Thomas Cokelaer

The paper compares transcriptomic responses of bank vole kidney and respiratory cells to three orthohantaviruses, identifying common and tissue-specific pathways involved in infection outcomes.

This study shows that the Kozak sequence context influences mRNA stability and protein expression in Leishmania by modulating translation-coupled decay and polysome recruitment.

The paper uses a five-layer systems analysis to show that protein degradation, not genomic changes, drives stage differentiation in Leishmania parasites.

KozakExplorer quantitatively analyzes translation initiation signals across genomes, revealing evolutionary patterns in eukaryotes and prokaryotes.

The paper identifies hybridization between Leishmania species as a driver of pathogenicity shift in Leishmania infantum causing cutaneous leishmaniasis.

This study shows bidirectional mitochondrial transfer via tunneling nanotubes between glioblastoma cells and astrocytes, both in vitro and in vivo, and highlights their role in tumor microenvironment interactions.

LORA is a long-read genome assembly pipeline that integrates multiple assemblers and provides quality assessment tools, demonstrating its use on bacterial and eukaryotic genomes.

This study sequences and analyzes genetic diversity in SGG isolates associated with colorectal cancer, revealing no specific pathogenicity island and highlighting surface proteins and other factors involved in host colonization.

This study compares macrophage biology between hamsters and mice to identify factors contributing to differential susceptibility to L. donovani infection.

This study investigates how a SOD-deficient bacterial pathogen adapts to superoxide stress through metabolic pathways rather than enzymatic defenses.

The paper generates a hybrid between Leishmania infantum and Leishmania tarentolae, showing genomic compatibility and transcriptomic differences driven by gene copy number and mRNA turnover.

This study shows that 5-aminolevulinic acid triggers shutdown of the HemKR signaling system in Leptospira by promoting HemK phosphatase activity, leading to gene expression changes and iron-deficit tolerance.

This study identifies ZCF15 and ZCF26 as biofilm regulators in Candida albicans that modulate metabolic reprogramming during the planktonic-to-biofilm transition.

The paper investigates how inverted sedentary chromosomal integrons (SCIs) in Vibrio cholerae recover their original orientation through homologous recombination, maintaining cassette stability and bacterial fitness.

This paper identifies a bile-induced RND efflux pump in Bacteroides thetaiotaomicron that facilitates magnesium efflux, reducing eDNA concentration and promoting biofilm formation.

This study uses TALENs to contract CTG repeats in DM1 cells, achieving 68% contraction with a recoded TALEN, while SaCas9 failed, and identifies potential off-target effects.

This paper presents 142 high-quality yeast genomes to improve pangenome understanding, identifying structural variants and complex genomic regions.

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

This study investigates SARS-CoV-2 infection in the olfactory system, showing viral persistence and inflammation linked to prolonged loss of smell in COVID-19 patients.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

Sequanix provides a graphical interface for Snakemake workflows to make them more accessible to a broader audience.

The paper introduces BiRewire 3, a tool for efficiently randomizing biological networks while preserving node functional characteristics, and demonstrates its application in network analysis.

The paper introduces a method to detect and characterize low and high coverage regions in genomes using a running median and double threshold approach.