List of works - Robert W Shafer

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

scientific article

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

scientific article

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

scientific article

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

scientific article

A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses

scientific article

African mitochondrial DNA subhaplogroups and peripheral neuropathy during antiretroviral therapy

scientific article

Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance

scientific article published on December 2004

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

scientific article

Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation

scientific article

Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance

scientific article published on 19 October 2012

Comparison of an Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing

article

Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays

scientific article published on April 2005

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

scientific article

Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations

scientific article

Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds

scientific article published on 09 September 2020

Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons

scientific article published on 09 March 2022

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

scientific article

Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens

scientific article published on 19 March 2019

Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations

scientific article

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery

scientific article published on 19 January 2018

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

scientific article

Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape

scientific article

Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots

scientific article published on 17 August 2016

Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors

scientific article published on 14 September 2017

Genetic Variability of HIV-1 for Drug Resistance Assay Development

scientific article published on 11 February 2016

Genotypic predictors of human immunodeficiency virus type 1 drug resistance

scholarly article

Genotypic testing for human immunodeficiency virus type 1 drug resistance

scientific article

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

scientific article

HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing

scientific article

HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance

scientific article published on 05 July 2005

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation

scientific article

HIV-1 drug resistance and resistance testing

scientific article

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure

scientific article

HIV-1 integrase inhibitor resistance and its clinical implications

scientific article

HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes

scientific article published on March 2006

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

scientific article published on January 2007

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

scientific article

Human immunodeficiency virus reverse transcriptase and protease sequence database

scientific article (publication date: 2003)

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

scientific article published on 17 February 2009

Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration

scientific article

Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors

scientific article

In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis

scientific article

Knowledge integration of software for HIV drug resistance research.

scientific article published on 11 October 2007

Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation

scientific article published on 10 July 2003

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

scientific article published on 20 August 2008

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

scientific article

Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa

article

Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients

scientific article

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

scientific article published on 15 February 2016

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration

scientific article published on 19 March 2017

Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing

scientific article published on 9 August 2013

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

scientific article published on 31 August 2009

Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation

scientific article

Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine

scientific article published on June 2013

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

scientific article

Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations

scientific article published on April 2005

Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector

scientific article published on 16 November 2009

Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine

scientific article published on 4 June 2012

Pharmacokinetics of nelfinavir and efavirenz in antiretroviral-naive, human immunodeficiency virus-infected subjects when administered alone or in combination with nucleoside analog reverse transcriptase inhibitors

scientific article

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

scientific article

Predictive value of HIV-1 genotypic resistance test interpretation algorithms

scientific article published on August 2009

Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing

scientific article published on August 2017

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

scientific article published on 10 September 2007

Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1

scientific article published on 24 June 2013

Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility

scientific article published on 23 March 2016

Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance

scientific article published on 5 February 2016

Similar prevalence of low-abundance drug-resistant variants in treatment-naive patients with genotype 1a and 1b hepatitis C virus infections as determined by ultradeep pyrosequencing

scientific article

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

scientific article

Site nurse-initiated adherence and symptom support telephone calls for HIV-positive individuals starting antiretroviral therapy, ACTG 5031: substudy of ACTG 384.

scientific article

Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes

scientific article (publication date: 3 May 2012)

Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis

scientific article

The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B data

scientific article

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

scientific article published on 20 March 2009

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

scientific article

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens

scientific article (publication date: 2013)

Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis

article

Viral population estimation using pyrosequencing

scientific article

Virologic efficacy of boosted double versus boosted single protease inhibitor therapy

scientific article published on July 2007

Virologic response to lopinavir-ritonavir-based antiretroviral regimens in a multicenter international clinical cohort: comparison of genotypic interpretation scores

scientific article published on 18 August 2008

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

scientific article

List of works by Robert W Shafer

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

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

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

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

A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses

African mitochondrial DNA subhaplogroups and peripheral neuropathy during antiretroviral therapy

Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance

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

Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation

Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance

Comparison of an Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing

Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays

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

Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations

Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds

Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons

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

Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens

Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery

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

Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape

Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots

Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors

Genetic Variability of HIV-1 for Drug Resistance Assay Development

Genotypic predictors of human immunodeficiency virus type 1 drug resistance

Genotypic testing for human immunodeficiency virus type 1 drug resistance

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

HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing

HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation

HIV-1 drug resistance and resistance testing

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure

HIV-1 integrase inhibitor resistance and its clinical implications

HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes

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

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

Human immunodeficiency virus reverse transcriptase and protease sequence database

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

Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration

Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors

In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis

Knowledge integration of software for HIV drug resistance research.

Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation

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

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

Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa

Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration

Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing

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

Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation

Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine

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

Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations

Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector

Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine

Pharmacokinetics of nelfinavir and efavirenz in antiretroviral-naive, human immunodeficiency virus-infected subjects when administered alone or in combination with nucleoside analog reverse transcriptase inhibitors

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

Predictive value of HIV-1 genotypic resistance test interpretation algorithms

Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing

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

Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1

Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility

Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance

Similar prevalence of low-abundance drug-resistant variants in treatment-naive patients with genotype 1a and 1b hepatitis C virus infections as determined by ultradeep pyrosequencing

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

Site nurse-initiated adherence and symptom support telephone calls for HIV-positive individuals starting antiretroviral therapy, ACTG 5031: substudy of ACTG 384.

Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes

Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis

The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B data

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

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens

Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis

Viral population estimation using pyrosequencing

Virologic efficacy of boosted double versus boosted single protease inhibitor therapy

Virologic response to lopinavir-ritonavir-based antiretroviral regimens in a multicenter international clinical cohort: comparison of genotypic interpretation scores