Yue Andy Qi

This study profiles proteomic changes in iPSC-derived neurons exposed to Aβ42A, revealing AD-related pathways and validating findings in postmortem AD brain tissue.

This study shows APOE genotypes alter astrocytic lipid droplet proteomes and dynamics, with APOE4 showing resistance to lipophagy, suggesting impaired clearance as a mechanism for AD risk.

SenCat catalogs senescence markers across 14 human cell types using transcriptomic and proteomic profiling, revealing shared metabolic pathways and enabling machine learning-based identification of senescent cells.

The paper identifies TMEM106B fibril accumulation as a shared mechanism in neurodegeneration linked to genetic variants in TMEM106B and GRN.

The paper identifies TDP-43-dependent molecular cascades in ALS/FTD by integrating multiomic data from iPSC-derived neurons and validates key genes through experimental assays.

The paper compares dopaminergic neurons from siblings with Gaucher disease to investigate genetic factors contributing to Parkinsonism.

The paper investigates how GBA1 mutations affect glycoprotein nonmetastatic melanoma protein B (GPNMB) expression in dopaminergic neurons, linking lipid accumulation to Parkinson's disease risk.

The paper profiles HLA immunopeptidomes and interactomes in microglia, identifying disease-associated epitopes and their interactions.

The paper profiles proteome and phosphoproteome dynamics during neuronal differentiation of the KOLF2.1J iPSC line, revealing distinct molecular signatures and kinase activity changes.

The paper investigates how endemic viral infections alter the neuronal proteome and links these changes to neurodegenerative disease pathways.

The paper identifies a non-coding risk variant in GBA1 associated with Parkinson's disease in African ancestry populations, showing it disrupts splicing and reduces glucocerebrosidase activity.

ProtPipe is a data analysis pipeline for proteomics and peptidomics that automates processing, quality control, and downstream analysis of mass spectrometry data.

This study investigates how knocking down RNA binding proteins affects mRNA transport and local translation in neurons, revealing distinct impacts on neuritic proteome and transcriptome.

The paper shows that loss of TDP-43 function leads to the expression of de novo proteins from mis-spliced mRNA transcripts in ALS/FTD.

The paper identifies novel cryptic polyadenylation events induced by TDP-43 loss in ALS/FTD using bioinformatic methods and shows their potential disease relevance and impact on protein translation.

This paper presents a cellular taxonomy of the adult human spinal cord using single nucleus RNA-sequencing and spatial transcriptomics, identifying 29 glial and 35 neuronal clusters and highlighting motoneuron vulnerability to ALS.

The paper identifies and characterizes a reference iPSC line, KOLF2.1J, for standardized use in collaborative studies across multiple differentiation protocols and assays.

This paper applies Aligned-UMAP to longitudinal biomedical datasets to reveal time-dependent patterns and provides best practices for its use.

The paper presents a fully automated FAIMS-DIA proteomic pipeline for iPSC-derived neurons, showing high protein identification and reproducibility, validated against single-cell RNA-Seq data.

The paper shows that ALS/FTD risk variants in UNC13A increase sensitivity to TDP-43 depletion by promoting cryptic exon inclusion and protein loss.