Helen & Robert Appel Alzheimer’s Disease Research Institute

Publications

Found 52 results
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2025
Sun Y, Wang X, Zhang DY, Zhang Z, Bhattarai JP, Wang Y, Park KH, Dong W, Hung Y-F, Yang Q et al..  2025.  Brain-wide neuronal circuit connectome of human glioblastoma.. Nature. 641(8061):222-231.
Hu W, Foord C, Hsu J, Fan L, Corley MJ, Lanjewar SN, Xu S, Belchikov N, He Y, Pang APS et al..  2025.  Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.. Nat Biotechnol.
Wang S, Qi C, Rajpurohit C, Ghosh B, Xiong W, Wang B, Qi Y, Hwang SHee, Hammock BD, Li H et al..  2025.  Inhibition of soluble epoxide hydrolase confers neuroprotection and restores microglial homeostasis in a tauopathy mouse model.. Mol Neurodegener. 20(1):44.
Naseri NN, Xu T, Chantarawong S, Patrie SM, Kelleher NL, Sharma M, Shalem O, Rhoades E.  2025.  Specific Combinations of Physiological Tau Phosphorylation Regulate Tau-Microtubule Interactions in Developing Neurons.. bioRxiv.
2024
Carling GK, Fan L, Foxe NR, Norman K, Wong MYing, Zhu D, Corona C, Razzoli A, Yu F, Yarahmady A et al..  2024.  Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model.. Neuron.
Carling GK, Fan L, Foxe NR, Norman K, Ye P, Wong MYing, Zhu D, Yu F, Xu J, Yarahmady A et al..  2024.  Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model.. bioRxiv.
Guiberson NGuy Lewis, Black LS, Haller JE, Brukner A, Abramov D, Ahmad S, Xie YXin, Sharma M, Burré J.  2024.  Disease-linked mutations in Munc18-1 deplete synaptic Doc2.. Brain.
Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Li J, Wang Z et al..  2024.  Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development.. Cell. 187(13):3236-3248.e21.
Barnett D, Zimmer TS, Booraem C, Palaguachi F, Meadows SM, Xiao H, Chouchani ET, Orr AG, Orr AL.  2024.  Mitochondrial complex III-derived ROS amplify immunometabolic changes in astrocytes and promote dementia pathology.. bioRxiv.
Wang C, Zhao C, Xiao H, Qiang J, Liu Z, Gu J, Zhang S, Li D, Zhang Y, Burré J et al..  2024.  N-acetylation of α-synuclein enhances synaptic vesicle clustering mediated by α-synuclein and lysophosphatidylcholine.. Elife. 13
Kong W, Frouard J, Xie G, Corley MJ, Helmy E, Zhang G, Schwarzer R, Montano M, Sohn P, Roan NR et al..  2024.  Neuroinflammation generated by HIV-infected microglia promotes dysfunction and death of neurons in human brain organoids.. PNAS Nexus. 3(5):pgae179.
Wallace CH, Oliveros G, Xie L, Serrano P, Rockwell P, Figueiredo-Pereira M.  2024.  Potential Alzheimer's early biomarkers in a transgenic rat model and benefits of diazoxide/dibenzoylmethane co-treatment on spatial memory and AD-pathology.. Sci Rep. 14(1):3730.
2023
Xie L, Xie L.  2023.  Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning.. PLoS Comput Biol. 19(8):e1010974.
Xie L, Xie L.  2023.  Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning.. PLoS Comput Biol. 19(8):e1010974.
Cai T, Xie L, Zhang S, Chen M, He D, Badkul A, Liu Y, Namballa HKrishna, Dorogan M, Harding WW et al..  2023.  End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins.. PLoS Comput Biol. 19(1):e1010851.
Cai T, Xie L, Zhang S, Chen M, He D, Badkul A, Liu Y, Namballa HKrishna, Dorogan M, Harding WW et al..  2023.  End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins.. PLoS Comput Biol. 19(1):e1010851.
Wu Y, Liu Q, Xie L.  2023.  Hierarchical multi-omics data integration and modeling predict cell-specific chemical proteomics and drug responses.. Cell Rep Methods. 3(4):100452.
Oliveros G, Wallace CH, Chaudry O, Liu Q, Qiu Y, Xie L, Rockwell P, Figueiredo-Pereira ME, Serrano PA.  2023.  Repurposing ibudilast to mitigate Alzheimer's disease by targeting inflammation.. Brain. 146(3):898-911.
Liao Z, Xie L, Mamitsuka H, Zhu S.  2023.  Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer.. Bioinformatics. 39(1)
Zhang S, Liu Y, Xie L.  2023.  A universal framework for accurate and efficient geometric deep learning of molecular systems.. Sci Rep. 13(1):19171.
2022
Pham T-H, Qiu Y, Liu J, Zimmer S, O'Neill E, Xie L, Zhang P.  2022.  Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing.. Patterns (N Y). 3(4):100441.
Wu Y, Liu Q, Qiu Y, Xie L.  2022.  Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer's disease drug repurposing.. PLoS Comput Biol. 18(8):e1010367.
Cai T, Abbu KAlyssa, Liu Y, Xie L.  2022.  DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity.. Bioinformatics. 38(9):2561-2570.
Liu Y, Lim H, Xie L.  2022.  Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding.. BMC Bioinformatics. 23(Suppl 3):158.
Chaudry O, Ndukwe K, Xie L, Figueiredo-Pereira M, Serrano P, Rockwell P.  2022.  Females exhibit higher GluA2 levels and outperform males in active place avoidance despite increased amyloid plaques in TgF344-Alzheimer's rats.. Sci Rep. 12(1):19129.