Gérémy Clair

The paper develops a computationally efficient, library-free DIA workflow for metaproteomics, improving throughput and reducing reliance on spectral libraries.

The paper introduces RomicsProcessor, a reproducible-by-design tool for multi-omics and spatial-omics analysis that enforces FAIR principles and ensures computational reproducibility.

The paper identifies carbamylation as a regulatory modification in β-cell metabolism and insulin processing in T1D by analyzing proteomic changes in NOD and MIN6 cells.

This study identifies CD248 as a co-activator of TGF-β receptor I in pulmonary arterial hypertension, supporting anti-CD248 therapy as a targeted alternative to systemic TGF-β inhibition.

This study uses mass spectrometry to identify caspase targets in primary intestinal epithelial cells following NAIP-NLRC4 inflammasome activation, revealing novel cleavage sites beyond known Caspase-1 substrates.

This study identifies sex-specific multi-omic responses to endurance exercise training in rat lungs, revealing differences in immune pathways and mitochondrial acetylation between males and females.

This study uses sorted-cell proteomics to identify BPD-specific proteome changes in epithelial and endothelial cells, revealing cornification-associated proteins and redox imbalance.

This study identifies changes in the skeletal muscle nuclear proteome after acute exercise, revealing post-transcriptional effects on mRNA processing and splicing.

This paper presents a multimodal imaging approach to characterize metabolic changes in bronchopulmonary dysplasia, revealing altered lipid distributions and collagen remodeling in affected tissues.

The paper integrates N-glycan analysis with CODEX imaging to identify cell-specific glycosylation patterns in healthy human lung tissue.

The study identifies loss of cell junctions and matrix dysregulation as drivers of epithelial desquamation and fibrosis in IPF distal bronchioles.

The paper constructs a single-cell reference atlas for human and mouse lung tissues to improve cell type annotation and data integration.

The paper describes the LungMAP Portal Ecosystem, a centralized resource integrating multi-omics and imaging data across species to enable standardized analysis of lung biology and disease.

This paper introduces TIFF, a method enhancing single-cell proteomics sensitivity and accuracy by filtering background ions and using 3D MS1 feature matching, achieving deep proteome analysis in single cells.

This paper introduces a nested nanowell chip to improve single-cell proteomics throughput and robustness, demonstrating the ability to quantify ~1500 proteins from ~100 cells with low abundance variation.