| Year |
Citation |
Score |
| 2024 |
Tao K, Zhou J, Nagarajan P, Tzou PL, Shafer RW. Comprehensive database of HIV mutations selected during antiretroviral in vitro passage experiments. Antiviral Research. 230: 105988. PMID 39154752 DOI: 10.1016/j.antiviral.2024.105988 |
0.527 |
|
| 2024 |
Duffey M, Shafer RW, Timm J, Burrows JN, Fotouhi N, Cockett M, Leroy D. Combating antimicrobial resistance in malaria, HIV and tuberculosis. Nature Reviews. Drug Discovery. PMID 38750260 DOI: 10.1038/s41573-024-00933-4 |
0.454 |
|
| 2024 |
Chu C, Tao K, Kouamou V, Avalos A, Scott J, Grant PM, Rhee SY, McCluskey SM, Jordan MR, Morgan RL, Shafer RW. Prevalence of Emergent Dolutegravir Resistance Mutations in People Living with HIV: A Rapid Scoping Review. Viruses. 16. PMID 38543764 DOI: 10.3390/v16030399 |
0.8 |
|
| 2023 |
Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations. The Journal of General Virology. 104. PMID 37801004 DOI: 10.1099/jgv.0.001898 |
0.647 |
|
| 2023 |
Tao K, Rhee SY, Chu C, Avalos A, Ahluwalia AK, Gupta RK, Jordan MR, Shafer RW. Treatment Emergent Dolutegravir Resistance Mutations in Individuals Naïve to HIV-1 Integrase Inhibitors: A Rapid Scoping Review. Viruses. 15. PMID 37766338 DOI: 10.3390/v15091932 |
0.469 |
|
| 2023 |
Inzaule SC, Siedner MJ, Little SJ, Avila-Rios S, Ayitewala A, Bosch RJ, Calvez V, Ceccherini-Silberstein F, Charpentier C, Descamps D, Eshleman SH, Fokam J, Frenkel LM, Gupta RK, Ioannidis JPA, ... ... Shafer RW, et al. Recommendations on data sharing in HIV drug resistance research. Plos Medicine. 20: e1004293. PMID 37738247 DOI: 10.1371/journal.pmed.1004293 |
0.819 |
|
| 2023 |
Mbuagbaw L, Garcia C, Brenner B, Cecchini D, Chakroun M, Djiadeu P, Holguin A, Mor O, Parkin N, Santoro MM, Ávila-Ríos S, Fokam J, Phillips A, Shafer RW, Jordan MR. Checklist for studies of HIV drug resistance prevalence or incidence: rationale and recommended use. The Lancet. Hiv. PMID 37716367 DOI: 10.1016/S2352-3018(23)00173-X |
0.514 |
|
| 2023 |
Nouhin J, Tzou P, Rhee SY, Sahoo MK, Pinsky BA, Krupkin MA, Puglisi JD, Puglisi EV, Shafer RW. HIV-1 5'-Leader Mutations in Plasma Viruses Before and After the Development of Reverse Transcriptase Inhibitor-Resistance Mutations. Medrxiv : the Preprint Server For Health Sciences. PMID 37333388 DOI: 10.1101/2023.06.04.23290942 |
0.698 |
|
| 2023 |
Tao K, Rhee SY, Tzou PL, Osman ZA, Pond SLK, Holmes SP, Shafer RW. HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing. Viruses. 15. PMID 37112972 DOI: 10.3390/v15040992 |
0.452 |
|
| 2023 |
Rhee SY, Schapiro JM, Saladini F, Zazzi M, Khoo S, Shafer RW. Potential role of doravirine for the treatment of HIV-1-infected persons with transmitted drug resistance. Aids Research and Therapy. 20: 8. PMID 36750835 DOI: 10.1186/s12981-023-00503-5 |
0.478 |
|
| 2023 |
Smith J, Bansi-Matharu L, Cambiano V, Dimitrov D, Bershteyn A, van de Vijver D, Kripke K, Revill P, Boily MC, Meyer-Rath G, Taramusi I, Lundgren JD, van Oosterhout JJ, Kuritzkes D, Schaefer R, ... ... Shafer R, et al. Predicted effects of the introduction of long-acting injectable cabotegravir pre-exposure prophylaxis in sub-Saharan Africa: a modelling study. The Lancet. Hiv. PMID 36642087 DOI: 10.1016/S2352-3018(22)00365-4 |
0.317 |
|
| 2022 |
Kassaye SG, Grossman Z, Vengurlekar P, Chai W, Wallace M, Rhee SY, Meyer WA, Kaufman HW, Castel A, Jordan J, Crandall KA, Kang A, Kumar P, Katzenstein DA, Shafer RW, et al. Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States. Viruses. 15. PMID 36680108 DOI: 10.3390/v15010068 |
0.677 |
|
| 2022 |
Tao K, Rhee SY, Tzou PL, Holmes S, Shafer RW. Highly Ambiguous HIV-1 pol Positions Encoding Multiple Amino Acids Usually Result from Antiviral or Immune Selection Pressure. Aids Research and Human Retroviruses. PMID 36515174 DOI: 10.1089/AID.2022.0094 |
0.535 |
|
| 2022 |
Wensing AM, Calvez V, Ceccherini-Silberstein F, Charpentier C, Günthard HF, Paredes R, Shafer RW, Richman DD. 2022 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine. 30: 559-574. PMID 36375130 |
0.509 |
|
| 2022 |
Tzou PL, Tao K, Sahoo MK, Kosakovsky Pond SL, Pinsky BA, Shafer RW. Sierra SARS-CoV-2 sequence and antiviral resistance analysis program. Journal of Clinical Virology : the Official Publication of the Pan American Society For Clinical Virology. 157: 105323. PMID 36334368 DOI: 10.1016/j.jcv.2022.105323 |
0.545 |
|
| 2022 |
Rhee SY, Parkin N, Harrigan PR, Holmes S, Shafer RW. Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir. Antiviral Research. 105427. PMID 36191692 DOI: 10.1016/j.antiviral.2022.105427 |
0.394 |
|
| 2022 |
Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clinical Microbiology Reviews. e0005222. PMID 36102816 DOI: 10.1128/cmr.00052-22 |
0.445 |
|
| 2022 |
Rhee SY, Boehm M, Tarasova O, Di Teodoro G, Abecasis AB, Sönnerborg A, Bailey AJ, Kireev D, Zazzi M, Shafer RW. Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations. Pathogens (Basel, Switzerland). 11. PMID 35631067 DOI: 10.3390/pathogens11050546 |
0.534 |
|
| 2022 |
Rhee SY, Kassaye SG, Jordan MR, Kouamou V, Katzenstein D, Shafer RW. Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review. The Lancet. Microbe. 3: e392-e398. PMID 35544100 DOI: 10.1016/S2666-5247(21)00250-0 |
0.805 |
|
| 2022 |
DeVos J, McCarthy K, Sewe V, Akinyi G, Junghae M, Opollo V, Nouhin J, Shafer R, Zeh C, Ramos A, Alexander H, Chang J. A Partially Multiplexed HIV Drug Resistance (HIVDR) Assay for Monitoring HIVDR Mutations of the Protease, Reverse-Transcriptase (PRRT), and Integrase (INT). Microbiology Spectrum. e0177621. PMID 35510849 DOI: 10.1128/spectrum.01776-21 |
0.472 |
|
| 2021 |
Hoffman SA, Costales C, Sahoo MK, Palanisamy S, Yamamoto F, Huang C, Verghese M, Solis DC, Sibai M, Subramanian A, Tompkins LS, Grant P, Shafer RW, Pinsky BA. SARS-CoV-2 Neutralization Resistance Mutations in Patient with HIV/AIDS, California, USA. Emerging Infectious Diseases. 27. PMID 34296992 DOI: 10.3201/eid2710.211461 |
