Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

Publications

Analysis | Database | Reviews | Related Viruses | Case Studies


Melikian (2013)

Copyright © 2013,
Oxford University Press
Melikian GL, Rhee SY, Varghese V, Porter D, White K, Taylor J, Towner W, Troia P, Burack J, Dejesus E, Robbins GK, Razzeca K, Kagan R, Liu TF, Fessel WJ, Israelski D, Shafer RW (2013). Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. J Antimicrob Chemother, 2013 Aug 9.
Van Zyl (2013)

Copyright © 2013,
Public library of science
Van Zyl GU, Liu TF, Claassen M, Engelbrecht S, de Oliveira T, Preiser W, Wood NT, Travers S, Shafer RW (2013). Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens. PLoS One, 2013 Jun 26.
Varghese (2013)

Varghese V, Mitsuya Y, Fessel WJ, Liu TF, Melikian GL, Katzenstein DA, Schiffer CA, Holmes SP, Shafer RW (2013). Prototypical Recombinant Multi-Protease Inhibitor Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type-1. Antimicrobial Agents and Chemotherapy, 2013 Jun 24.
Tang (2013)

Copyright © 2013,
University of Chicago Press
Tang MW, Rhee SY, Bertagnolio S, Ford N, Holmes S, Sigaloff KC, Hamers RL, de Wit TF, Fleury HJ, Kanki PJ, Ruxrungtham K, Hawkins CA, Wallis CL, Stevens W, van Zyl GU, Manosuthi W, Hosseinipour MC, Ngo-Giang-Huong N, Belec L, Peeters M, Aghokeng A, Bunupuradah T, Burda S, Cane P, Cappelli G, Charpentier C, Dagnra AY, Deshpande AK, El-Katib Z, Eshleman SH, Fokam J, Gody JC, Katzenstein D, Koyalta DD, Kumwenda JJ, Lallemant M, Lynen L, Marconi VC, Margot NA, Moussa S, Ndung'u T, Nyambi PN, Orrell C, Schapiro JM, Schuurman R, Sirivichayakul S, Smith D, Zolfo M, Jordan MR, Shafer RW (2013). Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. Journal of Infectious Diseases, 2013 Jun 15.
Babrzadeh (2012)

Copyright © 2012,
Oxford University Press
Babrzadeh F, Varghese V, Pacold M, Liu TF, Nyren P, Schiffer C, Fessel WJ, Shafer RW (2012). Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. J Antimicrob Chemother. 2012 Oct 19.
Balamane (2012)

Balamane M, Varghese V, Melikian GL, Fessel WJ, Katzenstein DA, Shafer RW (2012). Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine. Antimicrobial Agents and Chemother. 2012 Aug;56(8):4522-4.
Rhee (2012)

Copyright © 2012,
BioMed Central Ltd
Rhee SY, Blanco JL, Liu TF, Pere I, Kaiser R, Zazzi M, Incardona F, Towner W, Gatell JM, De Luca A, Fessel WJ, Shafer RW (2012). Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes. AIDS Res Ther. 2012 May 3;9(1):13.
Melikian (2012)

Melikian GL, Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia-Cancio PV, Zolopa A, Robbins GK, Kagan R, Israelski D, Shafer RW (2012). Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. Antimicrobial Agents and Chemother. 2012 May;56(5):2305-13.
Tang (2012)

Tang MW, Kanki PJ, Shafer RW (2012). A Review of the Virological Efficacy of the 4 World Health Organization-Recommended Tenofovir-Containing Regimens for Initial HIV Therapy. Clin Infect Dis. 2012 Mar;54(6):862-75.
Doherty (2011)

Copyright © 2011,
BioMed Central Ltd
Doherty KM, Nakka P, King BM, Rhee SY, Holmes SP, Shafer RW, Radhakrishnan ML (2011). A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinformatics2011 Dec 15;12(1):477

Fessel (2011)

Copyright © 2010,
Elsevier B.V.
Fessel WJ, Anderson B, Follansbee SE, Winters MA, Lewis ST, Weinheimer SP, Petropoulos CJ, Shafer RW (2011). The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment. Antiviral Res. 2011 Dec;92(3):484-7. Epub 2011 Oct 4.

