AIMC Topic: Bacterial Physiological Phenomena
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Risk-reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria.
Nature microbiology
May 26, 2025
Copiotrophic marine bacteria contribute to the control of carbon storage in the ocean by remineralizing organic matter. Motility presents copiotrophs with a risk-reward trade-off: it is highly beneficial in seeking out sparse nutrient hotspots, but e...
Using metabolic networks to predict cross-feeding and competition interactions between microorganisms.
Microbiology spectrum
Mar 20, 2024
Understanding the interactions between microorganisms and their impact on bacterial behavior at the community level is a key research topic in microbiology. Different methods, relying on experimental or mathematical approaches based on the diverse pr...
PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.
Viruses
Feb 8, 2022
The characterization of therapeutic phage genomes plays a crucial role in the success rate of phage therapies. There are three checkpoints that need to be examined for the selection of phage candidates, namely, the presence of temperate markers, anti...
Simulation and Prediction of Fungal Community Evolution Based on RBF Neural Network.
Computational and mathematical methods in medicine
Oct 8, 2021
Simulation and prediction of the scale change of fungal community. First, using the experimental data of a variety of fungal decomposition activities, a mathematical model of the decomposition rate and the relationship between the bacterial species w...
Misic, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities.
eLife
Sep 9, 2021
Studies of bacterial communities, biofilms and microbiomes, are multiplying due to their impact on health and ecology. Live imaging of microbial communities requires new tools for the robust identification of bacterial cells in dense and often inter-...
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions.
Cell host & microbe
Oct 28, 2020
Glycans, the most diverse biopolymer, are shaped by evolutionary pressures stemming from host-microbe interactions. Here, we present machine learning and bioinformatics methods to leverage the evolutionary information present in glycans to gain insig...
iQSP: A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou's 5-Steps Rule and Informative Physicochemical Properties.
International journal of molecular sciences
Dec 20, 2019
Understanding of quorum-sensing peptides (QSPs) in their functional mechanism plays an essential role in finding new opportunities to combat bacterial infections by designing drugs. With the avalanche of the newly available peptide sequences in the p...
Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima.
ACS synthetic biology
Jun 7, 2019
Enzymes that catalyze chemical reactions at high temperatures are used for industrial biocatalysis, applications in molecular biology, and as highly evolvable starting points for protein engineering. The optimal growth temperature (OGT) of organisms ...
Gradients of three coastal environments off the South China Sea and their impacts on the dynamics of heterotrophic microbial communities.
The Science of the total environment
Dec 27, 2018
Heterotrophic fungus-like marine protists are recognized to contribute significantly to the coastal carbon cycling largely due to their high biomass and ability to decompose recalcitrant organic matter. Yet, little is known about their dynamics at po...
Colony analysis and deep learning uncover 5-hydroxyindole as an inhibitor of gliding motility and iridescence in Cellulophaga lytica.
Microbiology (Reading, England)
Feb 5, 2018
Iridescence is an original type of colouration that is relatively widespread in nature but has been either incompletely described or entirely neglected in prokaryotes. Recently, we reported a brilliant 'pointillistic' iridescence in agar-grown colony...
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