0.64 |
|
| 2021 |
Rhee SY, Tzou PL, Shafer RW. Temporal Trends in HIV-1 Mutations Used for the Surveillance of Transmitted Drug Resistance. Viruses. 13. PMID 34064774 DOI: 10.3390/v13050879 |
0.533 |
|
| 2021 |
Bailey AJ, Rhee SY, Shafer RW. Integrase Strand Transfer Inhibitor Resistance in Integrase Strand Transfer Inhibitor-Naïve Persons. Aids Research and Human Retroviruses. PMID 33683148 DOI: 10.1089/AID.2020.0261 |
0.462 |
|
| 2021 |
Shafer RW, Dupnik K, Winters MA, Eshleman SH. A Guide to HIV-1 Reverse Transcriptase and Protease Sequencing for Drug Resistance Studies. Hiv Sequence Compendium. 2001: 1-51. PMID 22324021 |
0.608 |
|
| 2020 |
Ndembi N, Murtala-Ibrahim F, Tola M, Jumare J, Aliyu A, Alabi P, Mensah C, Abimiku A, Quiñones-Mateu ME, Crowell TA, Rhee SY, Shafer RW, Gupta R, Blattner W, Charurat ME, et al. Predictors of first-line antiretroviral therapy failure among adults and adolescents living with HIV/AIDS in a large prevention and treatment program in Nigeria. Aids Research and Therapy. 17: 64. PMID 33143751 DOI: 10.1186/s12981-020-00317-9 |
0.348 |
|
| 2020 |
Saladini F, Giammarino F, Hosseini BA, Giannini A, Boccuto A, Dragoni F, Vicenti I, Shafer RW, Zazzi M. In vitro cross-resistance to doravirine in a panel of HIV-1 clones harbouring multiple NNRTI resistance mutations. The Journal of Antimicrobial Chemotherapy. PMID 32974670 DOI: 10.1093/jac/dkaa401 |
0.541 |
|
| 2020 |
Rhee SY, Kassaye SG, Barrow G, Sundaramurthi JC, Jordan MR, Shafer RW. HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates. Journal of the International Aids Society. 23: e25611. PMID 32936523 DOI: 10.1002/jia2.25611 |
0.56 |
|
| 2020 |
Rhee SY, Clutter D, Hare CB, Tchakoute CT, Sainani K, Fessel WJ, Hurley L, Slome S, Pinsky BA, Silverberg MJ, Shafer RW. Virological Failure and Acquired Genotypic Resistance Associated With Contemporary Antiretroviral Treatment Regimens. Open Forum Infectious Diseases. 7: ofaa316. PMID 32904894 DOI: 10.1093/Ofid/Ofaa316 |
0.601 |
|
| 2020 |
Noguera-Julian M, Lee ER, Shafer RW, Kantor R, Ji H. Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses. 12. PMID 32575676 DOI: 10.3390/v12060666 |
0.498 |
|
| 2020 |
Ávila-Ríos S, Parkin N, Swanstrom R, Paredes R, Shafer R, Ji H, Kantor R. Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations. Viruses. 12. PMID 32516949 DOI: 10.3390/V12060617 |
0.442 |
|
| 2020 |
Duarte HA, Babigumira JB, Enns EA, Stauffer DC, Shafer RW, Beck IA, Garrison LP, Chung MH, Frenkel LM, Bendavid E. Cost-effectiveness analysis of pre-ART HIV drug resistance testing in Kenyan women. Eclinicalmedicine. 22: 100355. PMID 32490370 DOI: 10.1016/J.Eclinm.2020.100355 |
0.372 |
|
| 2020 |
Tzou PL, Kosakovsky Pond SL, Avila-Rios S, Holmes SP, Kantor R, Shafer RW. Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. Plos One. 15: e0225352. PMID 32102090 DOI: 10.1371/journal.pone.0225352 |
0.547 |
|
| 2020 |
Tzou PL, Descamps D, Rhee SY, Raugi DN, Charpentier C, Taveira N, Smith RA, Soriano V, de Mendoza C, Holmes SP, Gottlieb GS, Shafer RW. Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2. The Journal of Infectious Diseases. PMID 31965175 DOI: 10.1093/infdis/jiaa026 |
0.62 |
|
| 2019 |
Wensing AM, Calvez V, Ceccherini-Silberstein F, Charpentier C, Günthard HF, Paredes R, Shafer RW, Richman DD. 2019 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine. 27: 111-121. PMID 31634862 |
0.509 |
|
| 2019 |
Tzou PL, Rhee SY, Descamps D, Clutter DS, Hare B, Mor O, Grude M, Parkin N, Jordan MR, Bertagnolio S, Schapiro JM, Harrigan PR, Geretti AM, Marcelin AG, Shafer RW. Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance. The Journal of Antimicrobial Chemotherapy. PMID 31617907 DOI: 10.1093/jac/dkz417 |
0.527 |
|
| 2019 |
Weber J, Volkova I, Sahoo MK, Tzou PL, Shafer RW, Pinsky BA. Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing. The Journal of Molecular Diagnostics : Jmd. PMID 31382033 DOI: 10.1016/J.Jmoldx.2019.06.003 |
0.745 |
|
| 2019 |
Tzou PL, Rhee SY, Shafer R. Amino Acid Prevalence of HIV-1 pol Mutations by Direct PCR and Single Genome Sequencing. Aids Research and Human Retroviruses. PMID 31317771 DOI: 10.1089/AID.2018.0289 |
0.469 |
|
| 2019 |
Rhee SY, Grant PM, Tzou PL, Barrow G, Harrigan PR, Ioannidis JPA, Shafer RW. A systematic review of the genetic mechanisms of dolutegravir resistance. The Journal of Antimicrobial Chemotherapy. PMID 31280314 DOI: 10.1093/jac/dkz256 |
0.323 |
|
| 2019 |
Chimukangara B, Lessells RJ, Rhee SY, Giandhari J, Kharsany ABM, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, ... ... Shafer RW, et al. Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis. Eclinicalmedicine. 9: 26-34. PMID 31143879 DOI: 10.1016/J.Eclinm.2019.03.006 |
0.728 |
|
| 2019 |
Clutter DS, Mazarei G, Sinha R, Manasa J, Nouhin J, LaPrade E, Bolouki S, Tzou PL, Hannita-Hui J, Sahoo MK, Kuimelis P, Kuimelis RG, Pinsky BA, Schoolnik GK, Hassibi A, ... Shafer RW, et al. Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance. The Journal of Molecular Diagnostics : Jmd. PMID 31026601 DOI: 10.1016/J.Jmoldx.2019.02.005 |
0.801 |
|
| 2019 |
Inzaule SC, Hamers RL, Doherty M, Shafer RW, Bertagnolio S, Rinke de Wit TF. Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens. The Lancet. Infectious Diseases. PMID 30902440 DOI: 10.1016/S1473-3099(18)30710-2 |
0.52 |
|
| 2018 |
Chimukangara B, Kharsany AB, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer R, Hunt G, Pillay D, et al. Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa. Aids Research and Human Retroviruses. PMID 30430843 DOI: 10.1089/AID.2018.0202 |
0.784 |
|
| 2018 |
Rhee SY, Shafer RW. Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. Scientific Data. 5: 180148. PMID 30063225 DOI: 10.1038/sdata.2018.148 |
0.49 |
|
| 2018 |
Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD. Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 30052811 DOI: 10.1093/Cid/Ciy463 |
0.526 |
|
| 2018 |
Tzou PL, Rhee SY, Pond SLK, Manasa J, Shafer RW. Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy. Scientific Data. 5: 180147. PMID 30040081 DOI: 10.1038/sdata.2018.147 |
0.76 |
|
| 2018 |
Rhee SY, Clutter D, Fessel WJ, Klein D, Slome S, Pinsky BA, Marcus JL, Hurley L, Silverberg MJ, Kosakovsky Pond SL, Shafer RW. Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance in a Large U.S. Clinic Population. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 29846534 DOI: 10.1093/Cid/Ciy453 |
0.66 |
|
| 2018 |
Tzou PL, Ariyaratne P, Varghese V, Lee C, Rakhmanaliev E, Villy C, Yee M, Tan K, Michel G, Pinsky BA, Shafer RW. Comparison of anDiagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing. Journal of Clinical Microbiology. PMID 29618499 DOI: 10.1128/Jcm.00105-18 |
0.632 |
|
| 2017 |
Shafer RW. Human Immunodeficiency Virus Type 1 Drug Resistance Mutations Update. The Journal of Infectious Diseases. PMID 28968669 DOI: 10.1093/infdis/jix398 |
0.44 |
|
| 2017 |
Manasa J, Varghese V, Pond SLK, Rhee SY, Tzou PL, Fessel WJ, Jang KS, White E, Rögnvaldsson T, Katzenstein DA, Shafer RW. Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors. Scientific Reports. 7: 11559. PMID 28912582 DOI: 10.1038/s41598-017-11893-8 |
0.737 |
|
| 2017 |
Clutter DS, Zhou S, Varghese V, Rhee SY, Pinsky BA, Jeffrey Fessel W, Klein DB, Spielvogel E, Holmes SP, Hurley LB, Silverberg MJ, Swanstrom R, Shafer RW. Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing. The Journal of Infectious Diseases. 216: 387-391. PMID 28859436 DOI: 10.1093/Infdis/Jix338 |
0.694 |
|
| 2017 |
Paredes R, Tzou PL, van Zyl G, Barrow G, Camacho R, Carmona S, Grant PM, Gupta RK, Hamers RL, Harrigan PR, Jordan MR, Kantor R, Katzenstein DA, Kuritzkes DR, Maldarelli F, ... ... Shafer RW, et al. Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation. Plos One. 12: e0181357. PMID 28753637 DOI: 10.1371/journal.pone.0181357 |
0.745 |
|
| 2017 |
Rhee SY, Varghese V, Holmes SP, Van Zyl GU, Steegen K, Boyd MA, Cooper DA, Nsanzimana S, Saravanan S, Charpentier C, de Oliveira T, Etiebet MA, Garcia F, Goedhals D, Gomes P, ... ... Shafer RW, et al. Mutational correlates of virological failure in individuals receiving a WHO-recommended tenofovir-containing first-line regimen: An international collaboration. Ebiomedicine. PMID 28365230 DOI: 10.1016/J.Ebiom.2017.03.024 |
0.327 |
|
| 2017 |
Wensing AM, Calvez V, Günthard HF, Johnson VA, Paredes R, Pillay D, Shafer RW, Richman DD. 2017 Update of the Drug Resistance Mutations in HIV-1. Topics in Antiviral Medicine. 24: 132-133. PMID 28208121 |
0.509 |
|
| 2017 |
Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS. Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. Elife. 6. PMID 28103185 DOI: 10.7554/eLife.24879 |
0.508 |
|
| 2016 |
Gregson J, Kaleebu P, Marconi VC, van Vuuren C, Ndembi N, Hamers RL, Kanki P, Hoffmann CJ, Lockman S, Pillay D, de Oliveira T, Clumeck N, Hunt G, Kerschberger B, Shafer RW, et al. Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study. The Lancet. Infectious Diseases. PMID 27914856 DOI: 10.1016/S1473-3099(16)30469-8 |
0.527 |
|
| 2016 |
Clutter DS, Jordan MR, Bertagnolio S, Shafer RW. HIV-1 drug resistance and resistance testing. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 27587334 DOI: 10.1016/j.meegid.2016.08.031 |
0.486 |
|
| 2016 |
Sahoo MK, Varghese V, White E, Winslow M, Katzenstein DA, Shafer RW, Pinsky BA. Evaluation of the Aptima HIV-1 Quant Dx Assay using Plasma and Dried Blood Spots. Journal of Clinical Microbiology. PMID 27535684 DOI: 10.1128/JCM.01569-16 |
0.734 |
|
| 2016 |
Avila-Rios S, Sued O, Rhee SY, Shafer RW, Reyes-Teran G, Ravasi G. Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis. Plos One. 11: e0158560. PMID 27355626 DOI: 10.1371/journal.pone.0158560 |
0.555 |
|
| 2016 |
Kassaye SG, Grossman Z, Balamane M, Johnston-White B, Liu C, Kumar P, Young M, Sneller MC, Sereti I, Dewar R, Rehm C, Meyer W, Shafer R, Katzenstein D, Maldarelli F. Transmitted HIV Drug Resistance High and Longstanding in Metropolitan Washington, D.C. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 27307507 DOI: 10.1093/cid/ciw382 |
0.726 |
|
| 2016 |
Rhee SY, Sankaran K, Varghese V, Winters M, Hurt CB, Eron JJ, Parkin N, Holmes SP, Holodniy M, Shafer RW. HIV-1 Protease, Reverse Transcriptase, and Integrase Variation. Journal of Virology. PMID 27099321 DOI: 10.1128/JVI.00495-16 |
0.488 |
|
| 2016 |
Varghese V, Pinsky B, Smith DS, Klein DB, Shafer R. Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility. Aids Research and Human Retroviruses. PMID 27009474 DOI: 10.1089/Aid.2016.0038 |
0.665 |
|
| 2016 |
Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS. More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. Elife. 5. PMID 26882502 DOI: 10.7554/eLife.10670 |
0.564 |
|
| 2016 |
Clutter DS, Sánchez PR, Rhee SY, Shafer RW. Genetic Variability of HIV-1 for Drug Resistance Assay Development. Viruses. 8. PMID 26875985 DOI: 10.3390/v8020048 |
0.587 |
|
| 2016 |
Clutter DS, Fessel WJ, Rhee SY, Hurley LB, Klein DB, Ioannidis JP, Silverberg MJ, Shafer RW. Response to Therapy in Antiretroviral Therapy-Naïve Patients with Isolated Nonnucleoside Reverse-Transcriptase Inhibitor-Associated Transmitted Drug Resistance. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 26855248 DOI: 10.1097/QAI.0000000000000942 |
0.394 |
|
| 2015 |
Rhee SY, Jordan MR, Raizes E, Chua A, Parkin N, Kantor R, Van Zyl GU, Mukui I, Hosseinipour MC, Frenkel LM, Ndembi N, Hamers RL, Rinke de Wit TF, Wallis CL, Gupta RK, ... ... Shafer RW, et al. HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing. Plos One. 10: e0145772. PMID 26717411 DOI: 10.1371/Journal.Pone.0145772 |
0.737 |
|
| 2015 |
