[HTML][HTML] Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment

LJ Marcos-Zambrano… - Frontiers in …, 2021 - frontiersin.org
The number of microbiome-related studies has notably increased the availability of data on
human microbiome composition and function. These studies provide the essential material …

[HTML][HTML] From reads to insight: a hitchhiker's guide to ATAC-seq data analysis

F Yan, DR Powell, DJ Curtis, NC Wong - Genome biology, 2020 - Springer
Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …

[HTML][HTML] Gut microbiome dysbiosis contributes to abdominal aortic aneurysm by promoting neutrophil extracellular trap formation

Z Tian, Y Zhang, Z Zheng, M Zhang, T Zhang, J Jin… - Cell host & …, 2022 - cell.com
Abdominal aortic aneurysm (AAA) is an insidious and lethal vascular disease that lacks
effective nonsurgical interventions. Gut microbiota dysbiosis plays key roles in many …

Exploring epigenomic datasets by ChIPseeker

Q Wang, M Li, T Wu, L Zhan, L Li, M Chen… - Current …, 2022 - Wiley Online Library
In many aspects of life, epigenetics, or the altering of phenotype without changes in
sequences, play an essential role in biological function. A vast number of epigenomic …

[HTML][HTML] An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

F Xie, W Jin, H Si, Y Yuan, Y Tao, J Liu, X Wang… - Microbiome, 2021 - Springer
Background Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host
health and thus animal production. However, we lack an integrated understanding of …

A marine fungus Alternaria alternata FB1 efficiently degrades polyethylene

R Gao, R Liu, C Sun - Journal of Hazardous Materials, 2022 - Elsevier
Huge quantities of plastic wastes have been accumulating in the environment causing
serious ecological problems and significantly impacting the global carbon cycling. Plastic …

[HTML][HTML] Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma

Y Zheng, T Wang, X Tu, Y Huang, H Zhang… - … for immunotherapy of …, 2019 - Springer
Background Checkpoint-blockade immunotherapy targeting programmed cell death protein
1 (PD-1) has recently shown promising efficacy in hepatocellular carcinoma (HCC) …

Meta‐analysis of gut dysbiosis in Parkinson's disease

H Nishiwaki, M Ito, T Ishida, T Hamaguchi… - Movement …, 2020 - Wiley Online Library
Background PD may begin with the intestinal accumulation of α‐synuclein fibrils, which can
be causally associated with gut dysbiosis. The variability of gut microbiota across countries …

[HTML][HTML] A marine bacterial community capable of degrading poly (ethylene terephthalate) and polyethylene

R Gao, C Sun - Journal of Hazardous Materials, 2021 - Elsevier
Plastic wastes are becoming the most common form of marine debris and present a growing
global pollution problem. Here, we used a screening approach on hundreds of plastic waste …

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome

EM Hill‐Burns, JW Debelius, JT Morton… - Movement …, 2017 - Wiley Online Library
Background There is mounting evidence for a connection between the gut and Parkinson's
disease (PD). Dysbiosis of gut microbiota could explain several features of PD. Objective …