Thomas MacCarthy

Thomas MacCarthy

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Thomas MacCarthy

Thomas MacCarthy

Publications by authors named "Thomas MacCarthy"

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AID Overlapping and Polη Hotspots Are Key Features of Evolutionary Variation Within the Human Antibody Heavy Chain (IGHV) Genes.

Front Immunol 2020 30;11:788. Epub 2020 Apr 30.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States.

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http://dx.doi.org/10.3389/fimmu.2020.00788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204545PMC
April 2020

Evolutionary effects of the AID/APOBEC family of mutagenic enzymes on human gamma-herpesviruses.

Virus Evol 2019 Jan 11;5(1):vey040. Epub 2019 Feb 11.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.

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http://dx.doi.org/10.1093/ve/vey040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371749PMC
January 2019

Correction to: The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure.

BMC Bioinformatics 2018 07 4;19(1):256. Epub 2018 Jul 4.

Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA.

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http://dx.doi.org/10.1186/s12859-018-2259-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031183PMC
July 2018

The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure.

BMC Bioinformatics 2018 05 2;19(1):163. Epub 2018 May 2.

Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA.

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http://dx.doi.org/10.1186/s12859-018-2161-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930495PMC
May 2018

The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes.

PLoS Comput Biol 2017 03 31;13(3):e1005471. Epub 2017 Mar 31.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Book, New York, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1005471
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http://dx.doi.org/10.1371/journal.pcbi.1005471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391955PMC
March 2017

Potential for evolution of complex defense strategies in a multi-scale model of virus-host coevolution.

BMC Evol Biol 2016 10 26;16(1):233. Epub 2016 Oct 26.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.

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http://dx.doi.org/10.1186/s12862-016-0804-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080737PMC
October 2016

DNA polymerase ι functions in the generation of tandem mutations during somatic hypermutation of antibody genes.

J Exp Med 2016 08 25;213(9):1675-83. Epub 2016 Jul 25.

Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224

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http://dx.doi.org/10.1084/jem.20151227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995076PMC
August 2016

Regulatory evolution and voltage-gated ion channel expression in squid axon: selection-mutation balance and fitness cliffs.

PLoS One 2015 13;10(4):e0120785. Epub 2015 Apr 13.

Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America; Institute of Molecular Cardiology, Stony Brook University, Stony Brook, New York, United States of America; The Department of Research, Veterans Affairs Medical Center, Northport, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120785PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395378PMC
April 2016

Chronic lymphocytic leukemia cells diversify and differentiate in vivo via a nonclassical Th1-dependent, Bcl-6-deficient process.

JCI Insight 2016 Apr;1(4)

The Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, USA.; Department of Medicine, Hofstra Northwell School of Medicine, Manhasset, New York, USA.; Department of Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, New York, USA.

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http://dx.doi.org/10.1172/jci.insight.86288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855875PMC
April 2016

Cancer as the Disintegration of Robustness: Population-Level Variance in Gene Expression Identifies Key Differences Between Tobacco- and HPV-Associated Oropharyngeal Carcinogenesis.

Arch Pathol Lab Med 2015 Nov 1;139(11):1362-72. Epub 2015 Jul 1.

From the Departments of Pathology (Ms Ben-Dayan and Drs Belbin, Childs, and Prystowsky), Epidemiology and Population Health (Dr Schlecht), and Computational and Systems Biology (Dr Bergman), Albert Einstein College of Medicine, Bronx, New York; the Department of Applied Mathematics and Statistics, SUNY Stony Brook, Stony Brook, New York (Dr MacCarthy); and the Department of Otorhinolaryngology, Montefiore Medical Center, Bronx, New York (Dr Smith).

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http://dx.doi.org/10.5858/arpa.2014-0624-OADOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695554PMC
November 2015

Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks.

