This study creates a multi-omic atlas of the choroid plexus in Alzheimer's disease, identifying disease-associated cell state transitions and functional impairments.

bioRxiv · Nov 23, 2025 · PreprintGenomics

Uncovering Plaque-Glia Niches in Human Alzheimer's Disease Brains Using Spatial Transcriptomics

Denis R. Avey, Bernard Ng, Ricardo A. Vialle, Nicola A. Kearns, Kátia de Paiva Lopes, Artemis Iatrou, Sashini L De Tissera, Himanshu Vyas, Devin M. Saunders, Daniel J. Flood, Jishu Xu, Shinya Tasaki, Chris Gaiteri, David A. Bennett, Yanling Wang

The paper uses spatial transcriptomics to analyze Aβ plaques and glial interactions in AD brains, finding that low Aβ areas show more neuronal loss and high-glia areas show inflammation and neurodegeneration.

Molecular Neurodegeneration Advances · Jul 16, 2025Peer-reviewedGenomics

Integrated Spatial and Single-Nuclei Transcriptomic Analysis of Long Non-Coding RNAs in Alzheimer's Disease

Bernard Ng, Denis R. Avey, Faraz Sultan, Kátia de Paiva Lopes, Masashi Fujita, Devin Saunders, Ricardo A. Vialle, Himanshu Vyas, Nicola A. Kearns, Shinya Tasaki, Artemis Iatrou, Sashini L De Tissera, Amiko Krisa Lagrimas, Tien-Hao Chang, Jishu Xu, , Yanling Wang

The paper identifies AD-associated lncRNAs with spatial and cell-type-specific expression patterns and shows OIP5-AS1 contributes to microglial activation in AD.

bioRxiv · Oct 27, 2024 · PreprintNeuroscience

The YTHDF proteins shape the brain gene signatures of Alzheimer's disease

Shinya Tasaki, Denis R. Avey, Nicola A. Kearns, Chunjiang Yu, Sashini L De Tissera, Himanshu Vyas, Lin Cheng, Jishu Xu, Artemis Iatrou, Daniel J. Flood, Wenlong Li, Lisa Laverne Barnes, Katherine L. Rothamel, Aliza P. Wingo, Thomas S. Wingo, , Yanling Wang

This study identifies YTHDF proteins as key regulators of Alzheimer's disease brain gene signatures through m6A-dependent and independent mechanisms.

bioRxiv · Oct 23, 2024 · PreprintNeuroscience

SR-TWAS: Leveraging Multiple Reference Panels to Improve TWAS Power by Ensemble Machine Learning

Randy L. Parrish, Aron S. Buchman, Shinya Tasaki, Yanling Wang, Denis R. Avey, Jishu Xu, Philip L. De Jager, David Alan Bennett, Michael P. Epstein, Jingjing Yang

SR-TWAS improves TWAS power by combining multiple reference panels and regression methods through ensemble learning, identifying risk genes for Alzheimer's and Parkinson's diseases.

medRxiv · Jun 20, 2023 · PreprintGenetic & Genomic Medicine

High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation

Matthew A. Lalli, Denis R. Avey, Joseph D. Dougherty, Jeffrey Milbrandt, Robi David Mitra

This paper uses single-cell profiling to functionally analyze ASD genes, identifying two convergent modules affecting neuronal differentiation and predicting shared clinical phenotypes.

Genome Research · Sep 1, 2020Peer-reviewedGenomics

Single cell RNAseq uncovers a robust transcriptional response to morphine by oligodendrocytes

Denis R. Avey, Sumithra Sankararaman, Aldrin Kay‐Yuen Yim, Ruteja A. Barve, Robi David Mitra, Jeffrey Milbrandt

This study identifies morphine-induced gene expression changes in oligodendrocytes using single-cell RNA sequencing in mice, highlighting pathways related to myelination.

bioRxiv · Apr 24, 2018 · PreprintNeuroscience