The paper defines cognitive resilience as differential cognitive decline rates after adjusting for neuropathologies, develops a framework to quantify it using molecular signatures from post-mortem brain data, and translates these findings to living individuals.

bioRxiv · Aug 13, 2025 · PreprintNeuroscience

Genotyping TOMM40'523 Poly-T Polymorphisms Using Whole-Genome Sequencing

Ricardo A. Vialle, Lei Yu, Yan Li, Roberto Tadeu Raittz, José M. Farfel, Philip L. De Jager, Julie A. Schneider, Lisa Laverne Barnes, Shinya Tasaki, David A. Bennett

This paper introduces a computational pipeline for genotyping TOMM40 poly-T polymorphisms from whole-genome sequencing data, achieving high accuracy and consistency with PCR-based genotypes.

Human Genetics and Genomics Advances · Aug 7, 2025Peer-reviewedGenetic & Genomic Medicine

Brain Multi-Omic Subtypes of Neuroticism Reveal Molecular Signatures linked to Alzheimer's Disease

Andrea R. Zammit, Katia de Pavia Lopes, Caio M.P.F. Batalha, Lei Yu, Victoria N. Poole, Shinya Tasaki, Alifiya Kapasi, Yanling Wang, Philip L. De Jager, Vilas Menon, Nicholas T. Seyfried, Rima F Kaddurah-Daouk, Yasser Iturria‐Medina, David Alan Bennett

The paper identifies three brain multi-omic molecular subtypes of neuroticism linked to Alzheimer's disease traits, with subtype N1 showing the strongest associations.

bioRxiv · May 19, 2025 · PreprintNeuroscience

Translating the Post-Mortem Brain Multi-Omics Molecular Taxonomy of Alzheimer's Dementia to Living Humans

Yasser Iturria‐Medina, Victoria N. Poole, Andrea R. Zammit, Lei Yu, Shinya Tasaki, Joon Hwan Hong, Kátia de Paiva Lopes, Caio M.P.F. Batalha, Abdur Raquib Ridwan, Ricardo A. Vialle, Lazaro M. Sanchez-Rodriguez, Maiya Rachel Geddes, Peter M. Abadir, Eric A. Ortlund, Philip L. De Jager, , David Alan Bennett

This study translates post-mortem brain multi-omics AD dementia subtypes into blood, MRI, and psychological markers in living individuals.

bioRxiv · Mar 20, 2025 · PreprintNeuroscience

Multi-omic subtypes of Alzheimer's dementia are differentially associated with psychological traits

Andrea R. Zammit, Lei Yu, Victoria N. Poole, Konstantinos Arfanakis, Julie A. Schneider, Vladislav Petyuk, Philip L. De Jager, Rima F Kaddurah-Daouk, Yasser Iturria‐Medina, David Alan Bennett

The paper examines associations between three multi-omic AD subtypes and four psychological traits, finding differential links between subtypes and traits.

bioRxiv · Feb 21, 2025 · PreprintMolecular Biology

Polygenic Risk Associated with Alzheimer's Disease and Other Traits Influences Genes Involved in T Cell Signaling and Activation

Dallin Dressman, Shinya Tasaki, Lei Yu, Julie A. Schneider, David A. A Bennett, Wassim Elyaman, Badri Narayan Vardarajan

The paper computes polygenic risk scores for various disorders and correlates them with T cell gene expression in Alzheimer's patients and controls, identifying gene pathways related to T cell signaling and activation.

Frontiers in Immunology · Mar 25, 2024Peer-reviewedBioinformatics

Multi-region brain transcriptomes uncover two subtypes of aging individuals with differences in Alzheimer risk and the impact of APOEe4

Annie Lee, Yiyi Ma, Lei Yu, Robert J. Dawe, Cristin Aubin, Konstantinos Arfanakis, Richard P Mayeux, David Alan Bennett, Hans‐Ulrich Klein, Philip L. De Jager

The paper identifies two subtypes of aging brains with distinct Alzheimer's risk profiles and differential impacts of APOEε4.

bioRxiv · Jan 25, 2023 · PreprintNeuroscience

Genome-wide association study and functional validation implicates JADE1 in tauopathy

Kurt W. Farrell, SoongHo Kim, Natalia Han, Megan A. Iida, Elias M. Gonzalez, Marcos Otero‐García, Jamie M. Walker, Timothy E. Richardson, Alan Edward Renton, Shea J. Andrews, Brian Fulton‐Howard, Jack Humphrey, Ricardo A. Vialle, Kathryn R. Bowles, Kátia de Paiva Lopes, , John F. Crary

This study identifies JADE1 as a novel genetic factor in tauopathy through genome-wide association and functional validation in human and Drosophila models.

Acta Neuropathologica · Oct 31, 2021Peer-reviewedNeuroscience

Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans

Yiyi Ma, Lei Yu, Marta Olah, Rebecca G. Smith, Stephanie R. Oatman, Mariet Allen, Ehsan Pishva, Bin Zhang, Vilas Menon, Nilüfer Ertekin-Taner, Katie Lunnon, David Alan Bennett, Hans-Ulrich Klein, Philip L. De Jager

The paper identifies an epigenomic factor linked to reduced activated microglia that mitigates the risk of Alzheimer's disease in APOE ε4 carriers.

Alzheimer s & Dementia · Dec 1, 2020Peer-reviewedNeuroscience

Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach

Benjamin A. Logsdon, Thanneer Malai Perumal, Vivek Swarup, Minghui Wang, Cory C. Funk, Chris Gaiteri, Mariet Allen, Xue Bing Wang, Eric B. Dammer, Gyan Prakash Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen Dang, James A. Eddy, , Lara M. Mangravite

Coexpression meta-analysis of 2114 human brain RNA-seq samples across the AMP-AD consortium identifies five consensus Alzheimer's disease transcriptional clusters, including two sex-heterogeneous clusters and a previously unreported proteostasis cluster.

bioRxiv · Jan 3, 2019 · PreprintSystems Biology

A molecular network of the aging brain implicates INPPL1 and PLXNB1 in Alzheimer’s disease

Sara Mostafavi, Chris Gaiteri, Sarah E. Sullivan, Charles C. White, Shinya Tasaki, Jishu Xu, Mariko F. Taga, Hans‐Ulrich Klein, Ellis Patrick, Vitalina Komashko, Cristin Aubin, Robert V. Smith, Elizabeth M. Bradshaw, David E. Root, Aviv Regev, , Philip L. De Jager

Molecular network analysis of RNA sequencing data from the aging human cortex identifies new Alzheimer's and cognitive decline genes.

Nature Neuroscience · May 21, 2018Peer-reviewedSystems Biology