Varghese (2010)

Copyright © 2010,
Mary Ann Libert, Inc.
Varghese V, Liu TF, Rhee SY, Libiran P, Trevino C, Fessel WJ, Shafer RW. (2010). HIV-1 Integrase Sequence Variability in Antiretroviral Naive Patients and in Triple-Class Experienced Patients Subsequently Treated with Raltegravir. AIDS Res Hum Retroviruses, 2010 Oct

Rhee (2010)

Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW. (2010). HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrobial Agents and Chemotherapy, 2010 Oct

Varghese (2010)

Copyright © 2010,
Public library of science
Varghese V, Wang E, Babrzadeh F, Bachmann MH, Shahriar R, Liu T, Mappala SJ, Gharizadeh B, Fessel WJ, Katzenstein D, Kassaye S, Shafer RW. (2010). Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation. PLoS One, 2010 Jun 7

Reuman (2010)

Copyright © 2010,
Oxford University Press
Reuman EC, Rhee SY, Holmes SP, Shafer RW (2010). Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. Journal of Antinicrobial Chemotherapy, 2010 May 12

Reuman (2010)

Reuman EC, Bachmann MH, Varghese V, Fessel WJ, Shafer RW (2010). Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector. Antimicrobial Agents and Chemotherapy,2010 Feb;54(2):934-6.

Varghese (2009)

Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, Hanczaruk B, Blake LA, Gharizadeh B, Babrzadeh F, Bachmann MH, Fessel WJ, Shafer RW (2009). Minority Variants Associated with Transmitted and Acquired HIV-1 Nonnucleoside Reverse Transcriptase Inhibitor Resistance: Implications for the Use of Second-Generation Nonnucleoside Reverse Transcriptase Inhibitors. JAIDS, 2009 Sep 3

Shahriar (2009)

Shahriar R, Rhee SY, Liu TF, Fessel WJ, Scarcella A, Towner W, Holmes SP, Zolopa AR, Shafer RW (2009). Nonpolymorphic HIV-1 Protease and RT Treatment-Selected Mutations. Antimicrobial Agents and Chemotherapy, 2009 Aug 31

Rhee (2009)

Copyright © 2009,
University of Chicago Press
Rhee SY, Fessel WJ, Liu TF, Marlowe NM, Rowland CM, Rode RA, Vandamme AM, Van Laethem K, Brun-Vezinet F, Calvez V, Taylor J, Hurley L, Horberg M, Shafer RW (2009). Predictive Value of HIV-1 Genotypic Resistance Test Interpretation Algorithms. Journal of Infectious Diseases, 2009 Aug 1;200(3):453-463

Bennett (2009)

Copyright © 2008,
Public Library of Science
Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, Kiuchi M, Heneine W, Kantor R, Jordan MR, Schapiro JM, Vandamme AM, Sandstrom P, Boucher CA, van de Vijver D, Rhee SY, Liu TF, Pillay D, Shafer RW (2009). Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS ONE, 2009;4(3):e4724
Varghese (2009)

Varghese V, Mitsuya Y, Shahriar R, Bachmann MH, Fessel WJ, Kagan RM, Shafer RW (2009). HIV-1 Isolates with the RT Mutation Q145M Retain Nucleoside and Non-Nucleoside RT Inhibitor Susceptibility. Antimicrobial Agents and Chemotherapy, 2009 Feb 17
Rhee (2008)

Copyright © 2008,
Retrovirology
Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW (2008). Natural Variation of HIV-1 Group M Integrase: Implications for a New Class of Antiretroviral Inhibitors. Retrovirology, 2008 Aug 7;5:74
Mitsuya (2008)

Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, Jayakumar R, Gharizadeh B, Ronaghi M, Klein D, Fessel WJ, Shafer RW (2008). Minority HIV-1 Variants in Antiretroviral Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations. Journal of Virology, 2008 Aug 20 Epub
Bembom (2008)

Copyright © 2008,
Wiley InterScience
Bembom O, Petersen ML, Rhee SY, Fessel WJ, Sinisi SE, Shafer RW, van der Laan MJ (2008). Biomarker Discovery using Targeted Maximum-Likelihood Estimation: Application to the treatment of Antiretroviral-Resistant HIV Infection. Statistics in Medicine, 2008 Sep 29 Epub
Gifford (2008)

Copyright © 2008,
AIDS
Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, Shafer RW (2008). Sequence Editing by Apolipoprotein B RNA-editing Catalytic Component-B and Epidemiological Surveillance of Transmitted HIV-1 Drug Resistance. AIDS, 2008 Mar 30;22(6):717-25
Shafer (2008)

