Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network
Bacterial gene expression is orchestrated by numerous transcription factors (TFs).
Elucidating how gene expression is regulated is fundamental to understanding bacterial …
Elucidating how gene expression is regulated is fundamental to understanding bacterial …
Leveraging independent component analysis to unravel transcriptional regulatory networks: A critical review and future directions
Y Zhang, J Zhao, X Sun, Y Zheng, T Chen… - Biotechnology Advances, 2024 - Elsevier
Transcriptional regulatory networks (TRNs) play a crucial role in exploring microbial life
activities and complex regulatory mechanisms. The comprehensive reconstruction of TRNs …
activities and complex regulatory mechanisms. The comprehensive reconstruction of TRNs …
iModulonMiner and PyModulon: software for unsupervised mining of gene expression compendia
Public gene expression databases are a rapidly expanding resource of organism responses
to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics …
to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics …
Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942
Synechococcus elongatus is an important cyanobacterium that serves as a versatile and
robust model for studying circadian biology and photosynthetic metabolism. Its …
robust model for studying circadian biology and photosynthetic metabolism. Its …
Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome
Vibrio natriegens regulates natural competence through the TfoX and QstR transcription
factors, which are involved in external DNA capture and transport. However, the extensive …
factors, which are involved in external DNA capture and transport. However, the extensive …
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa
Pseudomonas aeruginosa is an opportunistic pathogen and major cause of hospital-
acquired infections. The virulence of P. aeruginosa is largely determined by its …
acquired infections. The virulence of P. aeruginosa is largely determined by its …
A multi-scale expression and regulation knowledge base for Escherichia coli
CR Lamoureux, KT Decker, AV Sastry… - Nucleic Acids …, 2023 - academic.oup.com
Transcriptomic data is accumulating rapidly; thus, scalable methods for extracting
knowledge from this data are critical. Here, we assembled a top-down expression and …
knowledge from this data are critical. Here, we assembled a top-down expression and …
Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance
Relationships between the genome, transcriptome, and metabolome underlie all evolved
phenotypes. However, it has proved difficult to elucidate these relationships because of the …
phenotypes. However, it has proved difficult to elucidate these relationships because of the …
Machine learning of all Mycobacterium tuberculosis H37Rv RNA-seq data reveals a structured interplay between metabolism, stress response, and infection
Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens,
posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its …
posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its …
Pan-genome analysis of transcriptional regulation in six Salmonella enterica serovar typhimurium strains reveals their different regulatory structures
Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-
characterized model strains. Using machine learning methods, we established the …
characterized model strains. Using machine learning methods, we established the …