Time series

  • Article
    | Open Access

    Yeast exhibit oscillations that share features with circadian rhythms. The authors show that bioenergetic constraints promote oscillatory behaviour: resources are stored until supplies can support translational bursting, this is licensed by ion transport and release from membrane-less compartments.

    • John S. O’ Neill
    • , Nathaniel P. Hoyle
    •  & Helen C. Causton
  • Article
    | Open Access

    Injury repair is characterized by the generation of transient cell states important for tissue recovery. Here, the authors present a single cell RNA-seq map of recovery from bleomycin lung injury in mice and uncover a Krt8+ transitional stem cell state that precedes the regeneration of AT1 cells and persists in human lung fibrosis.

    • Maximilian Strunz
    • , Lukas M. Simon
    •  & Herbert B. Schiller
  • Article
    | Open Access

    Gene activation requires an increase of successful initiation events. Here, by employing a genome-wide kinetic analysis of transcription, the authors showed that gene activation generally requires a decrease in RNA Polymerase II (Pol II) promoter-proximal pausing while transcription of enhancer elements is not limited by Pol II pausing.

    • Saskia Gressel
    • , Björn Schwalb
    •  & Patrick Cramer
  • Article
    | Open Access

    The first week of life impacts health for all of life, but the mechanisms are little-understood. Here the authors extract multi-omic data from small volumes of blood to study the dynamic molecular changes during the first week of life, revealing a robust developmental trajectory common to different populations.

    • Amy H. Lee
    • , Casey P. Shannon
    •  & Tobias R. Kollmann
  • Article
    | Open Access

    Causality inference in time series analysis based on temporal precedence principle between cause and effect fails to detect mutual causal interactions. Here, Yang et al. introduce a causal decomposition approach based on the covariation principle of cause and effect that overcomes this limitation.

    • Albert C. Yang
    • , Chung-Kang Peng
    •  & Norden E. Huang
  • Article
    | Open Access

    High-throughput time-series data is increasingly available, yet estimating time-derivatives from such data can remain a challenge. Here, the authors provide a non-parametric method for inferring the first and second time-derivatives from multiple replicates of time-series data and for estimating errors in this inference and in any summary statistics.

    • Peter S. Swain
    • , Keiran Stevenson
    •  & Teuta Pilizota