John M Coffin

John M Coffin

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John M Coffin

Publications by authors named "John M Coffin"

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HIV Proviral Sequence Database (PSD): A New Public Database for Near Full-Length HIV Proviral Sequences and Their Meta-Analyses.

AIDS Res Hum Retroviruses 2019 Sep 10. Epub 2019 Sep 10.

National Cancer Institute, HIV Dynamics and Replicaiton Program, Frederick, Maryland, United States;

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http://dx.doi.org/10.1089/AID.2019.0214DOI Listing
September 2019

Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans.

PLoS Pathog 2019 Jul 10;15(7):e1007869. Epub 2019 Jul 10.

HIV Dynamics and Replication Program, National Cancer Institute Frederick, National Institutes of Health, Frederick, MD, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1007869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619828PMC
July 2019

Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees.

Proc Natl Acad Sci U S A 2019 01 4;116(4):1337-1346. Epub 2019 Jan 4.

Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111;

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http://dx.doi.org/10.1073/pnas.1814203116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347686PMC
January 2019

Nomenclature for endogenous retrovirus (ERV) loci.

Retrovirology 2018 08 28;15(1):59. Epub 2018 Aug 28.

Biology Department, Boston College, Chestnut Hill, Massachusetts, 02467, USA.

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http://dx.doi.org/10.1186/s12977-018-0442-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114882PMC
August 2018

Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation.

J Virol 2018 01 14;92(1). Epub 2017 Dec 14.

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA

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http://jvi.asm.org/lookup/doi/10.1128/JVI.01258-17
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http://dx.doi.org/10.1128/JVI.01258-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5730778PMC
January 2018

Ongoing HIV Replication During ART Reconsidered.

Open Forum Infect Dis 2017 19;4(3):ofx173. Epub 2017 Sep 19.

Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts.

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https://academic.oup.com/ofid/article/doi/10.1093/ofid/ofx17
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http://dx.doi.org/10.1093/ofid/ofx173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172598PMC
September 2017

Pushing the envelope.

Elife 2017 04 13;6. Epub 2017 Apr 13.

Department of Molecular Biology and Microbiology, Tufts University, Boston, United States.

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http://dx.doi.org/10.7554/eLife.26397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391202PMC
April 2017

Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir.

PLoS Pathog 2017 03 22;13(3):e1006283. Epub 2017 Mar 22.

Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378418PMC
March 2017

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.

Retrovirology 2016 Dec 20;13(1):87. Epub 2016 Dec 20.

Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12977-016-0321-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175307PMC
December 2016

The Discovery of Reverse Transcriptase.

Annu Rev Virol 2016 09 22;3(1):29-51. Epub 2016 Jul 22.

Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697.

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http://dx.doi.org/10.1146/annurev-virology-110615-035556DOI Listing
September 2016

What Integration Sites Tell Us about HIV Persistence.

Cell Host Microbe 2016 May;19(5):588-98

Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA.

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http://dx.doi.org/10.1016/j.chom.2016.04.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4900157PMC
May 2016

Discovery of unfixed endogenous retrovirus insertions in diverse human populations.

Proc Natl Acad Sci U S A 2016 Apr 21;113(16):E2326-34. Epub 2016 Mar 21.

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111;

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http://dx.doi.org/10.1073/pnas.1602336113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843416PMC
April 2016

The discovery of HTLV-1, the first pathogenic human retrovirus.

Authors:
John M Coffin

Proc Natl Acad Sci U S A 2015 Dec;112(51):15525-9

Tufts University School of Medicine, Boston MA 02111

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http://dx.doi.org/10.1073/pnas.1521629112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697431PMC
December 2015

A mouse strain defective in both T cells and NK cells has enhanced sensitivity to tumor induction by plasmid DNA expressing both activated H-Ras and c-Myc.

PLoS One 2014 10;9(10):e108926. Epub 2014 Oct 10.

Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0108926PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193875PMC
June 2015

Differential expression of HERV-K (HML-2) proviruses in cells and virions of the teratocarcinoma cell line Tera-1.

Viruses 2015 Mar 4;7(3):939-68. Epub 2015 Mar 4.

Graduate Program in Molecular Biology and Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA.

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http://dx.doi.org/10.3390/v7030939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379556PMC
March 2015

HIV-1 infection leads to increased transcription of human endogenous retrovirus HERV-K (HML-2) proviruses in vivo but not to increased virion production.

J Virol 2014 Oct 23;88(19):11108-20. Epub 2014 Jul 23.

Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA

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http://jvi.asm.org/cgi/doi/10.1128/JVI.01623-14
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http://dx.doi.org/10.1128/JVI.01623-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178833PMC
October 2014

The distribution of insertionally polymorphic endogenous retroviruses in breast cancer patients and cancer-free controls.

