Data publication and archiving articles within Nature Communications

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  • Article
    | Open Access

    Here, the authors revealed molecular heterogeneity, developmental trajectory and regulatory network of early human pancreas development, and depict the whole progression of pancreatic organogenesis during the first trimester at the single-cell level.

    • Zhuo Ma
    • , Xiaofei Zhang
    •  & Tao Xu

  • Comment
    | Open Access

    Issues with data reuse have been recognized in synthetic biology and the broader scientific community. Policies and standards fall short as machine reasoning is not emphasised and enforcement is lacking. We discuss the progress, remaining challenges, and possible solutions.

    • Jeanet Mante
    •  & Chris J. Myers

  • Article
    | Open Access

    Radiation damages the healthy lung and triggers severe side effects. Here the authors provide a single cell atlas of the lung responses to radiation injury to explore the spatio-temporal dynamics of the mechanisms leading to radio-induced pulmonary fibrosis.

    • Sandra Curras-Alonso
    • , Juliette Soulier
    •  & Charles Fouillade

  • Article
    | Open Access

    Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.

    • Michel S. Naslavsky
    • , Marilia O. Scliar
    •  & Mayana Zatz

  • Comment
    | Open Access

    In this opinion piece, we discuss why computational tools to limit the identifiability of genomic data are a promising avenue for privacy-preservation and legal compliance. Even where these technologies do not eliminate all residual risk of individual identification, the law may still consider such data anonymised.

    • Alexander Bernier
    • , Hanshi Liu
    •  & Bartha Maria Knoppers

  • Perspective
    | Open Access

    The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and integrate them into ProteomeXchange repositories.

    • Chengxin Dai
    • , Anja Füllgrabe
    •  & Yasset Perez-Riverol

  • Comment
    | Open Access

    More and more clinical studies include potentially sensitive human proteomics or metabolomics datasets, but bioinformatics resources for managing the access to these data are not yet available. This commentary discusses current best practices and future perspectives for the responsible handling of clinical proteomics and metabolomics data.

    • Thomas M. Keane
    • , Claire O’Donovan
    •  & Juan Antonio Vizcaíno

  • Article
    | Open Access

    Placental dysfunction can have catastrophic or barely discernible effects ranging from miscarriage to apparently normal birth. Here the authors present a comprehensive analysis of the human placental transcriptome and identify circular RNAs and piRNAs.

    • Sungsam Gong
    • , Francesca Gaccioli
    •  & D. Stephen Charnock-Jones

  • Article
    | Open Access

    Modern biological research is complicated by the difficulty of collecting, transforming, annotating, and integrating datasets. Here, the authors present Go Get Data, a fast, reproducible approach to installing standardized data recipes, with an application to genomics data.

    • Michael J. Cormier
    • , Jonathan R. Belyeu
    •  & Aaron R. Quinlan

  • Perspective
    | Open Access

    The IMEx consortium provides one of the largest resources of curated, experimentally verified molecular interaction data. Here, the authors review how IMEx evolved into a fundamental resource for life scientists and describe how IMEx data can support biomedical research.

    • Pablo Porras
    • , Elisabet Barrera
    •  & Sandra Orchard

  • Article
    | Open Access

    Increasing amount of public omics data are important and valuable resources for the research community. Here, the authors develop a set of metrics to quantify the attention and impact of biomedical datasets and integrate them into the framework of Omics Discovery Index (OmicsDI).

    • Yasset Perez-Riverol
    • , Andrey Zorin
    •  & Henning Hermjakob

  • Article
    | Open Access

    Most databases of genotype-phenotype associations are manually curated. Here, Kuleshov et al. describe a machine curation system that extracts such relationships from the GWAS literature and synthesizes them into a structured knowledge base called GWASkb that can complement manually curated databases.

    • Volodymyr Kuleshov
    • , Jialin Ding
    •  & Michael Snyder

  • Review Article
    | Open Access

    Glycomics is gaining momentum in basic, translational and clinical research. Here, the authors review current reporting standards and analysis tools for mass-spectrometry-based glycomics, and propose an e-infrastructure for standardized reporting and online deposition of glycomics data.

    • Miguel A. Rojas-Macias
    • , Julien Mariethoz
    •  & Niclas G. Karlsson

  • Article
    | Open Access

    The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it could serve the crystallographic community.

    • Peter A. Meyer
    • , Stephanie Socias
    •  & Piotr Sliz

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