Denis Baurain

This paper shows that hyoid barbels in goatfishes drove rapid speciation and ecomorphological divergence, meeting criteria for adaptive radiation.

This study investigates the evolutionary origin of thylakoid membranes in cyanobacteria by analyzing phylogenomic data and structural models of membrane trafficking and Photosystem II assembly.

This study shows Gloeobacterales integrate horizontally transferred genes into their metabolism, enabling ribose uptake and central carbon metabolism remodeling, challenging their status as primitive relics.

The paper identifies an early-diverging sulfide quinone reductase in Antarctic Gloeobacterales, suggesting sulfide tolerance in thylakoid-lacking cyanobacteria and their adaptation to euxinic conditions.

This study reconstructs high-quality genomes of Antarctic and Arctic cyanobacteria, revealing an Out-of-Antarctica dispersal scenario within subcluster 5.2.

The paper develops a FAIR amplicon sequencing workflow for long-term environmental monitoring of microbial communities in Antarctica.

This study identifies a unique Lhce light-harvesting complex in Euglena gracilis that dynamically associates with PSII and expands PSI light harvesting, revealing an alternative strategy for light acclimation in secondary plastids.

This study shows that Barley Yellow Dwarf Viruses adapt differently to various Poaceae hosts, with some adaptations causing reduced fitness in other hosts, suggesting crop mixtures could help manage the virus.

This study identifies a mitochondrial carrier transporter in diatoms that facilitates energy exchange between mitochondria and plastids, supporting photosynthesis.

This study identifies and characterizes archaeal pseudomurein biosynthesis genes using pangenomics, revealing evolutionary relationships and horizontal gene transfer events.

The paper introduces the GEN-ERA toolbox, a unified bioinformatics workflow for microbial genomics that enables reproducible phylogenetic and metabolic analyses on bacteria and small eukaryotes.

CRACOT benchmarks six contamination detection tools across six taxonomic ranks, finding poor precision and recommending tool combination for better accuracy.

The paper uses whole genome sequences of 75 Snodgrassella strains to show the genus comprises at least seven species, with two formally named, and identifies 107 species-specific genes.

AMAW automates genome annotation for non-model eukaryotes by integrating MAKER2 and providing a Singularity container for easier deployment.

ORPER is a Nextflow workflow that determines the phylogenetic position of organisms by constraining SSU rRNA sequences in a reference tree, demonstrated on Cyanobacteria strains.

TQMD is a tool for dereplicating prokaryotic genomes using k-mer based methods, optimized for high taxonomic levels and complementary to existing tools.

The paper reports genome sequencing of 15 arctic/subarctic Cyanobacteria and their associated microbiome using a metagenomic pipeline, showing high-quality assemblies from non-axenic cultures.

The paper assesses contamination levels in 440 cyanobacterial genomes using a consensus of six methods, finding over 5% are highly contaminated.

PREDetector 2.0 improves gene regulatory network prediction by offering interactive parameter tuning, enhanced visualization, and expanded database access for bacterial genomes.