PubMed

Panel of Prototypical Raltegravir-Resistant Infectious Molecular Clones in a Novel Integrase-Deleted Cloning Vector.

Reuman EC, Bachmann MH, Varghese V, Fessel WJ, Shafer RW.

Antimicrob Agents Chemother. 2009 Nov 16. [Epub ahead of print]PMID: 19917747 [PubMed - as supplied by publisher]Related articles

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.

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.

J Acquir Immune Defic Syndr. 2009 Nov 1;52(3):309-15.PMID: 19734799 [PubMed - indexed for MEDLINE]Related articles

Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations.

Shahriar R, Rhee SY, Liu TF, Fessel WJ, Scarsella A, Towner W, Holmes SP, Zolopa AR, Shafer RW.

Antimicrob Agents Chemother. 2009 Nov;53(11):4869-78. Epub 2009 Aug 31.PMID: 19721070 [PubMed - in process]Related articles

Predictive value of HIV-1 genotypic resistance test interpretation algorithms.

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.

J Infect Dis. 2009 Aug 1;200(3):453-63.PMID: 19552527 [PubMed - indexed for MEDLINE]Related articles

Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype.

Altmann A, Sing T, Vermeiren H, Winters B, Van Craenenbroeck E, Van der Borght K, Rhee SY, Shafer RW, Schülter E, Kaiser R, Peres Y, Sönnerborg A, Fessel WJ, Incardona F, Zazzi M, Bacheler L, Van Vlijmen H, Lengauer T.

Antivir Ther. 2009;14(2):273-83.PMID: 19430102 [PubMed - indexed for MEDLINE]Related articles

The challenge of antiretroviral drug resistance in HIV-1-infected children.

Shafer RW.

J Pediatr (Rio J). 2009 Mar-Apr;85(2):91-4. English, Portuguese. No abstract available. PMID: 19319452 [PubMed - in process]Related articlesFree article

The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance.

Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW.

Bioinformatics. 2009 May 1;25(9):1197-8. Epub 2009 Mar 20.PMID: 19304876 [PubMed - indexed for MEDLINE]Related articlesFree article

Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients.

Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh B, Hanczaruk B, Simen BB, Egholm M, Shafer RW.

J Infect Dis. 2009 May 1;199(9):1275-85.PMID: 19301976 [PubMed - indexed for MEDLINE]Related articles

Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update.

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.

PLoS One. 2009;4(3):e4724. Epub 2009 Mar 6.PMID: 19266092 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.

Altmann A, Däumer M, Beerenwinkel N, Peres Y, Schülter E, Büch J, Rhee SY, Sönnerborg A, Fessel WJ, Shafer RW, Zazzi M, Kaiser R, Lengauer T.

J Infect Dis. 2009 Apr 1;199(7):999-1006.PMID: 19239365 [PubMed - indexed for MEDLINE]Related articles

Human immunodeficiency virus type 1 isolates with the reverse transcriptase (RT) mutation Q145M retain nucleoside and nonnucleoside RT inhibitor susceptibility.

Varghese V, Mitsuya Y, Shahriar R, Bachmann MH, Fessel WJ, Kagan RM, Shafer RW.

Antimicrob Agents Chemother. 2009 May;53(5):2196-8. Epub 2009 Feb 17.PMID: 19223644 [PubMed - indexed for MEDLINE]Related articlesFree article

Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options.

Shafer RW.

J Infect Dis. 2009 Mar 1;199(5):610-2. No abstract available. PMID: 19210160 [PubMed - indexed for MEDLINE]Related articles

Incomplete reconstitution of T cell subsets on combination antiretroviral therapy in the AIDS Clinical Trials Group protocol 384.

Robbins GK, Spritzler JG, Chan ES, Asmuth DM, Gandhi RT, Rodriguez BA, Skowron G, Skolnik PR, Shafer RW, Pollard RB; AIDS Clinical Trials Group 384 Team.

