Mathematical models to study the biology of pathogens and the infectious diseases they cause
Mathematical models have many applications in infectious diseases: epidemiologists use
them to forecast outbreaks and design containment strategies; systems biologists use them …
them to forecast outbreaks and design containment strategies; systems biologists use them …
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 …
Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators
The transcriptional regulatory network (TRN) of Pseudomonas aeruginosa coordinates
cellular processes in response to stimuli. We used 364 transcriptomes (281 publicly …
cellular processes in response to stimuli. We used 364 transcriptomes (281 publicly …
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 …
Reconstructing the transcriptional regulatory network of probiotic L. reuteri is enabled by transcriptomics and machine learning
J Josephs-Spaulding, A Rajput, Y Hefner, R Szubin… - Msystems, 2024 - Am Soc Microbiol
Limosilactobacillus reuteri, a probiotic microbe instrumental to human health and
sustainable food production, adapts to diverse environmental shifts via dynamic gene …
sustainable food production, adapts to diverse environmental shifts via dynamic gene …