The paper identifies 18 m6A sites in HIV-1 using Nanopore sequencing and reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications.

NAR Genomics and Bioinformatics · Oct 7, 2025Peer-reviewedBioinformatics

OKseqHMM: a genome-wide replication fork directionality analysis toolkit

Yaqun Liu, Xia Wu, Yves d’Aubenton-Carafa, Claude Thermes, Chun-Long Chen

OKseqHMM measures genome-wide replication fork directionality using OK-Seq data and related techniques to study transcription-replication conflicts and genome instability.

Nucleic Acids Research · Dec 20, 2022Peer-reviewedBioinformatics

GC content but not nucleosome positioning directly contributes to intron-splicing efficiency in Paramecium

Stefano Gnan, Mélody Matelot, Marion Weiman, Olivier Arnaiz, Frédéric Guèrin, Linda Sperling, Mireille Bétermier, Claude Thermes, Chun-Long Chen, Sandra Duharcourt

Genome Research · Apr 1, 2022Peer-reviewedGenomics

TRANSCRIPTION-MEDIATED ORGANIZATION OF THE REPLICATION INITIATION PROGRAM ACROSS LARGE GENES SETS UP COMMON FRAGILE SITES GENOME-WIDE

Olivier Brison, Sami El-Hilali, Dana Azar, Stéphane Koundrioukoff, Mélanie Schmidt, Viola Nähse, Yan Jaszczyszyn, Anne-Marie Lachagès, Bernard Dutrillaux, Claude Thermes, Michelle Debatisse, Chun-Long Chen

The paper shows that transcription suppresses replication initiation in large genes, leading to delayed replication and instability at common fragile sites.

Nature Communications · Dec 13, 2019Peer-reviewedGenomics