Gene ontology articles within Nature Communications

Featured

• Article
  29 March 2024 | Open Access

  Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets

  Combining experimental lineage tracing with single cell transcriptomics is technically demanding. Here, authors present GEMLI, a computational tool to annotate cell lineages in single cell RNA sequencing data solely based on gene expression.

  • A. S. Eisele
  • , M. Tarbier
  •  & D. M. Suter

• Article
  11 May 2021 | Open Access

  Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data

  Identifying enriched gene sets in transcriptomic data is routine analysis. Here, the authors show that conventional gene category enrichment analysis (GCEA) applied to brain-wide atlas data yields biased results and develop a flexible ensemble-based null model framework to enable appropriate inference in GCEA.

  • Ben D. Fulcher
  • , Aurina Arnatkeviciute
  •  & Alex Fornito

• Article
  05 March 2021 | Open Access

  Improving gene function predictions using independent transcriptional components

  Our understanding of the function of many transcripts is still incomplete, limiting the interpretability of transcriptomic data. Here the authors use consensus-independent component analysis, together with a guilt-by-association approach, to improve the prediction of gene function.

  • Carlos G. Urzúa-Traslaviña
  • , Vincent C. Leeuwenburgh
  •  & Rudolf S. N. Fehrmann

• Article
  23 March 2020 | Open Access

  Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions

  Mutations in human pluripotent stem cells (PSC) and whether any form during culture prior to use in a human clinical context are a concern. Here, the authors use hPSCs derived to cGMP standards and show they have low mutation rates after culture, noting this decreases on culturing in low (5%) oxygen conditions.

  • Oliver Thompson
  • , Ferdinand von Meyenn
  •  & Peter W. Andrews

• Article
  05 February 2020 | Open Access

  Integrative pathway enrichment analysis of multivariate omics data

  Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

  • Marta Paczkowska
  • , Jonathan Barenboim
  •  & Christian von Mering

• Article
  01 March 2018 | Open Access

  Elongator and codon bias regulate protein levels in mammalian peripheral neurons

  Familial dysautonomia is linked to mutations in IKBKAP, a scaffolding protein for the Elongator complex, which regulates codon-biased gene translation in yeast. Here the authors show in mammalian neurons that IKBKAP loss alters expression of codon-biased genes, including some involved in DNA damage.

  • Joy Goffena
  • , Frances Lefcort
  •  & Lynn George

• Article
  21 February 2018 | Open Access

  Analysis of cardiomyocyte clonal expansion during mouse heart development and injury

  During cardiac tissue formation it is unclear whether newly generated myocytes originate from cardiac progenitor cells or from pre-existing cardiomyocytes. Here, the authors use a stochastic four-colour reporter system (Rainbow) to identify the source of new cardiomyocytes during mouse development.

  • Konstantina-Ioanna Sereti
  • , Ngoc B. Nguyen
  •  & Reza Ardehali