Retrovirology 2014 Aug 12;11:62. Epub 2014 Aug 12.

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston 02111, MA, USA.

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http://dx.doi.org/10.1186/PREACCEPT-1720768941312026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149278PMC
August 2014

PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data.

J Virol Methods 2014 Jul 26;203:73-80. Epub 2014 Mar 26.

Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, United States.

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http://dx.doi.org/10.1016/j.jviromet.2014.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104926PMC
July 2014

Quantification of HIV-1 latency reversal in resting CD4+ T cells from patients on suppressive antiretroviral therapy.

Proc Natl Acad Sci U S A 2014 May 31;111(19):7078-83. Epub 2014 Mar 31.

Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261;

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http://www.pnas.org/cgi/doi/10.1073/pnas.1402873111
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http://dx.doi.org/10.1073/pnas.1402873111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4024870PMC
May 2014

Endogenous retroviruses and human cancer: is there anything to the rumors?

Cell Host Microbe 2014 Mar;15(3):255-9

Department of Molecular Biology and Microbiology, Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2014.02.013DOI Listing
March 2014

Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy.

PLoS Pathog 2014 Mar 20;10(3):e1004010. Epub 2014 Mar 20.

HIV-1 Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America.

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https://dx.plos.org/10.1371/journal.ppat.1004010
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http://dx.doi.org/10.1371/journal.ppat.1004010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961343PMC
March 2014

Fifteen years later: hard and soft selection sweeps confirm a large population number for HIV in vivo.

PLoS Genet 2014 Feb 20;10(2):e1004179. Epub 2014 Feb 20.

The Gladstone Institutes, Gladstone Institute of Virology and Immunology, University of California San Francisco, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930503PMC
February 2014

Virions at the gates: receptors and the host-virus arms race.

Authors:
John M Coffin

PLoS Biol 2013 28;11(5):e1001574. Epub 2013 May 28.

Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pbio.1001574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665852PMC
January 2014

Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class.

J Virol 2013 Feb 5;87(4):1937-46. Epub 2012 Dec 5.

Tufts University School of Medicine, Department of Molecular Biology and Microbiology, Boston, Massachusetts, USA.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.01442-12
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http://dx.doi.org/10.1128/JVI.01442-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571459PMC
February 2013

Studies on the restriction of murine leukemia viruses by mouse APOBEC3.

PLoS One 2012 29;7(5):e38190. Epub 2012 May 29.

HIV Drug Resistance Program, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038190PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3362552PMC
October 2012

Endogenous Murine Leukemia Viruses: Relationship to XMRV and Related Sequences Detected in Human DNA Samples.

Adv Virol 2011 24;2011:940210. Epub 2011 Oct 24.

Department of Molecular Biology and Microbiology and Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.

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http://dx.doi.org/10.1155/2011/940210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265319PMC
August 2012

Recombinant origin, contamination, and de-discovery of XMRV.

Curr Opin Virol 2012 Aug 19;2(4):499-507. Epub 2012 Jul 19.

Viral Mutation Section, NCI, HIV DRP, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.

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http://linkinghub.elsevier.com/retrieve/pii/S187962571200104
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http://dx.doi.org/10.1016/j.coviro.2012.06.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426297PMC
August 2012

Mus spicilegus endogenous retrovirus HEMV uses murine sodium-dependent myo-inositol transporter 1 as a receptor.

J Virol 2012 Jun 28;86(11):6341-4. Epub 2012 Mar 28.

Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1128/JVI.00083-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372175PMC
June 2012

Characterization, mapping, and distribution of the two XMRV parental proviruses.

J Virol 2012 Jan 26;86(1):328-38. Epub 2011 Oct 26.

Department of Molecular Biology and Microbiology, Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.06022-11
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http://dx.doi.org/10.1128/JVI.06022-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255884PMC
January 2012

Binding of more than one Tva800 molecule is required for ASLV-A entry.

Retrovirology 2011 Nov 18;8:96. Epub 2011 Nov 18.

Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

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http://dx.doi.org/10.1186/1742-4690-8-96DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267798PMC
November 2011

Recombinant origin of the retrovirus XMRV.

Science 2011 Jul 31;333(6038):97-101. Epub 2011 May 31.

Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA.

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http://dx.doi.org/10.1126/science.1205292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278917PMC
July 2011

Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection.

Proc Natl Acad Sci U S A 2011 Apr 21;108(14):5661-6. Epub 2011 Mar 21.

Department of Physics and Astronomy, Tufts University, Medford, MA 02155, USA.

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http://dx.doi.org/10.1073/pnas.1102036108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078368PMC
April 2011

Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy.

