Julien Roux

Chronic Infection Perturbs the Affinity Hierarchy of Antiviral B Cells

This study shows that chronic viral infection disrupts B cell affinity hierarchies by preferentially causing attrition of high-affinity B cells due to excessive antigen stimulation.

Characteristics of ectopic alveolar basal cells relative to airway basal cells in fibrosis

The paper compares ectopic alveolar basal cells with airway basal cells in ILD patients, finding transcriptomic and organoid-forming differences but no evidence of AT2 cell origin.

Distinct circulating monocytes up-regulate CD52 and sustain innate immune function in patients with cirrhosis unless acute decompensation emerges

The paper identifies CD52-expressing monocytes in cirrhosis that enhance innate immunity, but their loss during acute decompensation correlates with infection and poor outcomes.

Targeting the expansion of myeloid-derived suppressor cells in liver cirrhosis

This study investigates MDSC expansion in cirrhosis patients and murine models, showing poly(I:C) reduces MDSC and fibrosis in infected fibrotic mice.

Robust data-driven gene expression inference for RNA-seq using curated intergenic regions

The paper introduces a method to improve gene expression calling in RNA-Seq by using intergenic read counts as a background reference, showing better consistency across biological replicates.

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Bgee provides an integrated expression atlas and comparative transcriptomics resource for multiple animal species using curated healthy wild-type expression data.

A comparison of gene expression and DNA methylation patterns across tissues and species

The paper compares gene expression and DNA methylation across tissues and species in primates, finding that only 7-11% of inter-species expression differences are explained by methylation, with higher explanation in tissue-specific genes.

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

The paper compares gene expression and regulatory differences between human and chimpanzee iPSC-derived cardiomyocytes and primary heart tissues to assess their utility for comparative genomic studies.

Sex Differentiation In Grayling (Salmonidae) Goes Through An All-Male Stage And Is Delayed In Genetic Males Who Instead Grow Faster

Evaluation of tools for long read RNA-seq splice-aware alignment

This study evaluates RNA-seq splice-aware alignment tools for long-read sequencing technologies, showing that some tools perform well with error correction.

Sex-Specific Changes In Gene Expression And Delayed Sex Differentiation In Response To Estrogen Pollution In Grayling (Salmonidae)

This study shows that estrogen pollution affects gene expression and delays sex differentiation in grayling, with stronger effects in females and some feminization of males.

What to compare and how: comparative transcriptomics for Evo-Devo

The paper reviews challenges in comparative transcriptomics for Evo-Devo and discusses efforts to address them through bioinformatics tools and the Bgee database.

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels.