CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy

G Zuo, B Hao - Genomics, Proteomics and Bioinformatics, 2015 - academic.oup.com
A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each
other and ultimately follow the genome data. With the number of sequenced genomes …

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species

I Kjærbølling, TC Vesth, JC Frisvad… - Proceedings of the …, 2018 - National Acad Sciences
The fungal genus of Aspergillus is highly interesting, containing everything from industrial
cell factories, model organisms, and human pathogens. In particular, this group has a prolific …

CVTree: a parallel alignment-free phylogeny and taxonomy tool based on composition vectors of genomes

G Zuo - Genomics, Proteomics and Bioinformatics, 2021 - academic.oup.com
Abstract Composition Vector Tree (CVTree) is an alignment-free algorithm to infer
phylogenetic relationships from genome sequences. It has been successfully applied to …

Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants

W Bünger, X Jiang, J Müller, T Hurek… - Scientific Reports, 2020 - nature.com
Despite the relevance of complex root microbial communities for plant health, growth and
productivity, the molecular basis of these plant-microbe interactions is not well understood …

Development of an Online Genome Sequence Comparison Resource for Bacillus cereus sensu lato Strains Using the Efficient Composition Vector Method

K Wang, C Shu, A Bravo, M Soberón, H Zhang… - Toxins, 2023 - mdpi.com
An automated method was developed for differentiating closely related B. cereus sensu lato
(sl) species, especially biopesticide Bacillus thuringiensis, from other human pathogens, B …

Multiple approaches to phylogenomic reconstruction of the fungal kingdom

CGP McCarthy, DA Fitzpatrick - Advances in genetics, 2017 - Elsevier
Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species
and an evolutionary history dating back a billion years. Fungi have been at the forefront of …

Quercetin mitigates rheumatoid arthritis by inhibiting adenosine deaminase in rats

KS El-Said, A Atta, MA Mobasher, MO Germoush… - Molecular …, 2022 - Springer
Rheumatoid arthritis (RA) is a chronic inflammatory joint disease characterized by synovial
proliferation and bone destruction. Adenosine deaminase (ADA) is a key inflammatory …

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis

G Zuo, Z Xu, B Hao - Life, 2015 - mdpi.com
A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is
reported:(1) the whole-genome-based and alignment-free CVTree using 179 genomes;(2) …

Visnagin alleviates rheumatoid arthritis via its potential inhibitory impact on malate dehydrogenase enzyme: in silico, in vitro, and in vivo studies

AA Khamis, AH Sharshar, TM Mohamed… - Genes & Nutrition, 2024 - Springer
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disorder. The present study
aimed to evaluate the in silico, in vitro, and in vivo inhibitory effect of visnagin on malate …

Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome

W Li, J Freudenberg, J Freudenberg - Gene, 2019 - Elsevier
The nuclear human genome harbors sequences of mitochondrial origin, indicating an
ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments …