Using machine learning and big data to explore the drug resistance landscape in HIV
August 2021
PLOS Computational Biology

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 test for significant frequency differences of mutations between treated and naive patients. However, we then consider each mutation …

Origin, evolution and global spread of SARS-CoV-2
June 2021
Comptes Rendus. Biologies
A. Zhukova , L. Blassel , F. Lemoine , M. Morel , J. Voznica and O. Gascuel

COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM
October 2020
F. Lemoine , L. Blassel , J. Voznica and O. Gascuel

The first cases of the COVID-19 pandemic emerged in December 2019. Until the end of February 2020, the number of available genomes was below 1000 and their multiple alignment was easily achieved using standard approaches. Subsequently, the availability of genomes has grown dramatically. Moreover, …