Clin Infect Dis. 2009 Feb 1;48(3):350-61.PMID: 19123865 [PubMed - indexed for MEDLINE]Related articles

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution.

Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20362-7. Epub 2008 Dec 15.PMID: 19075221 [PubMed - indexed for MEDLINE]Related articlesFree article

A highly prevalent and genetically diversified Picornaviridae genus in South Asian children.

Kapoor A, Victoria J, Simmonds P, Slikas E, Chieochansin T, Naeem A, Shaukat S, Sharif S, Alam MM, Angez M, Wang C, Shafer RW, Zaidi S, Delwart E.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20482-7. Epub 2008 Nov 25.PMID: 19033469 [PubMed - indexed for MEDLINE]Related articlesFree article

Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infection.

Bembom O, Petersen ML, Rhee SY, Fessel WJ, Sinisi SE, Shafer RW, van der Laan MJ.

Stat Med. 2009 Jan 15;28(1):152-72.PMID: 18825650 [PubMed - indexed for MEDLINE]Related articles

Rational use of antiretroviral therapy in low-income and middle-income countries: optimizing regimen sequencing and switching.

Elliott JH, Lynen L, Calmy A, De Luca A, Shafer RW, Zolfo M, Clotet B, Huffam S, Boucher CA, Cooper DA, Schapiro JM.

AIDS. 2008 Oct 18;22(16):2053-67. Review. No abstract available. PMID: 18753937 [PubMed - indexed for MEDLINE]Related articles

Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations.

Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, Jayakumar P, Gharizadeh B, Ronaghi M, Klein D, Fessel WJ, Shafer RW.

J Virol. 2008 Nov;82(21):10747-55. Epub 2008 Aug 20.PMID: 18715933 [PubMed - indexed for MEDLINE]Related articlesFree article

Knowledge integration of software for HIV drug resistance research.

Hernandez G Jr, Rhee SY, Shafer RW, Das AK.

AMIA Annu Symp Proc. 2007 Oct 11:973.PMID: 18694073 [PubMed - indexed for MEDLINE]Related articles

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW.

Retrovirology. 2008 Aug 7;5:74.PMID: 18687142 [PubMed - indexed for MEDLINE]Related articlesFree article

HIV-1 drug resistance mutations: an updated framework for the second decade of HAART.

Shafer RW, Schapiro JM.

AIDS Rev. 2008 Apr-Jun;10(2):67-84. Review.PMID: 18615118 [PubMed - indexed for MEDLINE]Related articlesFree article

Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies.

Shafer RW, Rhee SY, Bennett DE.

Antivir Ther. 2008;13 Suppl 2:59-68. Review.PMID: 18575192 [PubMed - indexed for MEDLINE]Related articles

Viral population estimation using pyrosequencing.

Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N.

PLoS Comput Biol. 2008 May 9;4(4):e1000074.PMID: 18437230 [PubMed - indexed for MEDLINE]Related articlesFree article

Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance.

Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, Shafer RW.

AIDS. 2008 Mar 30;22(6):717-25. Erratum in: AIDS. 2008 Oct 18;22(16):2225. PMID: 18356601 [PubMed - indexed for MEDLINE]Related articles

Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients.

Kapoor A, Shapiro B, Shafer RW, Shulman N, Rhee SY, Delwart EL.

Retrovirology. 2008 Jan 25;5:7.PMID: 18221530 [PubMed - indexed for MEDLINE]Related articlesFree article

Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment.

Mitsuya Y, Liu TF, Rhee SY, Fessel WJ, Shafer RW.

J Infect Dis. 2007 Oct 15;196(8):1177-9. Epub 2007 Sep 10.PMID: 17955436 [PubMed - indexed for MEDLINE]Related articlesFree article

A highly divergent picornavirus in a marine mammal.

Kapoor A, Victoria J, Simmonds P, Wang C, Shafer RW, Nims R, Nielsen O, Delwart E.

