Kevin Rychel
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View article: Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of <i>Escherichia coli</i>
Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of <i>Escherichia coli</i> Open
Adaptive laboratory evolution is able to generate microbial strains, which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use adaptive laboratory evolution to evolve Escherichia coli strains th…
View article: Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase
Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase Open
The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the…
View article: iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets
iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets Open
iModulons—sets of co-expressed genes identified through independent component analysis (ICA) of high-quality transcriptomic datasets—provide an unbiased, modular view of an organism's transcriptional regulatory network. Established in 2020…
View article: iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia Open
Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription …
View article: A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of <i>Streptococcus pyogenes</i>
A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of <i>Streptococcus pyogenes</i> Open
Streptococcus pyogenes is responsible for a range of diseases in humans contributing significantly to morbidity and mortality. Among more than 200 serotypes of S. pyogenes , serotype M1 strains hold the greatest clinical relevance due to t…
View article: Deciphering the transcriptional regulatory network of<i>Yarrowia lipolytica</i>using machine learning
Deciphering the transcriptional regulatory network of<i>Yarrowia lipolytica</i>using machine learning Open
The transcriptional regulatory network (TRN) in Yarrowia lipolytica coordinates its cellular processes, including the response to various stimuli. The TRN has been difficult to study due to its complex nature. In industrial-size fermenters…
View article: Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing
Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing Open
As the availability of data sets increases, meta-analysis leveraging aggregated and interoperable data types is proving valuable. This study leveraged a meta-analysis workflow to identify mutations that could improve robustness to reactive…
View article: Proteome allocation is linked to transcriptional regulation through a modularized transcriptome
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome Open
View article: The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions Open
Fast growth phenotypes are achieved through optimal transcriptomic allocation, in which cells must balance tradeoffs in resource allocation between diverse functions. One such balance between stress readiness and unbridled growth in E. col…
View article: Laboratory evolution reveals transcriptional mechanisms underlying thermal adaptation of<i>Escherichia coli</i>
Laboratory evolution reveals transcriptional mechanisms underlying thermal adaptation of<i>Escherichia coli</i> Open
Adaptive laboratory evolution (ALE) is able to generate microbial strains which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use ALE to evolve Escherichia coli strains that grow at temperatur…
View article: Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in <i>Pseudomonas putida</i> KT2440
Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in <i>Pseudomonas putida</i> KT2440 Open
There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional rela…
View article: Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant <i>Acinetobacter baumannii</i>
Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant <i>Acinetobacter baumannii</i> Open
The rise in hospital outbreaks of multidrug-resistant Acinetobacter baumannii infections underscores the urgent need for alternatives to traditional broad-spectrum antibiotic therapies. The success of A. baumannii as a significant nosocomi…
View article: High-resolution temporal profiling of E. coli transcriptional response
High-resolution temporal profiling of E. coli transcriptional response Open
View article: Data-Driven Strain Design Towards Mitigating Biomanufacturing Stresses
Data-Driven Strain Design Towards Mitigating Biomanufacturing Stresses Open
Microbial strains used in large-scale biomanufacturing of melatonin often experience stresses like reactive oxygen species (ROS), SOS response, and acid stress, which can reduce productivity. This study leveraged a data-driven workflow to …
View article: A multi-scale expression and regulation knowledge base for<i>Escherichia coli</i>
A multi-scale expression and regulation knowledge base for<i>Escherichia coli</i> Open
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…
View article: Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance
Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance Open
Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently developed data …
View article: Machine learning uncovers the <i>Pseudomonas syringae</i> transcriptome in microbial communities and during infection
Machine learning uncovers the <i>Pseudomonas syringae</i> transcriptome in microbial communities and during infection Open
The transcriptional regulatory network (TRN) of the phytopathogen Pseudomonas syringae pv. tomato DC3000 regulates its response to environmental stimuli, including interactions with hosts and neighboring bacteria. Despite the importance of…
View article: Elucidation of independently modulated genes in <i>Streptococcus pyogenes</i> reveals carbon sources that control its expression of hemolytic toxins
Elucidation of independently modulated genes in <i>Streptococcus pyogenes</i> reveals carbon sources that control its expression of hemolytic toxins Open
Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. An underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt…
View article: Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome
Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome Open
Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency re…
View article: Machine learning uncovers the<i>Pseudomonas syringae</i>transcriptome in microbial communities and during infection
Machine learning uncovers the<i>Pseudomonas syringae</i>transcriptome in microbial communities and during infection Open
The transcriptional regulatory network (TRN) of the phytopathogen Pseudomonas syringae pv. tomato DC3000 regulates its response to environmental stimuli, including interactions with hosts and neighboring bacteria. Despite the importance of…
View article: The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions
The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions Open
View article: Proteome allocation is linked to transcriptional regulation through a modularized transcriptome
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome Open
It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus inves…
View article: Laboratory Evolution, Transcriptomics, and Modeling Reveal Mechanisms of Paraquat Tolerance
Laboratory Evolution, Transcriptomics, and Modeling Reveal Mechanisms of Paraquat Tolerance Open
View article: Predicting stress response and improved protein overproduction in Bacillus subtilis
Predicting stress response and improved protein overproduction in Bacillus subtilis Open
View article: Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance
Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance Open
Summary Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently develop…
View article: Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures
Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures Open
Salmonella enterica serovar Typhimurium is a pathogen involved in human nontyphoidal infections. Treating S .
View article: Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of <i>Pseudomonas aeruginosa</i>
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of <i>Pseudomonas aeruginosa</i> Open
Pseudomonas aeruginosa is an opportunistic pathogen and major cause of hospital-acquired infections. The virulence of P. aeruginosa is largely determined by its transcriptional regulatory network (TRN). We used 411 transcription profiles o…
View article: Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins
Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins Open
Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. The underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adap…
View article: Elucidation of independently modulated genes in <i>Streptococcus pyogenes</i> reveals carbon sources that control its expression of hemolytic toxins
Elucidation of independently modulated genes in <i>Streptococcus pyogenes</i> reveals carbon sources that control its expression of hemolytic toxins Open
Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. The underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adap…
View article: Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network
Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network Open