Copyright © 2008,
Antiviral Therapy
Shafer RW, Rhee SY, Bennett DE (2008). Consensus Drug Resistance Mutations for Epidemiological Surveillance: Basic Principles and Potential Controversies. Antiviral Therapy, Vol. 13 (2008) Suppl 2:59-68
Mitsuya (2007)

Copyright © 2007,
University of Chicago Press
Mitsuya Y, Liu TF, Rhee SY, Fessel WJ, Shafer RW (2007). Prevalence of Darunavir Resistance-Associated Mutations: Patterns of Occurrence and Association with Past Treatment. Journal of Infectious Diseases, Oct 15, 2007 196:1177-9

Petersen (2007)

Petersen ML, Wang Y, van der Laan MJ, Rhee SY, Shafer RW, Fessel WJ (2007). Virologic Efficacy of Boosted Double Versus Boosted Single Protease Inhibitor Therapy. AIDS July 31, 2007 ISSN 0269-9370

Wang (2007)

Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007). Characterization of Mutation Spectra with Ultra-Deep Pyrosequencing: Application to HIV-1 Drug Resistance. Genome Research June 28, 2007 ISSN 1088-9051/07

Rhee (2007)

Copyright © 2007,
PLoS Computational Biology
Rhee SY, Liu TF, Holmes SP, Shafer RW (2007). HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. PLoS Computational Biology May 2007 3:5(e87)

Shafer (2007)

Shafer RW, Rhee SY, Pillay D, Miller V, Sandstrom P, Schaprio JM, Kuritzkes DR, Bennett D.(2006). HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS Jan 11, 2007

Mitsuya (2006)

Copyright © 2006,
Mary Ann Libert, Inc.
Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW.(2006). N88D Facilitates the Co-occurrence of D30N and L90M and the Development of Multidrug Resistance in HIV Type 1 Protease following Nelfinavir Treatment Failure. AIDS Res Hum Retroviruses 22(12):1300-5

Rhee (2006)

Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW(2006). Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of National Academy of Sciences of the United States of America Oct 25, 2006

Click here to access the data sets and the results.

Mitsuya (2006)

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Slome S, Flamm J, Horberg M, Hurley L, Klein D, Shafer RW(2006). HIV-1 Drug Resistance Genotype Results in Patients With Plasma Samples With HIV-1 RNA Levels Less than 75 Copies/mL. JAIDS 43(1):56-9

Rhee (2006)

Rhee SY, Kantor R, Katzenstein DA, Camacho R, Morris L,Sirivichayakul S,Jorgensen L, Brigido LF, Schapiro JM,and Shafer RW for the international Non Subtype B HIV-1 Working Group(2006). HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS 20(5):643-651, March 21, 2006

Click here to access the HIVseq program

Rhee (2005)

Copyright © 2005,
University of Chicago Press
Rhee SY, Fessel WJ, Zolopa AR, Hurley L, Liu T, Taylor J, Nguyen DP, Slome S, Klein D, Horberg M, Flamm J, Follansbee S, Schapiro JM, Shafer RW (2005). HIV-1 Protease and Reverse-Transcriptase Mutations: Correlations with Antiretroviral Therapy in Subtype B Isolates and Implications for Drug-Resistance Surveillance. Journal of Infectious Diseases, Aug 1;192(3):456-65. Epub 2005 Jul 5.
Kantor (2005)

Copyright © 2005,
Public Library of Science
Kantor R, Katzenstein DA, Efron B, Carvalho AP, Wynhoven B, Cane P, Clarke J, Sirivichayakul S, Soares MA, Snoeck J, Pillay C, Rudich H, Rodrigues R, Holguin A, Ariyoshi K, Bouzas MB, Cahn P, Sugiura W, Soriano V, Brigido LF, Grossman Z, Morris L, Vandamme AM, Tanuri A, Phanuphak P, Weber JN, Pillay D, Harrigan PR, Camacho R, Schapiro JM and Shafer RW (2005). Impact of HIV-1 Subtype and Antiretroviral Therapy on Protease and Reverse Transcriptase Genotype: Results of a Global Collaboration. PLoS Med. Apr;2(4):e112.
Johnston (2005)

Johnston E, Dupnik KM, Gonzales MJ, Winters MA, Rhee SY, Imamichi T and Shafer RW (2005). Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. AIDS 19(7):731-3.

Click here to access sequences.

