AIMC Topic: Gene Expression Regulation, Bacterial

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Machine learning uncovers the transcriptional regulatory network for the production host Streptomyces albidoflavus.

Cell reports Mar 8, 2025
Streptomyces albidoflavus is a widely used strain for natural product discovery and production through heterologous biosynthetic gene clusters (BGCs). However, the transcriptional regulatory network (TRN) and its impact on secondary metabolism remain...
Gene Regulatory Networks Streptomyces Multigene Family Gene Expression Regulation, Bacterial Machine Learning Transcriptome
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Data-driven discovery of the interplay between genetic and environmental factors in bacterial growth.

Communications biology Dec 24, 2024
A complex interplay of genetic and environmental factors influences bacterial growth. Understanding these interactions is crucial for insights into complex living systems. This study employs a data-driven approach to uncover the principles governing ...
Culture Media Gene Expression Regulation, Bacterial Environment Machine Learning Gene Regulatory Networks Escherichia coli Gene-Environment Interaction
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Machine learning reveals the transcriptional regulatory network and circadian dynamics of PCC 7942.

Proceedings of the National Academy of Sciences of the United States of America Sep 13, 2024
is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it orchestrates the cell's adaptatio...
Machine Learning Transcriptome Gene Regulatory Networks Bacterial Proteins Synechococcus Circadian Rhythm Gene Expression Regulation, Bacterial Photosynthesis
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Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Sep 12, 2024
Streptomyces produces diverse secondary metabolites of biopharmaceutical importance, yet the rate of biosynthesis of these metabolites is often hampered by complex transcriptional regulation. Therefore, a fundamental understanding of transcriptional ...
Transcriptome Gene Regulatory Networks Machine Learning Multigene Family Gene Expression Regulation, Bacterial Gene Expression Profiling Secondary Metabolism Streptomyces coelicolor
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Novel candidate genes for environmental stresses response in Synechocystis sp. PCC 6803 revealed by machine learning algorithms.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] May 6, 2024
Cyanobacteria have developed acclimation strategies to adapt to harsh environments, making them a model organism. Understanding the molecular mechanisms of tolerance to abiotic stresses can help elucidate how cells change their gene expression patter...
Bacterial Proteins Light Genes, Bacterial Transcriptome Computational Biology Support Vector Machine Stress, Physiological Machine Learning Gene Expression Regulation, Bacterial Algorithms Synechocystis Gene Expression Profiling
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Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility.

mSphere Aug 25, 2021
antibiotic susceptibility testing often fails to accurately predict drug efficacies, in part due to differences in the molecular composition between standardized bacteriologic media and physiological environments within the body. Here, we investiga...
Iron Gene Expression Regulation, Bacterial Escherichia coli K12 Transcriptome Microbial Sensitivity Tests Culture Media Anti-Bacterial Agents Drug Resistance, Bacterial Gene Expression Profiling Humans Machine Learning
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Detecting operons in bacterial genomes via visual representation learning.

Scientific reports Jan 22, 2021
Contiguous genes in prokaryotes are often arranged into operons. Detecting operons plays a critical role in inferring gene functionality and regulatory networks. Human experts annotate operons by visually inspecting gene neighborhoods across pileups ...
Models, Genetic Escherichia coli Bacillus subtilis Gene Expression Regulation, Bacterial Genome, Bacterial Operon Deep Learning Genomics Computational Biology Humans Algorithms Reproducibility of Results
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Integrated meta-analysis and machine learning approach identifies acyl-CoA thioesterase with other novel genes responsible for biofilm development in Staphylococcus aureus.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Jan 1, 2021
Biofilm forming Staphylococcus aureus is a major threat to the health-care industry. It is important to understand the differences between planktonic and biofilm growth forms in the pathogen since conventional treatments targeting the planktonic form...
Supervised Machine Learning Staphylococcal Infections Datasets as Topic Biofilms Microarray Analysis RNA-Seq Humans Gene Expression Regulation, Bacterial Staphylococcus aureus Algorithms Transcriptome
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Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome.

Nature communications Dec 11, 2020
The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcrip...
Ethanol Gene Expression Regulation, Bacterial DNA Damage Transcriptome Machine Learning Data Mining Iron Chelating Agents Bacterial Proteins Gene Regulatory Networks Histidine Tryptophan Bacillus subtilis Quorum Sensing
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Molecules Autoinducer 2 and cjA and Their Impact on Gene Expression in Campylobacter jejuni.

Journal of molecular microbiology and biotechnology Jan 29, 2019
Quorum sensing is a widespread form of cell-to-cell communication, which is based on the production of signaling molecules known as autoinducers (AIs). The first group contains highly species-specific N-acyl homoserine lactones (N-AHLs), generally kn...
4-Butyrolactone Homoserine Biofilms Lactones Campylobacter jejuni Species Specificity Bacterial Proteins Stress, Physiological Gene Expression Regulation, Bacterial Virulence Factors Quorum Sensing
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