Drug resistance mutations in HIV: new bioinformatics approaches and challenges

L Blassel, A Zhukova, CJ Villabona-Arenas… - Current opinion in …, 2021 - Elsevier
Highlights•Machine learning is increasingly used to predict and understand drug resistance
in HIV.•Phylogenetics helps to track the emergence and spread of HIV drug resistance …

A fast likelihood method to reconstruct and visualize ancestral scenarios

SA Ishikawa, A Zhukova, W Iwasaki… - Molecular biology and …, 2019 - academic.oup.com
The reconstruction of ancestral scenarios is widely used to study the evolution of characters
along phylogenetic trees. One commonly uses the marginal posterior probabilities of the …

Using machine learning and big data to explore the drug resistance landscape in HIV

L Blassel, A Tostevin… - PLOS Computational …, 2021 - journals.plos.org
Drug resistance mutations (DRMs) appear in HIV under treatment pressure. DRMs are
commonly transmitted to naive patients. The standard approach to reveal new DRMs is to …

Application of molecular epidemiology in revealing HIV‐1 transmission network and recombination patterns in Tian**, China

Z Hehe, Z Minna, F Qin, N Tielin, F Yi… - Journal of Medical …, 2024 - Wiley Online Library
Using a comprehensive molecular epidemiological approach, we characterized the
transmission dynamics of HIV‐1 among the MSM population in Tian**, China. Our findings …

[HTML][HTML] Genetic Diversity and Antiretroviral Resistance in HIV-1-Infected Patients Newly Diagnosed in Cabo Verde

SDV Leal, V Pimentel, P Gonçalves… - Viruses, 2024 - mdpi.com
The high genetic variability of HIV-1 and the emergence of transmitted drug resistance
(TDR) can impact treatment efficacy. In this study, we investigated the prevalent HIV-1 …

Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability

JM Chang, EW Floden, J Herrero, O Gascuel… - …, 2021 - academic.oup.com
Motivation Most evolutionary analyses are based on pre-estimated multiple sequence
alignment. Wong et al. established the existence of an uncertainty induced by multiple …

Development and validation of a scoring system for the prediction of HIV drug resistance in Hubei province, China

J Yan, W Zhang, H Luo, X Wang… - Frontiers in Cellular and …, 2023 - frontiersin.org
Objective The present study aimed to build and validate a new nomogram-based scoring
system for the prediction of HIV drug resistance (HIVDR). Design and methods Totally 618 …

Early presence of HIV-1 subtype C in Washington, DC

Z Grossman, S Rico, K Cone, W Shao… - AIDS Research and …, 2018 - liebertpub.com
The presence of non-B HIV subtypes in the USA has been documented during the epidemic,
although the timing of early introductions of different subtypes remains uncertain. Subtype C …

HIV Drug Resistance and Transmission Networks among a justice-involved Population at the time of Community Reentry in Washington, DC

CG Beckwith, S Min, A Manne, V Novitsky… - AIDS Research and …, 2021 - liebertpub.com
Justice-involved (JI) populations bear a disproportionate burden of HIV infection and are at
risk of poor treatment outcomes. Drug resistance prevalence and emergence, and …