Wensing AM, Calvez V, Günthard HF, Johnson VA, Paredes R, Pillay D, Shafer RW, Richman DD. 2015 Update of the Drug Resistance Mutations in HIV-1. Topics in Antiviral Medicine. 23: 132-41. PMID 26713503 DOI: 10.5167/Uzh-122257 |
0.509 |
|
| 2015 |
Collins SE, Grant PM, Shafer RW. Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients. Drugs. PMID 26677129 DOI: 10.1007/s40265-015-0515-6 |
0.398 |
|
| 2015 |
Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, ... ... Shafer RW, et al. Correction: Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis. Plos Medicine. 12: e1001845. PMID 26030872 DOI: 10.1371/journal.pmed.1001845 |
0.714 |
|
| 2015 |
Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, ... ... Shafer RW, et al. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. Plos Medicine. 12: e1001810. PMID 25849352 DOI: 10.1371/Journal.Pmed.1001810 |
0.787 |
|
| 2015 |
Basson AE, Rhee SY, Parry CM, El-Khatib Z, Charalambous S, De Oliveira T, Pillay D, Hoffmann C, Katzenstein D, Shafer RW, Morris L. Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors. Antimicrobial Agents and Chemotherapy. 59: 960-71. PMID 25421485 DOI: 10.1128/AAC.04215-14 |
0.716 |
|
| 2014 |
Blanco JL, Montaner JS, Marconi VC, Santoro MM, Campos-Loza AE, Shafer RW, Miller MD, Paredes R, Harrigan R, Nguyen ML, Perno CF, Gonzalez-Hernandez LA, Gatell JM. Lower prevalence of drug resistance mutations at first-line virological failure to first-line therapy with atripla vs. tenofovir + emtricitabine/lamivudine + efavirenz administered on a multiple tablet therapy. Aids (London, England). 28: 2531-9. PMID 25574957 DOI: 10.1097/QAD.0000000000000424 |
0.342 |
|
| 2014 |
Kolomeets AN, Varghese V, Lemey P, Bobkova MR, Shafer RW. A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. Aids (London, England). 28: F1-8. PMID 25259833 DOI: 10.1097/QAD.0000000000000485 |
0.639 |
|
| 2014 |
Wensing AM, Calvez V, Günthard HF, Johnson VA, Paredes R, Pillay D, Shafer RW, Richman DD. 2014 Update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine. 22: 642-50. PMID 25101529 |
0.445 |
|
| 2014 |
Pennings PS, Holmes SP, Shafer RW. HIV-1 transmission networks in a small world. The Journal of Infectious Diseases. 209: 180-2. PMID 24151310 DOI: 10.1093/infdis/jit525 |
0.401 |
|
| 2014 |
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, ... ... Shafer RW, et al. Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. The Journal of Antimicrobial Chemotherapy. 69: 12-20. PMID 23934770 DOI: 10.1093/jac/dkt316 |
0.374 |
|
| 2013 |
Robbins G, Testa M, Su M, Safren S, Morse G, Lammert S, Shafer R, Reynolds N, Chesney M. Site nurse-initiated adherence and symptom support telephone calls for HIV-positive individuals starting antiretroviral therapy, ACTG 5031: Substudy of ACTG 384 Hiv Clinical Trials. 14: 235-253. PMID 24144900 DOI: 10.1310/hct1405-235 |
0.306 |
|
| 2013 |
Van Zyl GU, Liu TF, Claassen M, Engelbrecht S, de Oliveira T, Preiser W, Wood NT, Travers S, Shafer RW. 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. 8: e67188. PMID 23840622 DOI: 10.1371/journal.pone.0067188 |
0.469 |
|
| 2013 |
Varghese V, Mitsuya Y, Fessel WJ, Liu TF, Melikian GL, Katzenstein DA, Schiffer CA, Holmes SP, Shafer RW. Prototypical Recombinant Multi-Protease Inhibitor Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type-1. Antimicrobial Agents and Chemotherapy. PMID 23796938 DOI: 10.1128/Aac.00614-13 |
0.651 |
|
| 2013 |
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, ... ... Shafer RW, et al. Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. The Journal of Infectious Diseases. 207: S70-7. PMID 23687292 DOI: 10.1093/Infdis/Jit114 |
0.638 |
|
| 2013 |
Rath BA, Yousef KP, Katzenstein DK, Shafer RW, Schütte C, von Kleist M, Merigan TC. In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis. Plos One. 8: e61102. PMID 23613794 DOI: 10.1371/Journal.Pone.0061102 |
0.697 |
|
| 2013 |
Johnson VA, Calvez V, Günthard HF, Paredes R, Pillay D, Shafer RW, Wensing AM, Richman DD. Update of the drug resistance mutations in HIV-1: March 2013 Topics in Antiviral Medicine. 21: 6-14. PMID 23596273 |
0.626 |
|
| 2013 |
Sangeda RZ, Theys K, Beheydt G, Rhee SY, Deforche K, Vercauteren J, Libin P, Imbrechts S, Grossman Z, Camacho RJ, Van Laethem K, Pironti A, Zazzi M, Sönnerborg A, Incardona F, ... ... Shafer RW, et al. HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 19: 349-60. PMID 23523594 DOI: 10.1016/j.meegid.2013.03.014 |
0.43 |
|
| 2013 |
Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA. Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease. Acs Chemical Biology. 8: 513-8. PMID 23252515 DOI: 10.1021/Cb3006193 |
0.522 |
|
| 2013 |
Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, Martin R, Liu TF, Pacold M, Reuman EC, Holmes SP, Borroto-Esoda K, Shafer RW. Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of lamivudine treatment Antimicrobial Agents and Chemotherapy. 57: 343-349. PMID 23114756 DOI: 10.1128/Aac.01601-12 |
0.389 |
|
| 2013 |
Babrzadeh F, Varghese V, Pacold M, Liu TF, Nyrén P, Schiffer C, Fessel WJ, Shafer RW. Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance Journal of Antimicrobial Chemotherapy. 68: 414-418. PMID 23085775 DOI: 10.1093/Jac/Dks409 |
0.474 |
|
| 2012 |
Winters MA, Lloyd RM, Shafer RW, Kozal MJ, Miller MD, Holodniy M. Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations Plos One. 7. PMID 22815755 DOI: 10.1371/journal.pone.0040514 |
0.342 |
|
| 2012 |
Tang MW, Shafer RW. HIV-1 antiretroviral resistance: Scientific principles and clinical applications Drugs. 72: e1-e25. PMID 22686620 DOI: 10.2165/11633630-000000000-00000 |
0.497 |
|
| 2012 |
Balamane M, Varghese V, Melikian GL, Fessel WJ, Katzenstein DA, Shafer RW. Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine Antimicrobial Agents and Chemotherapy. 56: 4522-4524. PMID 22664973 DOI: 10.1128/AAC.00648-12 |
