Antimicrobial resistance (AMR) poses a growing threat to human health. Increasingly, genome sequencing is being applied for the surveillance of bacterial pathogens, producing a wealth of data to train machine learning (ML) applications to predict AMR...
Journal of agricultural and food chemistry
Dec 10, 2025
The diversity and functions of metallothioneins (MTs) in Archaea remain poorly understood. This study identifies 180 archaeal MTs from 406 genomes, revealing distinct evolutionary lineages and structural diversity. Phylogenetic analysis suggests a no...
The human microbiome is crucial for health regulation and disease progression, presenting a valuable opportunity for health state classification. Traditional microbiome-based classification relies on pre-trained machine learning (ML) or deep learning...
Proceedings of the National Academy of Sciences of the United States of America
Nov 17, 2025
Rubisco is the main gateway through which inorganic carbon enters the biosphere, catalyzing the vast majority of carbon fixation on Earth. This pivotal enzyme has long been observed to be kinetically constrained. Yet, this impression is based on kine...
Proceedings of the National Academy of Sciences of the United States of America
Nov 17, 2025
Throughout Earth's history, organic molecules from both abiogenic and biogenic sources have been buried in sedimentary rocks. Most of these organic molecules have been significantly altered by geologic processes through deep time. Nonetheless, the na...
The advancement of metagenomic sequencing has revealed a vast viral diversity while simultaneously exposing limitations of homology-based tools such as BLAST and HMMER, which often fail to detect highly divergent viral genomes. The integration of art...
The host-microbiome association is considered a coevolutionary process, in which the microbiome provides important functions for host development, physiology and health. However, the ecological and evolutionary forces shaping the diversity and struct...
Transposable elements (TEs) are repetitive DNA sequences that move within genomes and play important roles in gene regulation and genome evolution. Accurate TE annotation in genomes is crucial for downstream analyses but challenging due to their sequ...
Understanding microbial dynamics in natural environments remains a significant challenge. As an alternative approach, studying model bacterial strains under well-defined laboratory conditions can reveal ecological niche patterns and evolutionary cons...
International journal of food microbiology
Sep 15, 2025
Predicting bacterial behavior and strain variability is essential for quantitative microbial risk assessments in food safety. The growing availability of whole-genome sequencing (WGS) data enables deeper insights into microbial thermotolerance. Howev...
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