Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer's …

Y Wu, Q Liu, Y Qiu, L Xie - PLoS computational biology, 2022 - journals.plos.org
Predictive modeling of drug-induced gene expressions is a powerful tool for phenotype-
based compound screening and drug repurposing. State-of-the-art machine learning …

The role of mitochondrial genome abundance in Alzheimer's disease

NV Harerimana, D Paliwali… - Alzheimer's & …, 2023 - Wiley Online Library
Mitochondrial dysfunction is an early and prominent feature of Alzheimer's disease (AD),
with impaired energy metabolism preceding the onset of clinical symptoms. Here we …

[HTML][HTML] Functional genomics study of protein inhibitor of activated STAT1 in mouse hippocampal neuronal cells revealed by RNA sequencing

K He, J Zhang, J Liu, Y Cui, LG Liu, S Ye, Q Ban… - Aging (Albany …, 2021 - ncbi.nlm.nih.gov
Protein inhibitor of activated STAT1 (PIAS1), a small ubiquitin-like modifier (SUMO) E3
ligase, was considered to be an inhibitor of STAT1 by inhibiting the DNA-binding activity of …

MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication

T Kumar, R Sethuraman, S Mitra… - PLOS Computational …, 2023 - journals.plos.org
With the evolution of multicellularity, communication among cells in different tissues and
organs became pivotal to life. Molecular basis of such communication has long been …

Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks

HU Klein, M Schäfer, DA Bennett… - PLoS computational …, 2020 - journals.plos.org
Biomedical research studies have generated large multi-omic datasets to study complex
diseases like Alzheimer's disease (AD). An important aim of these studies is the …

Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer's disease related proteins

SR Oatman, JS Reddy, Z Quicksall… - Molecular …, 2023 - Springer
Background Alzheimer's disease (AD) is neuropathologically characterized by amyloid-beta
(Aβ) plaques and neurofibrillary tangles. The main protein components of these hallmarks …

Integrative multi-omics analysis identifies novel protein-coding genes and pathways in autism spectrum disorder: a comprehensive study

D Liu, Y Liu, X Fang - Journal of Translational Medicine, 2024 - Springer
Fig. 2 Single-cell analysis.(A) Cell annotation;(B) Violin plots of cell marker expression;(C)
Difference in SLC30A9 related gene scores between two groups;(D) Difference in SLC30A9 …

Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences

L Zhan, J Li, B Jew, JH Sul - PLoS Genetics, 2021 - journals.plos.org
Late-onset Alzheimer's disease (LOAD) is the most common type of dementia causing
irreversible brain damage to the elderly and presents a major public health challenge …

ESHRD: deconvolution of brain homogenate RNA expression data to identify cell-type-specific alterations in Alzheimer's disease

IS Piras, C Bleul, JS Talboom, MD De Both… - Aging (Albany …, 2020 - pmc.ncbi.nlm.nih.gov
Objective: We describe herein a bioinformatics approach that leverages gene expression
data from brain homogenates to derive cell-type specific differential expression results …

Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities

MA Scelsi, V Napolioni, MD Greicius… - PLoS Computational …, 2021 - journals.plos.org
State-of-the-art rare variant association testing methods aggregate the contribution of rare
variants in biologically relevant genomic regions to boost statistical power. However, testing …