ArticleNucleic acids research2003
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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Who cites it
99 citing papers in PubMed.
- Evolution of Multiple Domains of the HIV-1 Envelope Glycoprotein during Coreceptor Switch with CCR5 Antagonist Therapy.Microbiology spectrum · 2022Trial
- Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.The New England journal of medicine · 2019Trial
- Genotypic susceptibility scores and HIV type 1 RNA responses in treatment-experienced subjects with HIV type 1 infection.AIDS research and human retroviruses · 2008Trial
- Comprehensive mapping of the virus and host factors that guide the paths of HIV-1 escape from a therapeutic.Cell reports · 2026Article
- Protein language model embeddings improve HIV drug resistance prediction: a comprehensive benchmark with attention-based interpretability.Bioinformatics (Oxford, England) · 2026Article
- Comprehensive Mapping of the Virus and Host Factors that Guide the Paths of HIV-1 Escape from a Therapeutic.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking Machine Learning Models for HIV-1 Protease Inhibitor Resistance Prediction: Impact of Data Set Construction and Feature Representation.Journal of chemical information and modeling · 2025Article
- Therapeutic Approaches of Viral Gene Silencing by Small Interfering RNA: Strategies to Prevent the Emergence of Antiviral Resistant Escape Mutants.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Selective decline of intact HIV reservoirs during the first decade of ART followed by stabilization in memory T cell subsets.AIDS (London, England) · 2025Article
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Susceptibility to Lenacapavir Among Newly Diagnosed HIV-Positive Patients Followed Up in Mozambique That Presented With Primary Antiretroviral Resistance to Other Classes.Journal of medical virology · 2025Article
- In vivo evolution of env in SHIV-AD8Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Developing a Prototype Machine Learning Model to Predict Quality of Life Measures in People Living With HIV.Integrated pharmacy research & practice · 2025Article
- Article
- Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy's outcome for HIV-1.Bioinformatics (Oxford, England) · 2024Article
- SHIV-C109p5 NHP induces rapid disease progression in elderly macaques with extensive GI viral replication.Journal of virology · 2024Article
- Web Service for HIV Drug Resistance Prediction Based on Analysis of Amino Acid Substitutions in Main Drug Targets.Viruses · 2023Article
- Brain microglia serve as a persistent HIV reservoir despite durable antiretroviral therapy.The Journal of clinical investigation · 2023Article
- Article
- Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage.Viruses · 2022Article
39 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Therapeutic success of anti-HIV therapies is limited by the development of drug resistant viruses. These genetic variants display complex mutational patterns in their pol gene, which codes for protease and reverse transcriptase, the molecular targets of current antiretroviral therapy. Genotypic resistance testing depends on the ability to interpret such sequence data, whereas phenotypic resistance testing directly measures relative in vitro susceptibility to a drug. From a set of 650 matched genotype-phenotype pairs we construct regression models for the prediction of phenotypic drug resistance from genotypes. Since the range of resistance factors varies considerably between different drugs, two scoring functions are derived from different sets of predicted phenotypes. Firstly, we compare predicted values to those of samples derived from 178 treatment-naive patients and report the relative deviance. Secondly, estimation of the probability density of 2000 predicted phenotypes gives rise to an intrinsic definition of a susceptible and a resistant subpopulation. Thus, for a predicted phenotype, we calculate the probability of membership in the resistant subpopulation. Both scores provide standardized measures of resistance that can be calculated from the genotype and are comparable between drugs. The geno2pheno system makes these genotype interpretations available via the Internet (http://www.genafor.org/).
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