J Virol. 2008 Jan;82(1):311-20. Epub 2007 Oct 17.PMID: 17942560 [PubMed - indexed for MEDLINE]Related articlesFree article

World Antimalarial Resistance Network (WARN) III: molecular markers for drug resistant malaria.

Plowe CV, Roper C, Barnwell JW, Happi CT, Joshi HH, Mbacham W, Meshnick SR, Mugittu K, Naidoo I, Price RN, Shafer RW, Sibley CH, Sutherland CJ, Zimmerman PA, Rosenthal PJ.

Malar J. 2007 Sep 6;6:121.PMID: 17822535 [PubMed - indexed for MEDLINE]Related articlesFree article

The mitochondrial pharmacogenomics of haplogroup T: MTND2*LHON4917G and antiretroviral therapy-associated peripheral neuropathy.

Canter JA, Haas DW, Kallianpur AR, Ritchie MD, Robbins GK, Shafer RW, Clifford DB, Murdock DG, Hulgan T.

Pharmacogenomics J. 2008 Feb;8(1):71-7. Epub 2007 Aug 7.PMID: 17684475 [PubMed - indexed for MEDLINE]Related articles

Educational attainment and response to HAART during initial therapy for HIV-1 infection.

Marc LG, Testa MA, Walker AM, Robbins GK, Shafer RW, Anderson NB, Berkman LF; ACTG Data Analysis Concept Sheet Study Team.

J Psychosom Res. 2007 Aug;63(2):207-16.PMID: 17662759 [PubMed - indexed for MEDLINE]Related articles

Simple PCR assays improve the sensitivity of HIV-1 subtype B drug resistance testing and allow linking of resistance mutations.

Johnson JA, Li JF, Wei X, Lipscomb J, Bennett D, Brant A, Cong ME, Spira T, Shafer RW, Heneine W.

PLoS One. 2007 Jul 25;2(7):e638.PMID: 17653265 [PubMed]Related articlesFree article

Virologic efficacy of boosted double versus boosted single protease inhibitor therapy.

Petersen ML, Wang Y, van der Laan MJ, Rhee SY, Shafer RW, Fessel WJ.

AIDS. 2007 Jul 31;21(12):1547-54.PMID: 17630549 [PubMed - indexed for MEDLINE]Related articlesFree article

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance.

Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW.

Genome Res. 2007 Aug;17(8):1195-201. Epub 2007 Jun 28.PMID: 17600086 [PubMed - indexed for MEDLINE]Related articlesFree article

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance.

Altmann A, Beerenwinkel N, Sing T, Savenkov I, Doumer M, Kaiser R, Rhee SY, Fessel WJ, Shafer RW, Lengauer T.

Antivir Ther. 2007;12(2):169-78.PMID: 17503659 [PubMed - indexed for MEDLINE]Related articles

HIV-1 subtype B protease and reverse transcriptase amino acid covariation.

Rhee SY, Liu TF, Holmes SP, Shafer RW.

PLoS Comput Biol. 2007 May;3(5):e87.PMID: 17500586 [PubMed - indexed for MEDLINE]Related articlesFree article

Case files from Stanford University Medical Center: ten years of HAART: a long wait for full HIV suppression.

Shulman N, Shafer RW.

MedGenMed. 2007 Jan 16;9(1):10. No abstract available. PMID: 17435619 [PubMed - indexed for MEDLINE]Related articlesFree article

Case files from Stanford University Medical Center: Drug resistance testing in previously untreated patients with HIV--knowing what to look for and choosing appropriate therapy.

Shafer RW, Nguyen DP, Fessel WJ.

MedGenMed. 2006 Aug 7;8(3):32. No abstract available. PMID: 17406166 [PubMed - indexed for MEDLINE]Related articlesFree article

A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history.

Lin RS, Rhee SY, Shafer RW, Das AK.

Comput Syst Bioinformatics Conf. 2006:385-8.PMID: 17369658 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of HIV mutation changes based on treatment history.

Lin RS, Rhee SY, Shafer RW, Das AK.