Zhang (2005)

Jie Zhang, Soo-Yon Rhee, Jonathan Taylor and Robert W. Shafer (2005). Comparison of the Precision and Sensitivity of the Antivirogram and PhenoSense HIV Drug Susceptibility Assays. JAIDS 38(4):439-444.

Click here to access data sets and statistical analyses used.

Johnston (2004)

Johnston E, Winters MA, Rhee SY, Merigan TC, Schiffer CA and Shafer RW. (2004). Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Antimicrobial Agents and Chemotherapy 48(12):4864-8.
Rhee (2004)

Soo-Yon Rhee, Tommy Liu, Jaideep Ravela, Matthew J. Gonzales and Robert W. Shafer (2004). Distribution of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Mutation Patterns in 4,183 Persons Undergoing Genotypic Resistance Testing. Antimicrobial Agents and Chemotherapy 48(8):3122-3126.
Kantor (2004)

Rami Kantor, Robert W. Shafer, Stephen Follansbee, Jonathan Taylor, David Shilane, Leo Hurley, Dong-Phuong Nguyen, David Katzenstein, and W. Jeffrey Fessel (2004). Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. AIDS 18(11):1503-1511.
Kapoor (2004)

Amit Kapoor, Morris Jones, Robert W. Shafer, Soo-Yon Rhee, Powel Kazanjian, and Eric L. Delwart (2004). Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay.
Gonzales (2003)

Gonzales MJ, Johnson E, Dupnik KM, Imamichi T, Shafer RW.(2003) Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. JAIDS,1;34(4):398-402
Gonzales (2003)

Copyright © 2003,
Mary Ann Libert, Inc.
Matthew J. Gonzales, Ilana Belitskaya, Kathryn M. Dupnik, Soo-Yon Rhee and Robert W. Shafer. (2003) Protease and Reverse Transcriptase Mutation Patterns in HIV Type 1 Isolates from Heavily Treated Persons: Comparison of Isolates from Northern California with Isolates from Other Regions. AIDS Res Hum Retroviruses, 19:909-915
Gonzales (2003)

Copyright © 2003,
University of Chicago Press
Matthew J. Gonzales, Eric Delwart, Soo-Yon Rhee, Rose Tsui, Andrew R. Zolopa, Jonathan Taylor, and Robert W. Shafer. (2003) Lack of Detectable Human Immunodeficiency Virus Type 1 Superinfection during 1072 Person-Years of Observation. Journal of Infectious Diseases, 188(3):397-405
Ravela (2003)

Jaideep Ravela, Bradley J. Betts, Francoise Brun-Vézinet, Anne-Mieke Vandamme, Diane Descamps, Kristel Van Laethem, Kate Smith, Jonathan M. Schapiro, Dean Winslow, Caroline Reid, Robert W. Shafer (2003). HIV-1 Protease and Reverse Transcriptase Mutation Patterns Responsible for Discordances Between Genotypic Drug Resistance Interpretation Algorithms JAIDS 33(1):8-14

View Data

Wu (2003)

Thomas D. Wu, Celia A. Schiffer, Matthew J. Gonzales, Jonathan Taylor, Rami Kantor, Sunwen Chou, Dennis Israelski, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer (2003). Mutation Patterns and Structural Correlates in HIV-1 Protease Following Varying Degrees of Protease Inhibitor Treatment J. Virol. 77(8): 4836-4847.

View Data

Gonzales (2003)

Matthew J. Gonzales, Thomas D. Wu, Jonathan Taylor, Ilana Belitskaya, Rami Kantor, Dennis Israelski, Sunwen Chou, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer (2003). Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors AIDS 17(6):791-799.

View Data

Kantor (2002)

Copyright © 2002,
Mary Ann Libert, Inc.
Rami Kantor, Lynn S. Zijenah, Robert W. Shafer, Solomon Mutetwa, Elizabeth Johnston, Robert Lloyd, Andrea Von Lieven, Dennis Israelski, and David A. Katzenstein (2002). HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy AIDS Res Hum Retroviruses, 18(18):1407-13.
Palmer (2002)

Sarah Palmer, Dominique Vuitton, Matthew J. Gonzales, Agnés Bassignot, and Robert W. Shafer (2002) Reverse Transcriptase and Protease Sequence Evolution in Two HIV-1-Infected Couples JAIDS, 31(3):285-290.
Eshleman (2002)

