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

bioRxiv · Sep 25, 2026 · PreprintNeuroscience

ProtPipe2: Multi-Platform Downstream Proteomics Analysis Tool

Jacob Epstein, Cory A. Weller, Isabelle Kowal, Ying Hao, Cole Tindall, Benjamin Jin, Mark Cookson, Mike A. Nalls, Ziyi Li, Yue A. Qi

ProtPipe2 provides a unified framework for downstream proteomics analysis across mass spectrometry, Olink, and SomaScan platforms, enabling consistent workflows and reusable analyses.

bioRxiv · Sep 21, 2026 · PreprintBioinformatics

Large-scale HLA immunopeptidome and interactome profiling in microglia

Sydney Klaisner, Ying Hao, Alexandra G. Beilina, Jae Hyeon Park, Ziyi Li, Michiyo Iba, Cole Tindall, Benjamin Jin, Jacob Epstein, Isabelle Kowal, Caroline B. Pantazis, Nicole Carmiol, Paige Jarreau, Nicole Washecka, Cory A. Weller, , Yue Andy Qi

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

bioRxiv · Apr 23, 2025 · PreprintImmunology

Temporal dynamics of proteome and phosphorproteome during neuronal differentiation in the reference KOLF2.1J iPSC line

Ying Hao, Ziyi Li, Erika Lara, Daniel M. Ramos, Marianist Santiana, Benjamin Jin, Jacob Epstein, Jasmin J. Camacho, Nicole Carmiol, Isabelle Kowal, Paige Jarreau, Cory A. Weller, Sydney Klaisner, Laurel A. Screven, Caroline B. Pantazis, , Yue Andy Qi

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

bioRxiv · Mar 25, 2025 · PreprintNeuroscience