Time series articles within Nature Communications

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  • Article
    | Open Access

    H2O2 stress is known to activate a slew of transcription factors that restore redox balance. Here, the authors use live-cell imaging and single-cell analysis to reveal that the transcription factors that are activated and their timing of activation is dose dependent.

    • Elizabeth Jose
    • , Woody March-Steinman
    •  & Andrew L. Paek

  • Article
    | Open Access

    Many real-world systems are characterized by bursty dynamics with interchanging periods of intense activity and quiescence. The authors propose a method to construct temporal networks that match a given activity pattern, and apply it to empirical bursty patterns.

    • Anzhi Sheng
    • , Qi Su
    •  & Joshua B. Plotkin

  • Article
    | Open Access

    Understanding disease progression dynamics is critical for diagnostics and treatment, but capturing dynamics is difficult. Here, the authors present a method for modelling disease progression from high dimensional molecular data that enables patient stratification and high-risk disease state identification, showcased in bladder cancer.

    • Amit Frishberg
    • , Neta Milman
    •  & Shai S. Shen-Orr

  • Article
    | Open Access

    A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, the authors develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery of analyte-responsive promoters.

    • Aqib Hasnain
    • , Shara Balakrishnan
    •  & Enoch Yeung

  • Article
    | Open Access

    To understand why genetically identical cells die at different times the authors measured damage dynamics in individual cells. They report lifespan variation comes not from initial conditions but from stochastic accumulation of damage that saturates repair systems.

    • Yifan Yang
    • , Omer Karin
    •  & Uri Alon

  • Article
    | Open Access

    The analysis of longitudinal bulk and single-cell multi-omics data is a highly complex task. Here, the authors introduce PALMO, a software platform with five modules to analyse longitudinal bulk and single-cell multi-omics data, which is extensively tested in external datasets that include multiple omics modalities.

    • Suhas V. Vasaikar
    • , Adam K. Savage
    •  & Xiao-jun Li

  • Article
    | Open Access

    Epithelial-to-mesenchymal transition (EMT) is a complex process regulated at multiple molecular levels. Here, the authors implement an analytic framework - PAMAF - to integrate data from twelve distinct omics modalities, which they use to understand the molecular changes and regulation during EMT in vitro.

    • Indranil Paul
    • , Dante Bolzan
    •  & Andrew Emili

  • 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

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