Helen & Robert Appel Alzheimer’s Disease Research Institute

Publications

Found 20 results
Author Title Type [ Year(Desc)]
Filters: Author is Xie, Lei  [Clear All Filters]
2019
Ayed M, Lim H, Xie L.  2019.  Biological representation of chemicals using latent target interaction profile.. BMC Bioinformatics. 20(Suppl 24):674.
Poleksic A, Xie L.  2019.  Database of adverse events associated with drugs and drug combinations.. Sci Rep. 9(1):20025.
Xie L, Xie L.  2019.  Pathway-Centric Structure-Based Multi-Target Compound Screening for Anti-Virulence Drug Repurposing.. Int J Mol Sci. 20(14)
Liu Q, He D, Xie L.  2019.  Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature.. PLoS Comput Biol. 15(10):e1007480.
Lim H, He D, Qiu Y, Krawczuk P, Sun X, Xie L.  2019.  Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.. PLoS Comput Biol. 15(6):e1006619.
2021
Sayed FA, Kodama L, Fan L, Carling GK, Udeochu JC, Le D, Li Q, Zhou L, Wong MYing, Horowitz R et al..  2021.  AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation.. Sci Transl Med. 13(622):eabe3947.
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.
Liu Q, Lee B, Xie L.  2022.  Small molecule modulation of microbiota: a systems pharmacology perspective.. BMC Bioinformatics. 23(Suppl 3):403.
Wallace CH, Oliveros G, Serrano PA, Rockwell P, Xie L, Figueiredo-Pereira M.  2022.  Timapiprant, a prostaglandin D2 receptor antagonist, ameliorates pathology in a rat Alzheimer's model.. Life Sci Alliance. 5(12)
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.
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.
2024
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.