0.706 |
|
| 2012 |
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. Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes. Aids Research and Therapy. 9: 13. PMID 22554313 DOI: 10.1186/1742-6405-9-13 |
0.362 |
|
| 2012 |
Woods CK, Brumme CJ, Liu TF, Chui CK, Chu AL, Wynhoven B, Hall TA, Trevino C, Shafer RW, Harrigan PR. Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. Journal of Clinical Microbiology. 50: 1936-42. PMID 22403431 DOI: 10.1128/JCM.06689-11 |
0.568 |
|
| 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. Standardized comparison of the relative impacts of HIV-1 Reverse Transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility Antimicrobial Agents and Chemotherapy. 56: 2305-2313. PMID 22330916 DOI: 10.1128/AAC.05487-11 |
0.533 |
|
| 2012 |
Tang MW, Liu TF, Shafer RW. The HIVdb system for HIV-1 genotypic resistance interpretation Intervirology. 55: 98-101. PMID 22286876 DOI: 10.1159/000331998 |
0.594 |
|
| 2011 |
Doherty KM, Nakka P, King BM, Rhee SY, Holmes SP, Shafer RW, Radhakrishnan ML. A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes Bmc Bioinformatics. 12. PMID 22172090 DOI: 10.1186/1471-2105-12-477 |
0.607 |
|
| 2011 |
Johnson VA, Calvez V, Günthard HF, Paredes R, Pillay D, Shafer R, Wensing AM, Richman DD. 2011 update of the drug resistance mutations in HIV-1 Topics in Antiviral Medicine. 19: 156-164. PMID 22156218 |
0.585 |
|
| 2011 |
Fessel WJ, Anderson B, Follansbee SE, Winters MA, Lewis ST, Weinheimer SP, Petropoulos CJ, Shafer RW. The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment Antiviral Research. 92: 484-487. PMID 22001594 DOI: 10.1016/j.antiviral.2011.09.010 |
0.523 |
|
| 2011 |
Koh Y, Aoki M, Danish ML, Aoki-Ogata H, Amano M, Das D, Shafer RW, Ghosh AK, Mitsuya H. Loss of protease dimerization inhibition activity of darunavir is associated with the acquisition of resistance to darunavir by HIV-1. Journal of Virology. 85: 10079-89. PMID 21813613 DOI: 10.1128/Jvi.05121-11 |
0.565 |
|
| 2011 |
Blanco JL, Varghese V, Rhee SY, Gatell JM, Shafer RW. HIV-1 integrase inhibitor resistance and its clinical implications Journal of Infectious Diseases. 203: 1204-1214. PMID 21459813 DOI: 10.1093/infdis/jir025 |
0.554 |
|
| 2010 |
Margeridon-Thermet S, Shafer RW. Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C. Viruses. 2: 2696-739. PMID 21243082 DOI: 10.3390/v2122696 |
0.425 |
|
| 2010 |
Varghese V, Liu TF, Rhee SY, Libiran P, Trevino C, Fessel WJ, Shafer RW. HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravir Aids Research and Human Retroviruses. 26: 1323-1326. PMID 20961278 DOI: 10.1089/aid.2010.0123 |
0.482 |
|
| 2010 |
Rhee SY, Margeridon-Thermet S, Nguyen MH, Liu TF, Kagan RM, Beggel B, Verheyen J, Kaiser R, Shafer RW. Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery Antiviral Research. 88: 269-275. PMID 20875460 DOI: 10.1016/j.antiviral.2010.09.012 |
0.302 |
|
| 2010 |
Theys K, Deforche K, Beheydt G, Moreau Y, van Laethem K, Lemey P, Camacho RJ, Rhee SY, Shafer RW, Van Wijngaerden E, Vandamme AM. Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape Bmc Bioinformatics. 11. PMID 20682040 DOI: 10.1186/1471-2105-11-409 |
0.506 |
|
| 2010 |
Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW. HIV-1 protease mutations and protease inhibitor cross-resistance Antimicrobial Agents and Chemotherapy. 54: 4253-4261. PMID 20660676 DOI: 10.1128/AAC.00574-10 |
0.447 |
|
| 2010 |
Varghese V, Wang E, Babrzadeh F, Bachmann MH, Shahriar R, Liu T, Mappala SJM, Gharizadeh B, Jeffrey Fessel W, Katzenstein D, Kassaye S, Shafer RW. Nucleic acid template and the risk of a PCR-induced HIV-1 drug resistance mutation Plos One. 5. PMID 20539818 DOI: 10.1371/journal.pone.0010992 |
0.777 |
|
| 2010 |
Reuman EC, Rhee SY, Holmes SP, Shafer RW. Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations Journal of Antimicrobial Chemotherapy. 65: 1477-1485. PMID 20462946 DOI: 10.1093/jac/dkq140 |
0.477 |
|
| 2010 |
Talbot A, Grant P, Taylor J, Baril JG, Liu TF, Charest H, Brenner B, Roger M, Shafer R, Cantin R, Zolopa A. Predicting tipranavir and darunavir resistance using genotypic, phenotypic, and virtual phenotypic resistance patterns: An independent cohort analysis of clinical isolates highly resistant to all other protease inhibitors Antimicrobial Agents and Chemotherapy. 54: 2473-2479. PMID 20368406 DOI: 10.1128/Aac.00096-10 |
0.426 |
|
| 2010 |
De Oliveira T, Shafer RW, Seebregts C. Public database for HIV drug resistance in southern Africa Nature. 464: 673. PMID 20360715 DOI: 10.1038/464673c |
0.571 |
|
| 2010 |
Reuman EC, Bachmann MH, Varghese V, Fesse WJ, Shafer RW. Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector Antimicrobial Agents and Chemotherapy. 54: 934-936. PMID 19917747 DOI: 10.1128/AAC.01345-09 |
0.529 |
|
| 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. 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 Journal of Acquired Immune Deficiency Syndromes. 52: 309-315. PMID 19734799 DOI: 10.1097/QAI.0b013e3181bca669 |
0.507 |
|
| 2009 |
Shahriar R, Rhee SY, Liu TF, Fessel WJ, Scarsella A, Towner W, Holmes SP, Zolopa AR, Shafer RW. Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations Antimicrobial Agents and Chemotherapy. 53: 4869-4878. PMID 19721070 DOI: 10.1128/AAC.00592-09 |
0.462 |
|
| 2009 |
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. Predictive value of HIV-1 genotypic resistance test interpretation algorithms. The Journal of Infectious Diseases. 200: 453-63. PMID 19552527 DOI: 10.1086/600073 |
0.549 |
|
| 2009 |
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, et al. Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype Antiviral Therapy. 14: 273-283. PMID 19430102 |
0.355 |
|
| 2009 |
Shafer RW. The challenge of antiretroviral drug resistance in HIV-1-infected children. Jornal De Pediatria. 85: 91-4. PMID 19319452 DOI: doi:10.2223/JPED.1894 |
