 2014 Jul 7.

The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America; Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101665PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084998PMC
February 2015

Bird to human transmission biases and vaccine escape mutants in H5N1 infections.

PLoS One 2014 2;9(7):e100754. Epub 2014 Jul 2.

Department of Physics, Rutgers the State University of New Jersey, Piscataway, New Jersey, United States of America; The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America; The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America; Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America; BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100754PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079711PMC
February 2015

Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses.

Proc Natl Acad Sci U S A 2014 Apr 17;111(13):5054-9. Epub 2014 Mar 17.

The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540.

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http://dx.doi.org/10.1073/pnas.1402285111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977288PMC
April 2014

Evolution and diversity in human herpes simplex virus genomes.

J Virol 2014 Jan 13;88(2):1209-27. Epub 2013 Nov 13.

Department of Biochemistry and Molecular Biology, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.01987-13
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http://dx.doi.org/10.1128/JVI.01987-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911644PMC
January 2014

A statistical strategy to identify recombinant viral ribonucleoprotein of avian, human, and swine influenza A viruses with elevated polymerase activity.

Influenza Other Respir Viruses 2013 Nov 2;7(6):969-78. Epub 2013 May 2.

Centre of Influenza Research & School of Public Health, The University of Hong Kong, Hong Kong.

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http://dx.doi.org/10.1111/irv.12117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823691PMC
November 2013

The maintenance of epigenetic states by p53: the guardian of the epigenome.

Oncotarget 2012 Dec;3(12):1503-4

Institute for Advanced Study, Einstein Road, Princeton, NJ, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681489PMC
http://dx.doi.org/10.18632/oncotarget.780DOI Listing
December 2012

Viral reassortment as an information exchange between viral segments.

Proc Natl Acad Sci U S A 2012 Feb 13;109(9):3341-6. Epub 2012 Feb 13.

The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1073/pnas.1113300109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295259PMC
February 2012

Oligonucleotide motifs that disappear during the evolution of influenza virus in humans increase alpha interferon secretion by plasmacytoid dendritic cells.

J Virol 2011 Apr 9;85(8):3893-904. Epub 2011 Feb 9.

New York University Langone Medical Center, Smilow Research Building, 522 First Avenue, Room 1303, New York, NY 10016, USA.

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http://dx.doi.org/10.1128/JVI.01908-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3126114PMC
April 2011

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza.

PLoS Curr 2010 Jan 29;2:RRN1147. Epub 2010 Jan 29.

Columbia Unoiversity; Simons Center for Systems Biology, Institute for Advanced Study; Center for Infection and Immunity and Columbia University.

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http://dx.doi.org/10.1371/currents.RRN1147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814059PMC
January 2010

Patterns of evolution and host gene mimicry in influenza and other RNA viruses.

PLoS Pathog 2008 Jun 6;4(6):e1000079. Epub 2008 Jun 6.

BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1000079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390760PMC
June 2008

Semiclassics of the chaotic quantum-classical transition.

Phys Rev E Stat Nonlin Soft Matter Phys 2007 Oct 18;76(4 Pt 2):046215. Epub 2007 Oct 18.

Department of Physics, Columbia University, New York, New York 10027, USA.

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http://dx.doi.org/10.1103/PhysRevE.76.046215DOI Listing
October 2007

Conditions for the quantum-to-classical transition: trajectories versus phase-space distributions.

Phys Rev E Stat Nonlin Soft Matter Phys 2007 Sep 24;76(3 Pt 2):036213. Epub 2007 Sep 24.

Department of Physics, University of Massachusetts at Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125, USA.

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http://dx.doi.org/10.1103/PhysRevE.76.036213DOI Listing
September 2007

The semiclassical regime of the chaotic quantum-classical transition.

Chaos 2005 Sep;15(3):33302

Department of Physics, Columbia University, New York, New York 10027, USA.

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http://dx.doi.org/10.1063/1.1979227DOI Listing
September 2005

Chaos and quantum mechanics.

Ann N Y Acad Sci 2005 Jun;1045:308-32

MS B285, Theoretical Division, The University of California, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.

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http://dx.doi.org/10.1196/annals.1350.026DOI Listing
June 2005

Parameter scaling in the decoherent quantum-classical transition for chaotic systems.

Phys Rev Lett 2003 Jan 10;90(1):014103. Epub 2003 Jan 10.

Department of Physics, Carleton College, Northfield, Minnesota 55057, USA.

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http://dx.doi.org/10.1103/PhysRevLett.90.014103DOI Listing
January 2003