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2023
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)
Lopez-Lee C
,
Kodama L
,
Fan L
,
Wong MYing
,
Foxe NR
,
Jiaz L
,
Yu F
,
Ye P
,
Zhu J
,
Norman K
et al.
. 2023.
Sex Chromosomes and Gonads Shape the Sex-Biased Transcriptomic Landscape in Tlr7-Mediated Demyelination During Aging.
.
bioRxiv.
Udeochu JC
,
Amin S
,
Huang Y
,
Fan L
,
Torres ERuth S
,
Carling GK
,
Liu B
,
McGurran H
,
Coronas-Samano G
,
Kauwe G
et al.
. 2023.
Tau activation of microglial cGAS-IFN reduces MEF2C-mediated cognitive resilience.
.
Nat Neurosci. 26(5):737-750.
Evering TH
,
Marston JL
,
Gan L
,
Nixon DF
. 2023.
Transposable elements and Alzheimer's disease pathogenesis.
.
Trends Neurosci. 46(3):170-172.
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.
Sharma M
,
Burré J
. 2023.
α-Synuclein in synaptic function and dysfunction.
.
Trends Neurosci. 46(2):153-166.
2022
Burré J
,
Sharma M
. 2022.
Cellular And Small Animal Models Of Neurodegenerative Diseases.
.
J Vis Exp. (186)
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.
Dräger NM
,
Sattler SM
,
Huang CTzu-Ling
,
Teter OM
,
Leng K
,
Hashemi SHadi
,
Hong J
,
Aviles G
,
Clelland CD
,
Zhan L
et al.
. 2022.
A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states.
.
Nat Neurosci.
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.
Dong Q
,
Gentry NW
,
McMahon T
,
Yamazaki M
,
Benitez-Rivera L
,
Wang T
,
Gan L
,
Ptáček L
,
Fu Y-H
. 2022.
Familial natural short sleep mutations reduce Alzheimer pathology in mice.
.
iScience. 25(4):103964.
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.
Xie YXue
,
Naseri NN
,
Fels J
,
Kharel P
,
Na Y
,
Lane D
,
Burré J
,
Sharma M
. 2022.
Lysosomal exocytosis releases pathogenic α-synuclein species from neurons in synucleinopathy models.
.
Nat Commun. 13(1):4918.
Wang C
,
Fan L
,
Khawaja RR
,
Liu B
,
Zhan L
,
Kodama L
,
Chin M
,
Li Y
,
Le D
,
Zhou Y
et al.
. 2022.
Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy.
.
Nat Commun. 13(1):1969.
Kuo S-H
,
Tasset I
,
Cheng MM
,
Diaz A
,
Pan M-K
,
Lieberman OJ
,
Hutten SJ
,
Alcalay RN
,
Kim S
,
Ximénez-Embún P
et al.
. 2022.
Mutant glucocerebrosidase impairs α-synuclein degradation by blockade of chaperone-mediated autophagy.
.
Sci Adv. 8(6):eabm6393.
Xia D
,
Lianoglou S
,
Sandmann T
,
Calvert M
,
Suh JH
,
Thomsen E
,
Dugas J
,
Pizzo ME
,
DeVos SL
,
Earr TK
et al.
. 2022.
Novel App knock-in mouse model shows key features of amyloid pathology and reveals profound metabolic dysregulation of microglia.
.
Mol Neurodegener. 17(1):41.
Blackwell DJ
,
Faggioni M
,
Wleklinski MJ
,
Gomez-Hurtado N
,
Venkataraman R
,
Gibbs CE
,
Baudenbacher FJ
,
Gong S
,
Fishman GI
,
Boyle PM
et al.
. 2022.
The Purkinje-myocardial junction is the anatomical origin of ventricular arrhythmia in CPVT.
.
JCI Insight.
Hardwick SA
,
Hu W
,
Joglekar A
,
Fan L
,
Collier PG
,
Foord C
,
Balacco J
,
Lanjewar S
,
Sampson MMcGuirk
,
Koopmans F
et al.
. 2022.
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
.
Nat Biotechnol.
Liu Q
,
Lee B
,
Xie L
. 2022.
Small molecule modulation of microbiota: a systems pharmacology perspective.
.
BMC Bioinformatics. 23(Suppl 3):403.
Carnazza KE
,
Komer LE
,
Xie YXue
,
Pineda A
,
Briano JAntonio
,
Gao V
,
Na Y
,
Ramlall T
,
Buchman VL
,
Eliezer D
et al.
. 2022.
Synaptic vesicle binding of α-synuclein is modulated by β- and γ-synucleins.
.
Cell Rep. 39(2):110675.
Tracy TE
,
Madero-Pérez J
,
Swaney DL
,
Chang TS
,
Moritz M
,
Konrad C
,
Ward ME
,
Stevenson E
,
Huttenhain R
,
Kauwe G
et al.
. 2022.
Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.
.
Cell. 185(4):712-728.e14.
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)
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