0.5 |
|
| 2009 |
Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW. The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics (Oxford, England). 25: 1197-8. PMID 19304876 DOI: 10.1093/bioinformatics/btp134 |
0.53 |
|
| 2009 |
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. Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. The Journal of Infectious Diseases. 199: 1275-85. PMID 19301976 DOI: 10.1086/597808 |
0.407 |
|
| 2009 |
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, ... ... Shafer RW, et al. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. Plos One. 4: e4724. PMID 19266092 DOI: 10.1371/journal.pone.0004724 |
0.555 |
|
| 2009 |
Varghese V, Mitsuya Y, Shahriar R, Bachmann MH, Fessel WJ, Kagan RM, Shafer RW. Human immunodeficiency virus type 1 isolates with the reverse transcriptase (RT) mutation Q145M retain nucleoside and nonnucleoside RT inhibitor susceptibility Antimicrobial Agents and Chemotherapy. 53: 2196-2198. PMID 19223644 DOI: 10.1128/AAC.01593-08 |
0.347 |
|
| 2009 |
Shafer RW. Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. The Journal of Infectious Diseases. 199: 610-2. PMID 19210160 DOI: 10.1086/596737 |
0.569 |
|
| 2009 |
Bembom O, Petersen ML, Rhee SY, Fessel WJ, Sinisi SE, Shafer RW, van der Laan MJ. Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infection. Statistics in Medicine. 28: 152-72. PMID 18825650 DOI: 10.1002/Sim.3414 |
0.449 |
|
| 2008 |
Deforche K, Camacho RJ, Grossman Z, Soares MA, Van Laethem K, Katzenstein DA, Harrigan PR, Kantor R, Shafer R, Vandamme AM. Bayesian network analyses of resistance pathways against efavirenz and nevirapine. Aids (London, England). 22: 2107-15. PMID 18832874 DOI: 10.1097/QAD.0b013e32830fe940 |
0.712 |
|
| 2008 |
Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, Jayakumar P, Gharizadeh B, Ronaghi M, Klein D, Fessel WJ, Shafer RW. Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. Journal of Virology. 82: 10747-55. PMID 18715933 DOI: 10.1128/Jvi.01827-07 |
0.489 |
|
| 2008 |
Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW. Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology. 5: 74. PMID 18687142 DOI: 10.1186/1742-4690-5-74 |
0.523 |
|
| 2008 |
Shafer RW, Schapiro JM. HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. Aids Reviews. 10: 67-84. PMID 18615118 |
0.424 |
|
| 2008 |
Shafer RW, Rhee SY, Bennett DE. Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies. Antiviral Therapy. 13: 59-68. PMID 18575192 |
0.598 |
|
| 2008 |
Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N. Viral population estimation using pyrosequencing. Plos Computational Biology. 4: e1000074. PMID 18437230 DOI: 10.1371/Journal.Pcbi.1000074 |
0.307 |
|
| 2008 |
Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, Shafer RW. Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance. Aids (London, England). 22: 717-25. PMID 18356601 DOI: 10.1097/QAD.0b013e3282f5e07a |
0.495 |
|
| 2008 |
Koelsch KK, Liu L, Haubrich R, May S, Havlir D, Günthard HF, Ignacio CC, Campos-Soto P, Little SJ, Shafer R, Robbins GK, D'Aquila RT, Kawano Y, Young K, Dao P, et al. Dynamics of total, linear nonintegrated, and integrated HIV-1 DNA in vivo and in vitro. The Journal of Infectious Diseases. 197: 411-9. PMID 18248304 DOI: 10.1086/525283 |
0.466 |
|
| 2008 |
Kapoor A, Shapiro B, Shafer RW, Shulman N, Rhee SY, Delwart EL. Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients. Retrovirology. 5: 7. PMID 18221530 DOI: 10.1186/1742-4690-5-7 |
0.509 |
|
| 2007 |
Hernandez G, Rhee SY, Shafer RW, Das AK. Knowledge integration of software for HIV drug resistance research. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 973. PMID 18694073 |
0.386 |
|
| 2007 |
Mitsuya Y, Liu TF, Rhee SY, Fessel WJ, Shafer RW. Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment. The Journal of Infectious Diseases. 196: 1177-9. PMID 17955436 DOI: 10.1086/521624 |
0.487 |
|
| 2007 |
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. World Antimalarial Resistance Network (WARN) III: molecular markers for drug resistant malaria. Malaria Journal. 6: 121. PMID 17822535 DOI: 10.1186/1475-2875-6-121 |
0.344 |
|
| 2007 |
Johnson JA, Li JF, Wei X, Lipscomb J, Bennett D, Brant A, Cong ME, Spira T, Shafer RW, Heneine W. Simple PCR assays improve the sensitivity of HIV-1 subtype B drug resistance testing and allow linking of resistance mutations. Plos One. 2: e638. PMID 17653265 DOI: 10.1371/journal.pone.0000638 |
0.542 |
|
| 2007 |
Petersen ML, Wang Y, van der Laan MJ, Rhee SY, Shafer RW, Fessel WJ. Virologic efficacy of boosted double versus boosted single protease inhibitor therapy. Aids (London, England). 21: 1547-54. PMID 17630549 DOI: 10.1097/Qad.0B013E32825A69A8 |
0.346 |
|
| 2007 |
Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Research. 17: 1195-201. PMID 17600086 DOI: 10.1101/gr.6468307 |
0.43 |
|
| 2007 |
Altmann A, Beerenwinkel N, Sing T, Savenkov I, Doumer M, Kaiser R, Rhee SY, Fessel WJ, Shafer RW, Lengauer T. Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antiviral Therapy. 12: 169-78. PMID 17503659 |
0.36 |
|
| 2007 |
Rhee SY, Liu TF, Holmes SP, Shafer RW. HIV-1 subtype B protease and reverse transcriptase amino acid covariation. Plos Computational Biology. 3: e87. PMID 17500586 DOI: 10.1371/journal.pcbi.0030087 |
0.493 |
|
| 2007 |
Shulman N, Shafer RW. Case files from Stanford University Medical Center: ten years of HAART: a long wait for full HIV suppression. Medgenmed : Medscape General Medicine. 9: 10. PMID 17435619 |
0.354 |
|
| 2007 |
Shafer RW, Rhee SY, Pillay D, Miller V, Sandstrom P, Schapiro JM, Kuritzkes DR, Bennett D. HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. Aids (London, England). 21: 215-23. PMID 17197813 DOI: 10.1097/QAD.0b013e328011e691 |
0.591 |
|
| 2006 |
