AIMC Topic: Bacteria

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Reviewing on AI-Designed Antibiotic Targeting Drug-Resistant Superbugs by Emphasizing Mechanisms of Action.

Drug development research
The emergence of drug-resistant bacteria, often referred to as "superbugs," poses a profound and escalating challenge to global health systems, surpassing the capabilities of traditional antibiotic discovery methods. As resistance mechanisms evolve r...

A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information.

PeerJ
Understanding the behavior of microbial consortia is crucial for predicting metabolite production by microorganisms. Genome-scale network reconstructions enable the computation of metabolic interactions and specific associations within microbial cons...

Bacterial Autonomous Intelligent Microrobots for Biomedical Applications.

Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology
Micro/nanorobots are being increasingly utilized as new diagnostic and therapeutic platforms in the biomedical field, enabling remote navigation to hard-to-reach tissues and the execution of various medical procedures. Although significant progress h...

Investigating the Impact of Antibiotics on Environmental Microbiota Through Machine Learning Models.

IET systems biology
Antibiotic pollution in the environment can significantly impact soil microorganisms, such as altering the soil microbial community or emerging antibiotic-resistant bacteria. We propose three machine learning (ML) methods to investigate antibiotics' ...

Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits.

Methods in molecular biology (Clifton, N.J.)
One of the main challenges in food microbiology is to prevent the risk of outbreaks by avoiding the distribution of food contaminated by bacteria. This requires constant monitoring of the circulating strains throughout the food production chain. Bact...

Integrating MALDI-TOF Mass Spectrometry with Machine Learning Techniques for Rapid Antimicrobial Resistance Screening of Foodborne Bacterial Pathogens.

Methods in molecular biology (Clifton, N.J.)
Although MALDI-TOF mass spectrometry (MS) is considered as the gold standard for rapid and cost-effective identification of microorganisms in routine laboratory practices, its capability for antimicrobial resistance (AMR) detection has received limit...

Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.

Nucleic acids research
Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced D...

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Briefings in bioinformatics
Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial ...

DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes.

Briefings in bioinformatics
Phages, the natural predators of bacteria, were discovered more than 100 years ago. However, increasing antimicrobial resistance rates have revitalized phage research. Methods that are more time-consuming and efficient than wet-laboratory experiments...

Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning.

Environmental microbiology
Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative p...