J Virol 2011 Jan 17;85(2):1067-76. Epub 2010 Nov 17.

HIV Drug Resistance Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD 21702-1201, USA.

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http://dx.doi.org/10.1128/JVI.01701-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019993PMC
January 2011

Mouse DNA contamination in human tissue tested for XMRV.

Retrovirology 2010 Dec 20;7:108. Epub 2010 Dec 20.

Section of Infectious Diseases, Jefferiss Research Trust Laboratories, Imperial College London, St Mary's Campus, London, W2 1PG, UK.

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http://link.springer.com/content/pdf/10.1186%2F1742-4690-7-1
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http://www.retrovirology.com/content/7/1/108
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http://dx.doi.org/10.1186/1742-4690-7-108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019155PMC
December 2010

Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences.

Retrovirology 2010 Dec 20;7:109. Epub 2010 Dec 20.

Department of Pathology, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111, USA.

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http://dx.doi.org/10.1186/1742-4690-7-109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022687PMC
December 2010

Multi-site adaptation in the presence of infrequent recombination.

Theor Popul Biol 2010 May 10;77(3):189-204. Epub 2010 Feb 10.

Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA 02111, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S004058091000012
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http://dx.doi.org/10.1016/j.tpb.2010.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849900PMC
May 2010

RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy.

Retrovirology 2009 Nov 4;6:101. Epub 2009 Nov 4.

Advanced Biomedical Computing Center, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD, USA.

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http://dx.doi.org/10.1186/1742-4690-6-101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776578PMC
November 2009

Virology. A new virus for old diseases?

Science 2009 Oct 8;326(5952):530-1. Epub 2009 Oct 8.

Department of Molecular Microbiology, Tufts University, Boston, MA 02111, USA.

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http://dx.doi.org/10.1126/science.1181349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818280PMC
October 2009

Persistent low-level viremia in HIV-1 elite controllers and relationship to immunologic parameters.

J Infect Dis 2009 Sep;200(6):984-90

The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 149 13th St, Charlestown, MA 02129, USA.

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http://dx.doi.org/10.1086/605446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725728PMC
September 2009

Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance.

PLoS Pathog 2009 Apr 3;5(4):e1000367. Epub 2009 Apr 3.

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.

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http://dx.doi.org/10.1371/journal.ppat.1000367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659435PMC
April 2009

Effects of retroviruses on host genome function.

Annu Rev Genet 2008 ;42:709-32

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.

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http://dx.doi.org/10.1146/annurev.genet.42.110807.091501DOI Listing
February 2009

Attenuation by a thousand cuts.

Authors:
John M Coffin

N Engl J Med 2008 Nov;359(21):2283-5

Department of Molecular Biology and Microbiology, Tufts University, Boston, USA.

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http://www.nejm.org/doi/abs/10.1056/NEJMcibr0805820
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http://dx.doi.org/10.1056/NEJMcibr0805820DOI Listing
November 2008

Host-retrovirus arms race: trimming the budget.

Cell Host Microbe 2008 Sep;4(3):196-7

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA.

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http://dx.doi.org/10.1016/j.chom.2008.08.008DOI Listing
September 2008

HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.

Proc Natl Acad Sci U S A 2008 Aug 30;105(31):10943-8. Epub 2008 Jul 30.

Viral Mutation Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0804660105
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http://dx.doi.org/10.1073/pnas.0804660105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2491488PMC
August 2008

Interactions of murine APOBEC3 and human APOBEC3G with murine leukemia viruses.

J Virol 2008 Jul 30;82(13):6566-75. Epub 2008 Apr 30.

HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, MD 12702-1201, USA.

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http://dx.doi.org/10.1128/JVI.01357-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447093PMC
July 2008

Oncogenicity of DNA in vivo: tumor induction with expression plasmids for activated H-ras and c-myc.

Biologicals 2008 May 22;36(3):184-97. Epub 2008 Jan 22.

Division of Viral Products, OVRR, CBER, FDA, Building 29A, Room 3D08, 29 Lincoln Drive, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.biologicals.2007.11.003DOI Listing
May 2008

Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy.

Proc Natl Acad Sci U S A 2008 Mar 10;105(10):3879-84. Epub 2008 Mar 10.

HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, MD 21702-1201, USA.

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http://dx.doi.org/10.1073/pnas.0800050105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268833PMC
March 2008

Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase.

AIDS 2008 Feb;22(4):497-501

HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702-1201, USA.

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http://dx.doi.org/10.1097/QAD.0b013e3282f29478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921824PMC
February 2008

Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses.

PLoS Genet 2007 Oct 10;3(10):2014-22. Epub 2007 Sep 10.

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pgen.0030183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041998PMC
October 2007