Extracellular vesicle analysis

A Hendrix, L Lippens, C Pinheiro, C Théry… - Nature Reviews …, 2023 - nature.com
Cells release small, phospholipid membrane-enclosed particles, collectively referred to as
extracellular vesicles (EVs), into their surroundings to enable intercellular communication …

[PDF][PDF] A simple guide to de novo transcriptome assembly and annotation

V Raghavan, L Kraft, F Mesny… - Briefings in …, 2022 - academic.oup.com
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

Three differential expression analysis methods for RNA sequencing: limma, EdgeR, DESeq2

S Liu, Z Wang, R Zhu, F Wang, Y Cheng… - JoVE (Journal of Visualized …, 2021 - jove.com
RNA sequencing (RNA-seq) is one of the most widely used technologies in transcriptomics
as it can reveal the relationship between the genetic alteration and complex biological …

Omics approaches for the assessment of biological responses to nanoparticles

Y Abdelkader, L Perez-Davalos, R LeDuc… - Advanced Drug Delivery …, 2023 - Elsevier
Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and
drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein …

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species

L Wei, S Luan, LAE Nagai, R Su, Q Zou - Bioinformatics, 2019 - academic.oup.com
Motivation As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) is
recently shown to play crucial roles in restriction–modification systems. For better …

standR: spatial transcriptomic analysis for GeoMx DSP data

N Liu, DD Bhuva, A Mohamed, M Bokelund… - Nucleic Acids …, 2024 - academic.oup.com
To gain a better understanding of the complexity of gene expression in normal and diseased
tissues it is important to account for the spatial context and identity of cells in situ. State-of …

Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice

Y Zhang, G Chen, L Deng, B Gao, J Yang… - Nucleic Acids …, 2023 - academic.oup.com
Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and
thus ensure plant fitness to the environment. Genome-wide characterization and comparison …

[HTML][HTML] Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods

J Costa-Silva, DS Domingues, D Menotti… - Computational and …, 2023 - Elsevier
Abstract Analysis of differential gene expression from RNA-seq data has become a standard
for several research areas. The steps for the computational analysis include many data …

Blockage of VEGF function by bevacizumab alleviates early-stage cerebrovascular dysfunction and improves cognitive function in a mouse model of Alzheimer's …

M Zhang, Z Zhang, H Li, Y **a, M **ng, C **ao… - Translational …, 2024 - Springer
Background Alzheimer's disease (AD) is a neurodegenerative disorder and the predominant
type of dementia worldwide. It is characterized by the progressive and irreversible decline of …

Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease

K Barreiro, OP Dwivedi, G Leparc… - Journal of …, 2020 - Wiley Online Library
Abstract Urinary Extracellular Vesicles (uEV) have emerged as a source for biomarkers of
kidney damage, holding potential to replace the conventional invasive techniques including …