Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data. - Joel V. Earnest-DeYoung; Emmanuelle Lerat; Bernard M. E. Moret (WABI, 2004)

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data. - Laurent Modolo; Emmanuelle Lerat (BMC Bioinform., 2015)

Simulation-based estimation of branching models for LTR retrotransposons. - Serge Moulin; Nicolas Seux; Stéphane Chrétien; Christophe Guyeux; Emmanuelle Lerat (Bioinform., 2017)

Repeat in Genomes: How and Why You Should Consider Them in Genome Analyses? - Emmanuelle Lerat (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)