Shafer RW, Nguyen DP, Fessel WJ. 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. Medgenmed : Medscape General Medicine. 8: 32. PMID 17406166 |
0.483 |
|
| 2006 |
Lin RS, Rhee SY, Shafer RW, Das AK. A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 385-8. PMID 17369658 |
0.503 |
|
| 2006 |
Lin RS, Rhee SY, Shafer RW, Das AK. Prediction of HIV mutation changes based on treatment history. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1011. PMID 17238630 |
0.568 |
|
| 2006 |
Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW. 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 Research and Human Retroviruses. 22: 1300-5. PMID 17209774 DOI: 10.1089/Aid.2006.22.1300 |
0.513 |
|
| 2006 |
Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW. Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of the National Academy of Sciences of the United States of America. 103: 17355-60. PMID 17065321 DOI: 10.1073/Pnas.0607274103 |
0.486 |
|
| 2006 |
Shafer RW. Rationale and uses of a public HIV drug-resistance database. The Journal of Infectious Diseases. 194: S51-8. PMID 16921473 DOI: 10.1086/505356 |
0.57 |
|
| 2006 |
Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Slome S, Flamm J, Horberg M, Hurley L, Klein D, Shafer RW. HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL. Journal of Acquired Immune Deficiency Syndromes (1999). 43: 56-9. PMID 16885777 DOI: 10.1097/01.qai.0000232609.99705.a2 |
0.514 |
|
| 2006 |
Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, Pillay D. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. Aids (London, England). 20: 1521-9. PMID 16847407 DOI: 10.1097/01.Aids.0000237368.64488.Ae |
0.516 |
|
| 2006 |
Kallianpur AR, Hulgan T, Canter JA, Ritchie MD, Haines JL, Robbins GK, Shafer RW, Clifford DB, Haas DW. Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy. Aids (London, England). 20: 1503-13. PMID 16847405 DOI: 10.1097/01.Aids.0000237366.56864.3C |
0.308 |
|
| 2006 |
Liu TF, Shafer RW. Web resources for HIV type 1 genotypic-resistance test interpretation. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 42: 1608-18. PMID 16652319 DOI: 10.1086/503914 |
0.588 |
|
| 2006 |
Rhee SY, Kantor R, Katzenstein DA, Camacho R, Morris L, Sirivichayakul S, Jorgensen L, Brigido LF, Schapiro JM, Shafer RW. HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. Aids (London, England). 20: 643-51. PMID 16514293 DOI: 10.1097/01.aids.0000216363.36786.2b |
0.667 |
|
| 2006 |
Snoeck J, Kantor R, Shafer RW, Van Laethem K, Deforche K, Carvalho AP, Wynhoven B, Soares MA, Cane P, Clarke J, Pillay C, Sirivichayakul S, Ariyoshi K, Holguin A, Rudich H, et al. Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent. Antimicrobial Agents and Chemotherapy. 50: 694-701. PMID 16436728 DOI: 10.1128/AAC.50.2.694-701.2006 |
0.622 |
|
| 2005 |
Kantor R, Shafer RW, Katzenstein D. The HIV-1 Non-subtype B Workgroup: An International Collaboration for the Collection and Analysis of HIV-1 Non-subtype B Data. Journal of the International Aids Society. 7: 71. PMID 19825127 DOI: 10.1186/1758-2652-7-1-71 |
0.673 |
|
| 2005 |
Kantor R, Shafer RW, Katzenstein D. The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B data. Medgenmed : Medscape General Medicine. 7: 71. PMID 16369376 |
0.673 |
|
| 2005 |
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. HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance. The Journal of Infectious Diseases. 192: 456-65. PMID 15995959 DOI: 10.1086/431601 |
0.601 |
|
| 2005 |
Zolopa AR, Lazzeroni LC, Rinehart A, Vezinet FB, Clavel F, Collier A, Conway B, Gulick RM, Holodniy M, Perno CF, Shafer RW, Richman DD, Wainberg MA, Kuritzkes DR. Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: an international comparison (The GUESS Study). Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 41: 92-9. PMID 15937768 DOI: 10.1086/430706 |
0.463 |
|
| 2005 |
Shulman NS, Delgado J, Bosch RJ, Winters MA, Johnston E, Shafer RW, Katzenstein DA, Merigan TC. Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assays. Journal of Acquired Immune Deficiency Syndromes (1999). 39: 78-81. PMID 15851917 DOI: 10.1097/01.Qai.0000159517.78100.7B |
0.645 |
|
| 2005 |
Shafer RW, Schapiro JM. Drug resistance and antiretroviral drug development Journal of Antimicrobial Chemotherapy. 55: 817-820. PMID 15845781 DOI: 10.1093/jac/dki127 |
0.382 |
|
| 2005 |
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, ... ... Shafer RW, et al. Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. Plos Medicine. 2: e112. PMID 15839752 DOI: 10.1371/journal.pmed.0020112 |
0.734 |
|
| 2005 |
Johnston E, Dupnik KM, Gonzales MJ, Winters MA, Rhee SY, Imamichi T, Shafer RW. Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. Aids (London, England). 19: 731-3. PMID 15821401 DOI: 10.1097/01.aids.0000166098.54564.0c |
0.6 |
|
| 2005 |
Zhang J, Rhee S, Taylor J, Shafer RW. Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays. Journal of Acquired Immune Deficiency Syndromes. 38: 439-444. PMID 15764961 DOI: 10.1097/01.Qai.0000147526.64863.53 |
0.472 |
|
| 2005 |
Lecossier D, Shulman NS, Morand-Joubert L, Shafer RW, Joly V, Zolopa AR, Clavel F, Hance AJ. Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine. Journal of Acquired Immune Deficiency Syndromes (1999). 38: 37-42. PMID 15608522 DOI: 10.1097/00126334-200501010-00007 |
0.402 |
|
| 2004 |
Johnston E, Winters MA, Rhee SY, Merigan TC, Schiffer CA, Shafer RW. 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: 4864-8. PMID 15561868 DOI: 10.1128/Aac.48.12.4864-4868.2004 |
0.434 |
|
| 2004 |
Brun-Vézinet F, Costagliola D, Khaled MA, Calvez V, Clavel F, Clotet B, Haubrich R, Kempf D, King M, Kuritzkes D, Lanier R, Miller M, Miller V, Phillips A, Pillay D, ... ... Shafer R, et al. Clinically validated genotype analysis: guiding principles and statistical concerns. Antiviral Therapy. 9: 465-78. PMID 15456077 |
0.376 |
|
| 2004 |