Copyright © 2002,
Mary Ann Libert, Inc.
Susan H. Eshleman, Matthew J. Gonzales, Graziella Becker-Pergola, Shawn C. Cunningham, Laura A. Guay, G. Brooks Jackson, and Robert W. Shafer (2002) Identification of Ugandan HIV Type 1 Variants with Unique Patterns of Recombination in pol Involving Subtypes A and D AIDS Research and Human Retroviruses, 18:507-511.
Kantor (2002)

Rami Kantor, W. Jeffrey Fessel, Andrew R. Zolopa, Dennis Israelski, Nancy Shulman, Jose G. Montoya Michael Harbour, Jonathan M. Schapiro and Robert W. Shafer. (2002) Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy Antimicrobial Agents and Chemotherapy, 46:1086-1092.
Gonzales (2001)

Copyright © 2001,
University of Chicago Press.
Matthew J. Gonzales, Rhoderick N. Machekano, and Robert W. Shafer. (2001) Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern california clinic-based population. Journal of Infectious Diseases, 184:998-1006.
Shafer (2001)

Shafer RW, Hertogs K, Zolopa AR, Warford A, Bloor S, Betts BJ, Merigan TC, Harrigan R, Larder BA(2001). High Degree of Interlaboratory Reproducibility of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Sequencing of Plasma Samples from Heavily Treated Patients. Journal of Clinical Microbiology 39(4):1522-9

Shafer (1999)

Robert W. Shafer, Phillip Hsu, Amy K. Patick, Charles Craig, and Volker Brendel. (1999) Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. Journal of Virology, 73:6197-6202.
Zolopa (1999)

Copyright © 1999,
Annals of Internal Medicine
Andrew R. Zolopa, MD; Robert W. Shafer, MD; Ann Warford, PhD; Jose G. Montoya, MD; Philip Hsu, BA; David Katzentein, MD; Thomas C. Merigan, MD; and Brad Efron, PhD. (1999) HIV-1 Genotypic Resistance Patterns Predict Response to Saquinavir-Ritonavir Therapy in Patients in Whom Previous Protease Inhibitor Therapy Had Failed. Annals of Internal Medicine, 131(11):813-21
Tang (2012)

Copyright © 2012,
S.Karger AG, Basel
Tang MW, Liu TF, Shafer RW. (2012). The HIVdb system for HIV-1 genotypic resistance interpretation. Intervirology 2012;55(2):98-101. Epub 2012 Jan 24

de Oliveira (2010)

Copyright © 2010,
Nature
de Oliveira T, Shafer RW, Seebregts C (2010). Public database for HIV drug resistance in southern Africa. Nature, 2010 Apr 1;464(7289):673
Gifford (2009)

Copyright © 2009,
Oxford University Press
Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW (2009). The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics, 2009 Mar 20.
Betts (2003)

Reproduced with Permission from
American Society for Microbiology
Bradley J. Betts and Robert W. Shafer, (2003) Algorithm Specification Interface for Human Immunodeficiency Virus Type 1 Genotypic Interpretation. Journal of Clinical Microbiology, 41(6), 2792-4.
Rhee (2003)

Reproduced with Permission from
NAR Online
Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 31(1), 298-303.
Gonzales (2002)

Copyright © 2002,
Oxford Journals.
Matthew J. Gonzales, Jonathan M. Dugan, and Robert W. Shafer (2002) Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN) Bioinformatics, 18(6), 886-887.
Kantor (2001)

Reproduced with Permission from
NAR Online
Rami Kantor, Rhoderick Machekano, Matthew J. Gonzales, Kathryn Dupnik, Jonathan M. Shapiro, and Robert W. Shafer. (2001) Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs Nucleic Acids Research, 29(1), 296-299.
Shafer (2000)

Copyright © 2000,
Nature America, Inc.
Robert W. Shafer, Duane R. Jung, and Bradley J. Betts. (2000) Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. Nature Medicine, 6(11), 1290-1292.
Shafer (2000)

Reproduced with Permission from
NAR Online
Robert W. Shafer, Duane R. Jung, Bradley J. Betts, Yinong Xi, and Matthew J. Gonzales. (2000) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 28(1), 346-348.
Shafer (1999)

Reproduced with Permission from
NAR Online
Robert W. Shafer, Derek Stevenson, and Bryan Chan. (1999) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 27(1), 348-352.

