Statistical methods articles within Nature Communications

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  • Article
    | Open Access

    Single-cell RNA sequencing has enabled great advances in understanding developmental biology but reconstructing cellular lineages from this data remains challenging. Here the authors develop an algorithm,dpath, which models the lineage relationships of underlying single cells based on single cell RNA seq data and apply it to study lineage progression of Etv2 expressing progenitors.

    • Wuming Gong
    • , Tara L. Rasmussen
    •  & Daniel J. Garry

  • Article
    | Open Access

    Plasticity and clonal population structure in bacterial genomes can hinder traditional SNP-based genetic association studies. Here, Corander and colleagues present a method to identify variable-length sequence elements enriched in a phenotype of interest, and demonstrate its use in human pathogens.

    • John A. Lees
    • , Minna Vehkala
    •  & Jukka Corander

  • Article
    | Open Access

    Clinical RNA-seq datasets can predict clinical outcomes. Here, Shen et al. report a statistical method for survival analysis of mRNA isoform variation using clinical RNA-seq datasets, and the identified isoform based survival predictors outperform gene expression based survival predictors using TCGA data on six cancer types.

    • Shihao Shen
    • , Yuanyuan Wang
    •  & Yi Xing

  • Article
    | Open Access

    Stochastic reaction-diffusion systems are used for modelling spatial dynamics in many disciplines, but parameter inference and model selection remain challenging. Here the authors offer a solution enabled by a connection between reaction-diffusion and the well-studied spatio-temporal Cox processes.

    • David Schnoerr
    • , Ramon Grima
    •  & Guido Sanguinetti

  • Article
    | Open Access

    Use of general linear mixed models (GLMMs) in genetic variance analysis can quantify the relative contribution of additive effects from genetic variation on a given trait. Here, Jonathan Mosley and colleagues apply GLMM in a phenome-wide analysis and show that genetic variations in the HLA region are associated with 44 phenotypes, 5 phenotypes which were not previously reported in GWASes.

    • Jonathan D. Mosley
    • , John S. Witte
    •  & Joshua C. Denny

  • Article
    | Open Access

    The influence of species conservation on food webs is less well understood than the effects of species loss. Here, the authors test several indices against optimal food web management and find no current metrics are reliably effective at identifying species conservation priorities.

    • E. McDonald-Madden
    • , R. Sabbadin
    •  & H. P. Possingham

  • Article
    | Open Access

    Das et al. present a novel Bayesian approach called expression Quantitative Trait enhancer Loci (eQTeL), which effectively integrates genetic and epigenetic information to identify combination of regulatory genomic variants underlying expression variance. Using various functional data, the authors show the variants identified by eQTeL are likely to be causal.

    • Avinash Das
    • , Michael Morley
    •  & Sridhar Hannenhalli

  • Article |

    Body plan complexity is associated with the number of different cell types, yet the processes that create this diversity are unclear. Here the authors use transcriptomics to test the hypothesis that unlike cancer cells, novel normal cell types arise through sub-specialization of an ancestral cell type.

    • Cong Liang
    • , Alistair R.R. Forrest
    •  & Günter P. Wagner

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