Systems analysis

  • Article |

    Two complete volumetric reconstructions of the Caenorhabditis elegans main neuropil (the nerve ring) reveal multi-scale spatial organization that supports both conserved and variable circuitry, and enables the derivation of a modular structure–function model of the neuropil.

    • Christopher A. Brittin
    • , Steven J. Cook
    •  & Netta Cohen
  • Article |

    Thermal proteome profiling combined with a reverse genetics approach provides insights into the abundance and thermal stability of the global proteome of Escherichia coli.

    • André Mateus
    • , Johannes Hevler
    •  & Mikhail M. Savitski
  • Article |

    An advanced proteomics workflow is used to identify 340,000 proteins from 100 taxonomically diverse species, providing a comparative view of proteomes across the evolutionary range.

    • Johannes B. Müller
    • , Philipp E. Geyer
    •  & Matthias Mann
  • Article |

    Insights into the interactions between pro- and anti-vaccination clusters on Facebook can enable policies and approaches that attempt to interrupt the shift to anti-vaccination views and persuade undecided individuals to adopt a pro-vaccination stance.

    • Neil F. Johnson
    • , Nicolas Velásquez
    •  & Yonatan Lupu
  • Article |

    Single-cell RNA sequencing is used to generate a dataset covering all major human organs in both adult and fetal stages, enabling comparison with similar datasets for mouse tissues.

    • Xiaoping Han
    • , Ziming Zhou
    •  & Guoji Guo
  • Article
    | Open Access

    The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

    • Jason Lloyd-Price
    • , Cesar Arze
    •  & Curtis Huttenhower
  • Letter |

    The authors devise an algorithm that can cluster T cell receptor (TCR) sequences sharing the same specificity, predict the HLA restriction of these TCR clusters on the basis of subjects’ genotypes and help to identify specific peptide major histocompatibility complex ligands.

    • Jacob Glanville
    • , Huang Huang
    •  & Mark M. Davis
  • Article
    | Open Access

    This paper describes molecular subtypes of cervical cancers, including squamous cell carcinoma and adenocarcinoma clusters defined by HPV status and molecular features, and distinct molecular pathways that are activated in cervical carcinomas caused by different somatic alterations and HPV types.

    • Robert D. Burk
    • , Zigui Chen
    •  & David Mutch
  • Letter |

    A protein degradation pathway is found at the inner nuclear membrane that is distinct from, but complementary to, endoplasmic-reticulum-associated protein degradation, and which is mediated by the Asi protein complex; a genome-wide library screening of yeast identifies more than 20 substrates of this pathway, which is shown to target mislocalized integral membrane proteins for degradation.

    • Anton Khmelinskii
    • , Ewa Blaszczak
    •  & Michael Knop
  • Article |

    Cyclic AMP, one of the earliest discovered and most intensely studied signalling molecules in molecular biology, is widely believed to signal the carbon status in mediating catabolite repression in bacteria; here a quantitative approach reveals a much broader physiological role for cAMP signalling, whereby it coordinates the allocation of proteomic resources with the global metabolic needs of the cell, including, for example, nitrogen or sulphur.

    • Conghui You
    • , Hiroyuki Okano
    •  & Terence Hwa