PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer

X Tang, J Shang, Y Ji, Y Sun - Nucleic Acids Research, 2023 - academic.oup.com
Plasmids are mobile genetic elements that carry important accessory genes. Cataloging
plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer …

[HTML][HTML] Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess

MK Yu, EC Fogarty, AM Eren - Nature Microbiology, 2024 - nature.com
Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness
in changing environments across clades. Yet our ecological and evolutionary understanding …

Artificial intelligence tools for the identification of antibiotic resistance genes

I Olatunji, DKR Bardaji, RR Miranda… - Frontiers in …, 2024 - frontiersin.org
The fight against bacterial antibiotic resistance must be given critical attention to avert the
current and emerging crisis of treating bacterial infections due to the inefficacy of clinically …

[HTML][HTML] A cryptic plasmid is among the most numerous genetic elements in the human gut

EC Fogarty, MS Schechter, K Lolans, ML Sheahan… - Cell, 2024 - cell.com
Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing
features. However, many bacteria carry" cryptic" plasmids that do not confer clear beneficial …

Accurate identification of bacteriophages from metagenomic data using Transformer

J Shang, X Tang, R Guo, Y Sun - Briefings in Bioinformatics, 2022 - academic.oup.com
Motivation Bacteriophages are viruses infecting bacteria. Being key players in microbial
communities, they can regulate the composition/function of microbiome by infecting their …

DCiPatho: deep cross-fusion networks for genome scale identification of pathogens

G Jiang, J Zhang, Y Zhang, X Yang, T Li… - Briefings in …, 2023 - academic.oup.com
Pathogen detection from biological and environmental samples is important for global
disease control. Despite advances in pathogen detection using deep learning, current …

[HTML][HTML] Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

M Anda, S Yamanouchi, S Cosentino… - Nature …, 2023 - nature.com
It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on
the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry …

Machine learning-enabled prediction of antimicrobial resistance in foodborne pathogens

B Yun, X Liao, J Feng, T Ding - CyTA-Journal of Food, 2024 - Taylor & Francis
ABSTRACT The World Health Organization (WHO) has identified antimicrobial resistance
(AMR) as one of the top three global dangers to public health. One of the most vital factors …

Conditional Wasserstein generative adversarial networks applied to acoustic metamaterial design

P Lai, F Amirkulova, P Gerstoft - The Journal of the Acoustical Society …, 2021 - pubs.aip.org
This work presents a method for the reduction of the total scattering cross section (TSCS) for
a planar configuration of cylinders by means of generative modeling and deep learning …

Adaptive sequencing using nanopores and deep learning of mitochondrial DNA

A Danilevsky, AL Polsky… - Briefings in …, 2022 - academic.oup.com
Nanopore sequencing is an emerging technology that reads DNA by utilizing a unique
method of detecting nucleic acid sequences and identifies the various chemical …