AIMC Topic: Gene Expression Regulation, Bacterial

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Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities.

Physical biology Jul 19, 2017
Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely ...
Gene Expression Regulation, Bacterial Bacterial Proteins Models, Biological Bacterial Physiological Phenomena Quorum Sensing Microbial Interactions Signal Transduction Staphylococcus aureus Decision Making Neural Networks, Computer
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Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm.

Journal of bioinformatics and computational biology Jun 13, 2017
Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the mo...
Gene Expression Regulation, Bacterial Gene Regulatory Networks Neural Networks, Computer Escherichia coli Computational Biology Models, Genetic Algorithms Escherichia coli Proteins
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A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data.

PloS one Feb 15, 2017
Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribut...
Transcriptome Salmonella enteritidis Humans Alzheimer Disease Gene Expression Regulation, Bacterial Databases, Nucleic Acid Gene Ontology
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Prediction of recombinant protein overexpression in Escherichia coli using a machine learning based model (RPOLP).

Computers in biology and medicine Sep 30, 2015
Recombinant protein overexpression, an important biotechnological process, is ruled by complex biological rules which are mostly unknown, is in need of an intelligent algorithm so as to avoid resource-intensive lab-based trial and error experiments i...
Recombinant Proteins Escherichia coli Databases, Protein Reproducibility of Results Machine Learning Gene Expression Regulation, Bacterial Artificial Intelligence Gene Expression Profiling Algorithms
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Improving prediction of bacterial sRNA regulatory targets with expression data.

NAR genomics and bioinformatics Jun 1, 2025
Small regulatory RNAs (sRNAs) are widespread in bacteria. However, characterizing the targets of sRNA regulation in a way that scales with the increasing number of identified sRNAs has proven challenging. Computational methods offer one means for eff...
RNA, Bacterial Computational Biology RNA, Small Untranslated Escherichia coli Gene Expression Regulation, Bacterial Machine Learning Salmonella
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Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.

Nucleic acids research Nov 27, 2024
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...
Phylogeny Deep Learning Biofilms Promoter Regions, Genetic Genome, Bacterial Metagenome Evolution, Molecular Bacteria Gene Expression Regulation, Bacterial
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A multi-scale expression and regulation knowledge base for Escherichia coli.

Nucleic acids research Oct 27, 2023
Transcriptomic data is accumulating rapidly; thus, scalable methods for extracting knowledge from this data are critical. Here, we assembled a top-down expression and regulation knowledge base for Escherichia coli. The expression component is a 1035-...
Gene Expression Profiling Escherichia coli Proteins Escherichia coli Gene Expression Regulation, Bacterial Knowledge Bases Transcriptome
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iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.

Nucleic acids research Jan 8, 2021
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their ass...
Software Gene Expression Profiling Transcriptome Machine Learning Escherichia coli Staphylococcus aureus Bacillus subtilis Gene Regulatory Networks Transcription Factors Transcription, Genetic Internet Knowledge Bases Databases, Genetic Gene Expression Regulation, Bacterial Bacterial Proteins
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Semi-supervised prediction of gene regulatory networks using machine learning algorithms.

Journal of biosciences Oct 1, 2015
Use of computational methods to predict gene regulatory networks (GRNs) from gene expression data is a challenging task. Many studies have been conducted using unsupervised methods to fulfill the task; however, such methods usually yield low predicti...
Gene Expression Regulation, Fungal Saccharomyces cerevisiae Proteins Escherichia coli Proteins Saccharomyces cerevisiae Gene Expression Regulation, Bacterial Escherichia coli Datasets as Topic Computational Biology Transcription Factors Support Vector Machine Gene Regulatory Networks
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