A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
H37Rv is the most widely used Mycobacterium tuberculosis strain, and its genome is
globally used as the M. tuberculosis reference sequence. Here, we present Bact-Builder, a …
globally used as the M. tuberculosis reference sequence. Here, we present Bact-Builder, a …
High-resolution temporal profiling of E. coli transcriptional response
Understanding how cells dynamically adapt to their environment is a primary focus of
biology research. Temporal information about cellular behavior is often limited by both small …
biology research. Temporal information about cellular behavior is often limited by both small …
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 …
Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis
Transcriptional regulation is a critical adaptive mechanism that allows bacteria to respond to
changing environments, yet the concept of transcriptional plasticity (TP)–the variability of …
changing environments, yet the concept of transcriptional plasticity (TP)–the variability of …
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 …
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 …
An overview of next generation sequencing strategies and genomics tools used for tuberculosis research
S Deb, J Basu, M Choudhary - Journal of Applied Microbiology, 2024 - academic.oup.com
Tuberculosis (TB) is a grave public health concern and is considered the foremost
contributor to human mortality resulting from infectious disease. Due to the stringent clonality …
contributor to human mortality resulting from infectious disease. Due to the stringent clonality …
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 …
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 …