CellTypeAI improves scRNA-seq cell type annotation by using local generative-AI models, outperforming conventional and cloud-based methods in accuracy and sensitivity.

bioRxiv · Mar 5, 2026 · PreprintBioinformatics

Blood-brain barrier dysfunction predicts cognitive trajectory after ischemic stroke

Lei Xue, Olivia A Jones, Lauren L. Drag, Kristy A. Zera, Li Zhu, Michael Mlynash, Natasha S. Carmichael, Chi-Hung Shu, Zuzanna Biesiada, David Seong, Owen Thomas, Epiphani C. Simmons, Emily Huang, Kacey Berry, Philip Chung, , Marion S. Buckwalter

The paper identifies a plasma proteomic signature linked to blood-brain barrier dysfunction, which predicts cognitive decline after ischemic stroke.

bioRxiv · Mar 2, 2026 · PreprintNeuroscience

Integration of Unpaired and Heterogeneous Clinical Flow Cytometry Data

Mike Phuycharoen, Verena Kästele, Thomas Williams, Lijing Lin A, Tracy Hussell, John R. Grainger, Magnus Rattray

This paper introduces UVAE to integrate unpaired clinical flow cytometry data, improving cell type signal and clustering by correcting batch effects.

iScience · Feb 7, 2026Peer-reviewedBioinformatics

Comprehensive analysis of myeloid reporter mice

Yidan Wang, Samuel D. Dowling, Vanessa Rodriguez, Jessica Maciuch, Meghan Mayer, Tyler Therron, Tovah N. Shaw, Miranda G. Gurra, Caroline L. Shah, Hadijat M. Makinde, Florent Ginhoux, David Voehringer, Cole A. Harrington, Toby Lawrence, John R. Grainger, , Harris Perlman

This study presents lineage tracing results from 18 myeloid-specific fate-mapping models in mouse peripheral blood and synovial tissue, validating synovial macrophage identification through flow cytometry and CITE-seq.

bioRxiv · Feb 24, 2025 · PreprintImmunology