Zuo‐Fei Yuan

This study evaluates false discovery rate and statistical power in DIA proteomics using technical replicates and spike-in experiments, revealing discrepancies between nominal and true FDR and showing power dependence on fold change and abundance.

JUMPlion improves DIA proteomics by recovering missing ion-level values, enhancing protein quantification accuracy in low-input and single-cell analyses.

This study identifies APOE as a presynaptic protein enriched in aged female mice, showing it modulates neurotransmitter release and affects synaptic function.

This paper demonstrates that bioPROTACs can reprogram CAR T-cells by targeting DNMT3A, offering a tunable alternative to gene editing for enhancing T-cell function.

The paper presents a cell type-resolved proteomic atlas of Alzheimer's disease mouse models, identifying thousands of cell-specific protein changes and highlighting astrocyte-microglia signaling.

The paper quantifies the proteomic composition of amyloid plaques in AD models and human brains, revealing stage-dependent remodeling and conserved proteins across species.

The paper identifies H3K27me3's dual role in regulating transposons and cell type-specific genes in choanoflagellates, suggesting ancestral chromatin mechanisms in development.

This study shows sorbate induces lysine sorbylation via Class I HDACs, altering inflammation gene expression without affecting histone acetylation.

The paper identifies glycerophospholipid biosynthesis upregulation as a mechanism of chemoresistance in SLFN11-loss Ewing sarcoma and shows that inhibiting this pathway enhances DNA-damaging agent efficacy.

Alzheimer's mouse model proteomes capture 30% (amyloid-only models) to 42% (adding tau and splicing models) of consensus human AD protein changes; in 5xFAD, plaques slow degradation of plaque-associated proteins.

This study shows that KAT2A and KAT2B prevent dsRNA accumulation and interferon signaling, which is critical for maintaining intestinal stem cells in mice.

This study shows that ATM-mediated phosphorylation of 53BP1-serine 25 is essential for neural progenitor cell proliferation and neuronal differentiation in cortical organoids.

The paper investigates the role of H3.3K27me3 in mouse embryonic stem cell differentiation, showing it regulates distinct terminal differentiation genes compared to canonical H3K27me3.