AIMC Topic: RNA, Bacterial

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Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.

Nature communications Nov 6, 2024
mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried ou...
Ribosomes RNA Stability Nucleic Acid Conformation Escherichia coli Machine Learning Protein Biosynthesis Kinetics RNA, Messenger RNA, Bacterial
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sRNAdeep: a novel tool for bacterial sRNA prediction based on DistilBERT encoding mode and deep learning algorithms.

BMC genomics Oct 31, 2024
BACKGROUND: Bacterial small regulatory RNA (sRNA) plays a crucial role in cell metabolism and could be used as a new potential drug target in the treatment of pathogen-induced disease. However, experimental methods for identifying sRNAs still require...
Software Computational Biology Mycobacterium tuberculosis Genome, Bacterial Algorithms Deep Learning RNA, Bacterial RNA, Small Untranslated
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OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data.

PLoS computational biology Jan 5, 2022
Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have...
RNA, Bacterial Sequence Analysis, RNA Operon Bacteria Computational Biology Machine Learning Algorithms
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sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction.

RNA biology Dec 31, 2021
Bacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A multitude of sRNAs have been identified in many bacterial species; however, their function has yet to be elucidated. A ke...
Machine Learning RNA, Bacterial Software RNA, Messenger Gene Expression Profiling RNA, Small Untranslated Databases, Genetic Bacteria Transcriptome Computational Biology Web Browser
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Prediction of bacterial small RNAs in the RsmA (CsrA) and ToxT pathways: a machine learning approach.

BMC genomics Aug 22, 2017
BACKGROUND: Small RNAs (sRNAs) constitute an important class of post-transcriptional regulators that control critical cellular processes in bacteria. Recent research using high-throughput transcriptomic approaches has led to a dramatic increase in th...
RNA, Bacterial Vibrio cholerae Bacterial Proteins Machine Learning Base Sequence Computational Biology
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An improved method for identification of small non-coding RNAs in bacteria using support vector machine.

Scientific reports Apr 6, 2017
Bacterial small non-coding RNAs (sRNAs) are not translated into proteins, but act as functional RNAs. They are involved in diverse biological processes like virulence, stress response and quorum sensing. Several high-throughput techniques have enable...
Support Vector Machine Databases, Genetic Reproducibility of Results Computational Biology RNA, Small Untranslated Machine Learning Genome, Bacterial RNA, Bacterial
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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...
Computational Biology RNA, Small Untranslated Gene Expression Regulation, Bacterial Machine Learning Escherichia coli Salmonella RNA, Bacterial
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GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.

BMC bioinformatics May 21, 2025
Bacterial small RNAs (sRNAs) are pivotal in post-transcriptional regulation, affecting functions like virulence, metabolism, and gene expression by binding specific mRNA targets. Identifying these targets is crucial to understanding sRNA regulation a...
Neural Networks, Computer Machine Learning Escherichia coli Computational Biology RNA, Bacterial RNA, Messenger RNA, Small Untranslated
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Heterocyclic-Based Analogues against Sarcine-Ricin Loop RNA from : Molecular Docking Study and Machine Learning Classifiers.

Medicinal chemistry (Shariqah (United Arab Emirates)) Jan 1, 2024
BACKGROUND: Heterocyclic-based drugs have strong bioactivities, are active pharmacophores, and are used to design several antibacterial drugs. Due to the diverse biodynamic properties of well-known heterocyclic cores, such as quinoline, indole, and i...
RNA, Bacterial Escherichia coli Heterocyclic Compounds Machine Learning Anti-Bacterial Agents Molecular Docking Simulation
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