Rhee SY, Liu T, Ravela J, Gonzales MJ, Shafer RW. 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: 3122-6. PMID 15273130 DOI: 10.1128/AAC.48.8.3122-3126.2004 |
0.442 |
|
| 2004 |
Kantor R, Shafer RW, Follansbee S, Taylor J, Shilane D, Hurley L, Nguyen DP, Katzenstein D, Fessel WJ. Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. Aids (London, England). 18: 1503-11. PMID 15238768 DOI: 10.1097/01.Aids.0000131358.29586.6B |
0.691 |
|
| 2003 |
Zazzi M, Romano L, Venturi G, Shafer RW, Reid C, Dal Bello F, Parolin C, Palù G, Valensin PE. Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotype. The Journal of Antimicrobial Chemotherapy. 53: 356-60. PMID 14688053 DOI: 10.1093/JAC/DKH021 |
0.478 |
|
| 2003 |
Shafer RW, Smeaton LM, Robbins GK, De Gruttola V, Snyder SW, D'Aquila RT, Johnson VA, Morse GD, Nokta MA, Martinez AI, Gripshover BM, Kaul P, Haubrich R, Swingle M, McCarty SD, et al. Comparison of four-drug regimens and pairs of sequential three-drug regimens as initial therapy for HIV-1 infection. The New England Journal of Medicine. 349: 2304-15. PMID 14668456 DOI: 10.1056/Nejmoa030265 |
0.369 |
|
| 2003 |
Robbins GK, De Gruttola V, Shafer RW, Smeaton LM, Snyder SW, Pettinelli C, Dubé MP, Fischl MA, Pollard RB, Delapenha R, Gedeon L, van der Horst C, Murphy RL, Becker MI, D'Aquila RT, et al. Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection. The New England Journal of Medicine. 349: 2293-303. PMID 14668455 DOI: 10.1056/Nejmoa030264 |
0.443 |
|
| 2003 |
Gonzales MJ, Johnson E, Dupnik KM, Imamichi T, Shafer RW. Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. Journal of Acquired Immune Deficiency Syndromes (1999). 34: 398-402. PMID 14615657 DOI: 10.1097/00126334-200312010-00006 |
0.424 |
|
| 2003 |
Gonzales MJ, Belitskaya I, Dupnik KM, Rhee SY, Shafer RW. 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 Research and Human Retroviruses. 19: 909-15. PMID 14601580 DOI: 10.1089/088922203322493085 |
0.497 |
|
| 2003 |
Kuiken C, Korber B, Shafer RW. HIV sequence databases. Aids Reviews. 5: 52-61. PMID 12875108 |
0.504 |
|
| 2003 |
Gonzales MJ, Delwart E, Rhee SY, Tsui R, Zolopa AR, Taylor J, Shafer RW. Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation. The Journal of Infectious Diseases. 188: 397-405. PMID 12870121 DOI: 10.1086/376534 |
0.442 |
|
| 2003 |
D'Aquila RT, Schapiro JM, Brun-Vézinet F, Clotet B, Conway B, Demeter LM, Grant RM, Johnson VA, Kuritzkes DR, Loveday C, Shafer RW, Richman DD. Drug resistance mutations in HIV-1. Topics in Hiv Medicine : a Publication of the International Aids Society, Usa. 11: 92-6. PMID 12837968 |
0.625 |
|
| 2003 |
Ravela J, Betts BJ, Brun-Vézinet F, Vandamme AM, Descamps D, van Laethem K, Smith K, Schapiro JM, Winslow DL, Reid C, Shafer RW. HIV-1 protease and reverse transcriptase mutation patterns responsible for discordances between genotypic drug resistance interpretation algorithms. Journal of Acquired Immune Deficiency Syndromes (1999). 33: 8-14. PMID 12792349 DOI: 10.1097/00126334-200305010-00002 |
0.443 |
|
| 2003 |
Wu TD, Schiffer CA, Gonzales MJ, Taylor J, Kantor R, Chou S, Israelski D, Zolopa AR, Fessel WJ, Shafer RW. Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. Journal of Virology. 77: 4836-47. PMID 12663790 DOI: 10.1128/Jvi.77.8.4836-4847.2003 |
0.515 |
|
| 2003 |
Gonzales MJ, Wu TD, Taylor J, Belitskaya I, Kantor R, Israelski D, Chou S, Zolopa AR, Fessel WJ, Shafer RW. Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. Aids (London, England). 17: 791-9. PMID 12660525 DOI: 10.1097/00002030-200304110-00003 |
0.448 |
|
| 2003 |
Rhee SY, Gonzales MJ, Kantor R, Betts BJ, Ravela J, Shafer RW. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research. 31: 298-303. PMID 12520007 DOI: 10.1093/nar/gkg100 |
0.502 |
|
| 2002 |
D'Aquila RT, Schapiro JM, Brun-Vézinet F, Clotet B, Conway B, Demeter LM, Grant RM, Johnson VA, Kuritzkes DR, Loveday C, Shafer RW, Richman DD. Drug Resistance Mutations in HIV-1. Topics in Hiv Medicine : a Publication of the International Aids Society, Usa. 10: 21-25. PMID 12717052 |
0.625 |
|
| 2002 |
Kantor R, Zijenah LS, Shafer RW, Mutetwa S, Johnston E, Lloyd R, von Lieven A, Israelski D, Katzenstein DA. HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy. Aids Research and Human Retroviruses. 18: 1407-13. PMID 12512512 DOI: 10.1089/088922202320935483 |
0.825 |
|
| 2002 |
Palmer S, Vuitton D, Gonzales MJ, Bassignot A, Shafer RW. Reverse transcriptase and protease sequence evolution in two HIV-1-infected couples. Journal of Acquired Immune Deficiency Syndromes (1999). 31: 285-90. PMID 12439203 DOI: 10.1097/00126334-200211010-00003 |
0.413 |
|
| 2002 |
Shulman NS, Hughes MD, Winters MA, Shafer RW, Zolopa AR, Hellmann NS, Bates M, Whitcomb JM, Katzenstein DA. Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patients. Journal of Acquired Immune Deficiency Syndromes (1999). 31: 121-7. PMID 12394789 DOI: 10.1097/00126334-200210010-00001 |
0.682 |
|
| 2002 |
Eshleman SH, Gonzales MJ, Becker-Pergola G, Cunningham SC, Guay LA, Jackson JB, Shafer RW. 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: 507-11. PMID 12015904 DOI: 10.1089/088922202317406655 |
0.373 |
|
| 2002 |
Shafer RW. Genotypic testing for human immunodeficiency virus type 1 drug resistance Clinical Microbiology Reviews. 15: 247-277. PMID 11932232 DOI: 10.1128/CMR.15.2.247-277.2002 |
0.631 |
|
| 2002 |
Kantor R, Fessel WJ, Zolopa AR, Israelski D, Shulman N, Montoya JG, Harbour M, Schapiro JM, Shafer RW. Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy Antimicrobial Agents and Chemotherapy. 46: 1086-1092. PMID 11897594 DOI: 10.1128/AAC.46.4.1086-1092.2002 |
0.487 |
|
| 2000 |
Shafer RW, Kantor R, Gonzales MJ. The Genetic Basis of HIV-1 Resistance to Reverse Transcriptase and Protease Inhibitors. Aids Reviews. 2: 211-228. PMID 19096725 |
0.537 |
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