Marie A. Brunet

This paper demonstrates that using ionbot with OpenProt improves detection of non-canonical proteins by reducing FDR and increasing reproducibility compared to TPP.

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

The paper integrates a comprehensive loss-of-function dataset with ncORF information in Medicago truncatula, revealing their potential impact on phenotypes and highlighting ambiguities in mutant studies.

The paper uses brain age gaps to identify developmental trajectories in youth, finding distinct patterns in ADHD and cognitive profiles.

sf-pediatric provides an age-adaptable dMRI pipeline for pediatric studies, improving modeling and reproducibility across brain development.

The paper uses proximity labeling to identify proteins interacting with 23 human RAB GTPases, revealing novel functional connections and interactions.

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

The paper assesses MS-based identifications of unannotated human microproteins, finding large variation in reported proteins and PSM quality across studies.

The paper identifies chimeric peptides and potential mosaic proteins in Medicago truncatula proteomic data, providing indirect evidence for the mosaic translation hypothesis.

The paper introduces a multiplexing strategy for scRNA-seq of adult mouse brain samples using anti-Thy1.2 antibodies and secondary oligonucleotide-labeled antibodies, enabling pooled sequencing with efficient demultiplexing and cost reduction.

This study identifies differentially expressed genes in peripheral blood monocytes across Alzheimer's disease stages, highlighting chemokine/cytokine pathways and potential biomarkers for early detection.

The paper identifies 280 alternative proteins in human protein-protein interaction networks using proteogenomic data and experimental validation, revealing new interactions and functional roles.

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

The paper identifies a new protein, MTALTND4, encoded by an alternative ATG in the human mitochondrial nd4 gene, which affects mitochondrial bioenergetics.

The paper identifies an alternative open reading frame (altORF) within the FUS gene that contributes to toxicity in neurodegenerative models.