Tang (2012)

Copyright © 2012,
Drugs
Tang MW, and Shafer RW (2012). HIV-1 Antiretroviral Resistance: Scientific Principles and Clinical Applications. Drugs 2012 Jun 18;72(9)
Blanco (2011)

Blanco JL, Varghese V, Rhee SY, Gatell JM, Shafer RW (2011). HIV-1 integrase inhibitor resistance and its clinical implications. JID 2011 May 1;203(9):1204-14
Shafer (2009)

Shafer RW (2009). The challenge of antiretroviral drug resistance in HIV-1-infected children. Jornal de pediatria 2009 Mar-Apr;85(2):91-4
Shafer (2009)

Shafer RW (2009). Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. Journal of Infectious Diseases 2009 Mar 1;199(5):610-2
Shafer (2008)

Copyright © 2008,
AIDS
Shafer RW, Schapiro JM (2008). HIV-1 Drug Resistance Mutations: an Updated Framework for the Second Decade of HAART. AIDS, Rev. 2008;10:67-84
Shafer (2006)

Shafer RW(2006). Rationale and Uses of a Public HIV Drug-Resistance Database. Journal of Infectious Diseases 194 Suppl 1:S51-8

Liu (2006)

Liu TF, Shafer RW(2006). Web Resources for HIV type 1 Genotypic-Resistance Test Interpretation. Clin Infect Dis 42(11):1608-18. Epub 2006 Apr 28

Shafer (2005)

Shafer RW and Schapiro JM. (2005) Drug resistance and antiretroviral drug development. J Antimicrob Chemother
Shafer (2002)

Robert W. Shafer (2002) Genotypic testing for human immunodeficiency virus type 1 drug resistance Clinical Microbiology Reviews 15:247-277
Shafer (2001)

Robert W. Shafer, Kathryn M. Dupnik, Mark A. Winters, and Susan H. Eshleman. (2001) A guide to HIV-1 reverse transcriptase and protease sequencing for drug resistance studies. Human Retroviruses and AIDS, Theoretical Biology and Biophysics. Los Alamos National Laboratories.
Shafer (2000)

Copyright © 2000,
Permanyer Publications
Robert W. Shafer, Rami Kantor, and Matthew J. Gonzales. (2000) The genetic basis of HIV-1 resistance to reverse transcriptase and protease inhibitors AIDS Reviews, 2, 211-228.
Shafer (2000)

Copyright © 2000,
University of Chicago Press.
Robert W. Shafer, Stanley C. Deresinski (2000) Human immunodeficiency virus information on the web: A guided tour. Clin Infect Dis, 31(2):568-77.
 

Margeridon-Thermet (2013)

Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, Martin R, Liu TF, Pacold M, Reuman EC, Holmes SP, Borroto-Esoda K, Shafer RW (2013). Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment. Antimicrobial Agents and Chemotherapy, 2013 Jan.
Reuman (2010)

Copyright © 2010,
Oxford Journals
Reuman EC, Margeridon-Thermet S, Caudill HB, Liu T, Borroto-Esoda K, Svarovskaia ES, Holmes S, Shafer RW. (2010). A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads.   Bioinformatics, 2010 Oct.
Rhee (2010)

Copyright © 2010,
Elsevier B.V.
Rhee SY, Margeridon-Thermet S, Nguyen MH, Liu TF, Kagan RM, Beggel B, Verheyen J, Kaiser R, Shafer RW. (2010). Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery.   Antiviral Res., 2010 Sept.
Margeridon-Thermet (2009)

Copyright © 2009,
University of Chicago Press
Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh F, Hanczaruk B, Simen BB, Egholm M and Shafer RW (2009) Nancy Shulman, Robert W. Shafer (2007) Ultra-Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse-Transcriptase Inhibitor (NRTI)-Treated Patients and NRTI-Naive Patients   Journal of Infectious Diseases, 2009 May 1;199(9):1275-85.
Gifford (2008)


Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW (2008). A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of National Academy of Sciences of the United States of America, 2008 Dec 23;105(51):20362-7

Shulman (2007)

Nancy Shulman, Robert W. Shafer (2007) Case files from Stanford University Medical Center: Ten Years of HAART: A Long Wait for Full HIV Suppression   Medscape General Medicine 2007;9(1):10.
Liu (2006)

Minghsun Liu, Mark Holodniy, Andrew R. Zolopa, Robert W. Shafer (2006) Case files from Stanford University Medical Center: The Initial Presentation of HIV-1 Infection -- Where Public and Personal Health Meet   Medscape General Medicine 2006;8(1):24.