PLoS Comput Biol 2015 Oct 9;11(10):e1004432. Epub 2015 Oct 9.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599961PMC
October 2015

Overlapping hotspots in CDRs are critical sites for V region diversification.

Proc Natl Acad Sci U S A 2015 Feb 2;112(7):E728-37. Epub 2015 Feb 2.

Department of Applied Mathematics and Statistics, State University of New York, Stony Brook, NY 11794

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http://dx.doi.org/10.1073/pnas.1500788112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343087PMC
February 2015

Host restriction of murine gammaherpesvirus 68 replication by human APOBEC3 cytidine deaminases but not murine APOBEC3.

Virology 2014 Apr 13;454-455:215-26. Epub 2014 Mar 13.

Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2014.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036618PMC
April 2014

Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity?

PLoS Comput Biol 2014 Mar 6;10(3):e1003450. Epub 2014 Mar 6.

Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945085PMC
March 2014

The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks.

PLoS Comput Biol 2013 3;9(1):e1002865. Epub 2013 Jan 3.

Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536627PMC
June 2013

Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies.

Cell Host Microbe 2013 Apr;13(4):417-28

Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1016/j.chom.2013.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633089PMC
April 2013

Recombinase-mediated cassette exchange as a novel method to study somatic hypermutation in Ramos cells.

mBio 2011 11;2(5). Epub 2011 Oct 11.

Departments of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA.

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http://dx.doi.org/10.1128/mBio.00186-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190358PMC
January 2012

Differential regulation drives plasticity in sex determination gene networks.

BMC Evol Biol 2010 Dec 16;10:388. Epub 2010 Dec 16.

CoMPLEX, University College London, UK.

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http://dx.doi.org/10.1186/1471-2148-10-388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022605PMC
December 2010

V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment.

Proc Natl Acad Sci U S A 2009 May 14;106(21):8629-34. Epub 2009 May 14.

Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx NY 10461, USA.

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http://dx.doi.org/10.1073/pnas.0903803106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682541PMC
May 2009

SHMTool: a webserver for comparative analysis of somatic hypermutation datasets.

DNA Repair (Amst) 2009 Jan 8;8(1):137-41. Epub 2008 Nov 8.

Dept of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1016/j.dnarep.2008.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659805PMC
January 2009

Ubiquitylated PCNA plays a role in somatic hypermutation and class-switch recombination and is required for meiotic progression.

Proc Natl Acad Sci U S A 2008 Oct 14;105(42):16248-53. Epub 2008 Oct 14.

Departments of Cell Biology and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1073/pnas.0808182105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2571010PMC
October 2008

The limits of subfunctionalization.

BMC Evol Biol 2007 Nov 7;7:213. Epub 2007 Nov 7.

Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1186/1471-2148-7-213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2213666PMC
November 2007

Buffering mechanisms in aging: a systems approach toward uncovering the genetic component of aging.

PLoS Comput Biol 2007 Aug 18;3(8):e170. Epub 2007 Jul 18.

Department of Pathology, Albert Einstein College of Medicine, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1963511PMC
August 2007

Coevolution of robustness, epistasis, and recombination favors asexual reproduction.

Proc Natl Acad Sci U S A 2007 Jul 23;104(31):12801-6. Epub 2007 Jul 23.

Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1073/pnas.0705455104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1931480PMC
July 2007

Using large-scale perturbations in gene network reconstruction.

BMC Bioinformatics 2005 Jan 19;6:11. Epub 2005 Jan 19.

COMPLEX, University College London, 4 Stephenson Way, London NW1 2HE, UK.

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http://dx.doi.org/10.1186/1471-2105-6-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548128PMC
January 2005

The evolutionary potential of the Drosophila sex determination gene network.

J Theor Biol 2003 Dec;225(4):461-8

CoMPLEX, University College London, 4 Stephenson Way, NW1 2HE London, UK.

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http://dx.doi.org/10.1016/s0022-5193(03)00282-0DOI Listing
December 2003