ArticleNucleic acids research2009
jpHMM: improving the reliability of recombination prediction in HIV-1.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed.
- Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America.Scientific reports · 2021Trial
- HIV-1 diversity in an antiretroviral treatment naïve cohort from Bushbuckridge, Mpumalanga Province, South Africa.Virology journal · 2015Trial
- Non-Canonical Binding of Nelfinavir in HIV-1 Protease Variants Reveals Structural Mechanisms of Antiretroviral Resistance.Viruses · 2026Article
- Emergence of newly reported HIV-1 recombinants CRF120_0107 and CRF149_01B in Guangxi Zhuang Autonomous Region, China: Molecular evidence and public health challenges.Biosafety and health · 2026Article
- Evolutionary dynamics of HIV-1 recombinants: analysis of contemporary and historical viral populations in East Africa.Virology journal · 2026Article
- Analysis of HIV-1 subtypes and drug resistance mutations in people who inject drugs in Aizawl and nearby districts of Mizoram, India.Virulence · 2025Article
- Molecular characterization of a unique Recombinant form of HIV-1 subtype F2/CRF02_AG identified in Guangdong, China.Virology journal · 2025Article
- Review
- Characterization of a New HIV-1 Second-Generation Circulating Recombinant Form CRF173_63A6 in the Jewish Autonomous Region of Russia.Pathogens (Basel, Switzerland) · 2025Article
- Molecular analysis of multiple HIV-1 BC recombinant strains circulating worldwide shows predominance of the C genotype in the viral genomic structure.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Phylogenetic analysis and transmission networks highlight the role of older adults in the transmission of HIV-1 in northern Zhejiang, China.Virology journal · 2025Article
- Unique genetic signatures in HIV-1 subtype A1 and A1D recombinant envelope glycoprotein distinguish contemporary transmitted/founder viruses from historical strains in East Africa.Frontiers in microbiology · 2025Article
- Hepatitis B virus (HBV) viremia despite tenofovir disoproxil fumarate-containing antiretroviral therapy in persons with HBV/HIV coinfection.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2024Article
- Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations.Scientific reports · 2024Article
- High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA.Virus evolution · 2024Article
- Article
- Description of the new HIV-1 intersubtype B/C circulating recombinant form (CRF146_BC) detected in Brazil.Memorias do Instituto Oswaldo Cruz · 2024Article
- Robustness of Felsenstein's Versus Transfer Bootstrap Supports With Respect to Taxon Sampling.Systematic biology · 2023Article
- Article
- Article
52 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of 'uncertainty' regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/.
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