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Showing 1–10 of 10 results
Advanced filters: Author: Anand Sastry Clear advanced filters
  • Adaptive laboratory evolution experiments in Escherichia coli show that the pseudogene efeU can be repaired to restore the bacterium’s iron uptake system, demonstrating that pseudogenes may serve as an ‘adaptive repertoire’ of selectable traits.

    • Amitesh Anand
    • Connor A. Olson
    • Bernhard O. Palsson
    Research
    Nature Microbiology
    Volume: 4, P: 386-389
  • Understanding how cells dynamically adapt to their environment is important, but temporal information about cellular behaviour is often limited. Here, Miano et al. apply unsupervised machine learning to a dataset describing the activity of over 1,800 promoters in E. coli, measured every 10 minutes, defining three primary stages of promoter activation in response to heavy metal stress.

    • Arianna Miano
    • Kevin Rychel
    • Jeff Hasty
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-10
  • The systems-level regulatory structure underlying gene expression in bacteria can be inferred using machine learning algorithms. Here we show this structure for Bacillus subtilis, present five hypotheses gleaned from it, and analyse the process of sporulation from its perspective.

    • Kevin Rychel
    • Anand V. Sastry
    • Bernhard O. Palsson
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-10
  • Translating omics data sets into biological insight is one of the great challenges of our time. Here, the authors make headway by synchronising pairs of omics data types via invariants across conditions and by integrating datasets into a genome-scale model of E. coli metabolism and gene expression.

    • Ali Ebrahim
    • Elizabeth Brunk
    • Bernhard O. Palsson
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-9
  • Mechanistic insight into the regulation of transcriptional modules remains scarce. Here, the authors identify statistically independent gene sets by applying independent component analysis to a high-quality E. coli RNA-seq data compendium and find that most gene sets represent the effects of specific transcriptional regulators.

    • Anand V. Sastry
    • Ye Gao
    • Bernhard O. Palsson
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-14
  • Rodionova et al. find that the putative transporter gene, ydhC and its regulator ydhB are involved in purine transportation and that the expression of the ydhC gene is activated by the YdhB in E. coli. The authors suggest renaming the regulator PunR and the transporter PunC, respectively.

    • Irina A. Rodionova
    • Ye Gao
    • Bernhard O. Palsson
    ResearchOpen Access
    Communications Biology
    Volume: 4, P: 1-10