AMIA Annu Symp Proc. 2006:1011.PMID: 17238630 [PubMed - indexed for MEDLINE]Related articlesFree article

Butting heads with resistance.

Shafer RW.

IAPAC Mon. 2006 Jun;12(6):180-9. No abstract available. PMID: 17233105 [PubMed - indexed for MEDLINE]Related articles

N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure.

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW.

AIDS Res Hum Retroviruses. 2006 Dec;22(12):1300-5.PMID: 17209774 [PubMed - indexed for MEDLINE]Related articlesFree article

HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance.

Shafer RW, Rhee SY, Pillay D, Miller V, Sandstrom P, Schapiro JM, Kuritzkes DR, Bennett D.

AIDS. 2007 Jan 11;21(2):215-23. Review.PMID: 17197813 [PubMed - indexed for MEDLINE]Related articlesFree article

Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors.

Deforche K, Camacho R, Grossman Z, Silander T, Soares MA, Moreau Y, Shafer RW, Van Laethem K, Carvalho AP, Wynhoven B, Cane P, Snoeck J, Clarke J, Sirivichayakul S, Ariyoshi K, Holguin A, Rudich H, Rodrigues R, Bouzas MB, Cahn P, Brigido LF, Soriano V, Sugiura W, Phanuphak P, Morris L, Weber J, Pillay D, Tanuri A, Harrigan PR, Shapiro JM, Katzenstein DA, Kantor R, Vandamme AM.

Infect Genet Evol. 2007 Jun;7(3):382-90. Epub 2006 Nov 28.PMID: 17127103 [PubMed - indexed for MEDLINE]Related articles

Genotypic predictors of human immunodeficiency virus type 1 drug resistance.

Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW.

Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17355-60. Epub 2006 Oct 25.PMID: 17065321 [PubMed - indexed for MEDLINE]Related articlesFree article

Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group study.

Motsinger AA, Ritchie MD, Shafer RW, Robbins GK, Morse GD, Labbe L, Wilkinson GR, Clifford DB, D'Aquila RT, Johnson VA, Pollard RB, Merigan TC, Hirsch MS, Donahue JP, Kim RB, Haas DW.

Pharmacogenet Genomics. 2006 Nov;16(11):837-45.PMID: 17047492 [PubMed - indexed for MEDLINE]Related articles

Rationale and uses of a public HIV drug-resistance database.

Shafer RW.

J Infect Dis. 2006 Sep 15;194 Suppl 1:S51-8. Review.PMID: 16921473 [PubMed - indexed for MEDLINE]Related articlesFree article

Case files from Stanford University Medical Center: the initial presentation of HIV-1 infection--where public and personal health meet.

Liu M, Holodniy M, Zolopa AR, Shafer RW.

MedGenMed. 2006 Jan 26;8(1):24. No abstract available. PMID: 16915154 [PubMed - indexed for MEDLINE]Related articlesFree article

HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL.

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Slome S, Flamm J, Horberg M, Hurley L, Klein D, Shafer RW.

J Acquir Immune Defic Syndr. 2006 Sep;43(1):56-9.PMID: 16885777 [PubMed - indexed for MEDLINE]Related articlesFree article

Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy.

Kallianpur AR, Hulgan T, Canter JA, Ritchie MD, Haines JL, Robbins GK, Shafer RW, Clifford DB, Haas DW.

AIDS. 2006 Jul 13;20(11):1503-13.PMID: 16847405 [PubMed - indexed for MEDLINE]Related articles

Effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy in HIV-1-positive subjects: results from ACTG 384.

Gandhi RT, Spritzler J, Chan E, Asmuth DM, Rodriguez B, Merigan TC, Hirsch MS, Shafer RW, Robbins GK, Pollard RB; ACTG 384 Team.

J Acquir Immune Defic Syndr. 2006 Aug 1;42(4):426-34.PMID: 16810109 [PubMed - indexed for MEDLINE]Related articles