Frédéric Lemoine

DIPScan detects and corrects defective viral genomes in sequencing data to improve consensus genome accuracy for influenza virus.

This study analyzes the global evolutionary patterns of Yersinia pestis, revealing its introduction into Africa and key genomic adaptations contributing to its persistence.

The paper introduces a Bayesian phylogenetic bootstrap method to improve branch support interpretation in phylogenetics, showing higher expected support for correct branches compared to the frequentist Felsenstein bootstrap.

The paper evaluates the neutralization activity of two new monoclonal antibodies against emerging SARS-CoV-2 variants and finds reduced efficacy against some sublineages.

This study characterizes SARS-CoV-2 variants XBB and BA.2.86/JN.1, finding they show increased fitness and antibody evasion while maintaining antiviral sensitivity.

The paper demonstrates that integron integrase can insert cassettes outside classical att sites, leading to new recombination sites called attG and expanding integron roles in bacterial evolution.

This study compares Felsenstein's bootstrap proportions and Transfer Bootstrap Expectation in assessing phylogenetic support under varying taxon sampling and finds TBE more robust in most cases.

BioConvert simplifies life science data format conversion by aggregating tools and providing a unified interface, supporting 50 formats and 100 conversions.

The paper introduces a deep learning method for phylodynamic analysis that outperforms existing approaches on simulated data and applies to HIV outbreak dynamics.

Gotree/Goalign provides a toolkit and Go API for phylogenetic workflows, offering 120 commands and an API for sequence alignment and tree manipulations.

This study analyzes how global and regional public health interventions affected SARS-CoV-2 transmission clusters using genetic sequence data and phylogenetic analysis.

The paper introduces COVID-Align, a tool for efficiently aligning SARS-CoV-2 genomes using profile HMM, enabling rapid and accurate analysis of large datasets.