Publications by authors named "John M Coffin"

100Publications

Correction to: An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses.

BMC Genomics 2020 07 29;21(1):517. Epub 2020 Jul 29.

Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, 21702, USA.

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http://dx.doi.org/10.1186/s12864-020-06924-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7388206PMC
July 2020

HIV-DRLink: A Tool for Reporting Linked HIV-1 Drug Resistance Mutations in Large Single-Genome Data Sets Using the Stanford HIV Database.

AIDS Res Hum Retroviruses 2020 Aug 27. Epub 2020 Aug 27.

HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA.

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http://dx.doi.org/10.1089/AID.2020.0109DOI Listing
August 2020

An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses.

BMC Genomics 2020 Mar 9;21(1):216. Epub 2020 Mar 9.

Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, 21702, USA.

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http://dx.doi.org/10.1186/s12864-020-6647-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7063773PMC
March 2020

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

AIDS Res Hum Retroviruses 2020 01 29;36(1):1-3. Epub 2019 Oct 29.

HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland.

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http://dx.doi.org/10.1089/AID.2019.0214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944138PMC
January 2020

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

PLoS Pathog 2019 07 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

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

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

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

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

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

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/s12977-014-0062-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149278PMC
August 2014

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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