Systems biology articles within Nature

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  • News & Views Forum |

    Engineering approaches allow biological structures and behaviours to be reconstituted in vitro. A biologist and a physicist discuss the potential and limitations of this bottom-up philosophy in providing insights into complex biological processes.

    • Matthew Good
    •  & Xavier Trepat

  • Letter |

    Integrative analyses identify host proteins that are modulated by Zika virus at multiple levels and provide a comprehensive framework for the understanding of Zika virus-induced changes to cellular pathways.

    • Pietro Scaturro
    • , Alexey Stukalov
    •  & Andreas Pichlmair

  • Letter |

    Experimental data from, and mathematical modelling of, colonies of the clonal raider ant Ooceraea biroi demonstrate that increases in group size generate division of labour among similar individuals, increased homeostasis and higher colony fitness.

    • Y. Ulrich
    • , J. Saragosti
    •  & D. J. C. Kronauer

  • Letter |

    Screening pairwise combinations of antibiotics and other drugs against three bacterial pathogens reveals that antagonistic and synergistic drug–drug interactions are specific to microbial species and strains.

    • Ana Rita Brochado
    • , Anja Telzerow
    •  & Athanasios Typas

  • Letter |

    Maternal age is found to be a major source of phenotypic variation in isogenic C. elegans populations living in a controlled environment, with the progeny of young mothers impaired for multiple fitness traits.

    • Marcos Francisco Perez
    • , Mirko Francesconi
    •  & Ben Lehner

  • Article |

    Profiling of 53,193 individual epithelial cells from the mouse small intestine identifies previously unknown cell subtypes and corresponding gene markers, providing insight into gut homeostasis and response to pathogens.

    • Adam L. Haber
    • , Moshe Biton
    •  & Aviv Regev

  • Letter |

    Metabolic flux analysis in mice reveals that lactate often acts as the primary carbon source for the tricarboxylic acid cycle both in normal tissues and in tumour microenvironments.

    • Sheng Hui
    • , Jonathan M. Ghergurovich
    •  & Joshua D. Rabinowitz

  • Letter |

    Introducing a single ‘sticky’ (hydrophobic) amino acid by point mutation into symmetric protein complexes frequently triggers their association into higher-order assemblies, without affecting their native fold and structure.

    • Hector Garcia-Seisdedos
    • , Charly Empereur-Mot
    •  & Emmanuel D. Levy

  • 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

  • Letter |

    Through drug exposure, a rare, transient transcriptional program characterized by high levels of expression of known resistance drivers can get ‘burned in’, leading to the selection of cells endowed with a transcriptional drug resistance and thus more chemoresistant cancers.

    • Sydney M. Shaffer
    • , Margaret C. Dunagin
    •  & Arjun Raj

  • News & Views |

    The development of a microscopy technique that enables observation of the interactions between six types of organelle, in 3D and over time, holds promise for improving our understanding of intracellular processes. See Letter p.162

    • Sang-Hee Shim

  • Article |

    The identification of the positions and patterns of amino acids that form the selectivity determinants for the entire human G-protein and G-protein-coupled receptor signalling system.

    • Tilman Flock
    • , Alexander S. Hauser
    •  & M. Madan Babu

  • News & Views |

    A systematic analysis of bipolar cells, which act as a central signalling conduit in the retina, reveals that the neurons' diverse responses to light are generated largely by feedback from neighbouring amacrine cells. See Article p.439

    • Richard H. Masland

  • 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

  • News & Views |

    A system that introduces random modifications to barcode sequences embedded in cells' DNA allows lineage relationships between cells to be discerned, while preserving the cells' spatial relationships. See Letter p.107

    • Lauren E. Beck
    •  & Arjun Raj

  • Brief Communications Arising |

    • Zhaleh Safikhani
    • , Nehme El-Hachem
    •  & Benjamin Haibe-Kains

  • News & Views |

    A 16-year-old synthetic genetic circuit that produces gene-expression oscillations in bacterial cells has been given an upgrade, making it an exceptionally precise biological clock. See Letter p.514

    • Xiaojing J. Gao
    •  & Michael B. Elowitz

  • Letter |

    The first synthetic genetic oscillator or ‘repressilator’ is simplified using insights from stochastic theory, thus achieving remarkably precise and robust oscillations and informing current debates about the next generation of synthetic circuits and their potential applications in cell-based therapies.

    • Laurent Potvin-Trottier
    • , Nathan D. Lord
    •  & Johan Paulsson

  • Letter |

    Clinically relevant bacteria have been engineered to lyse synchronously at a threshold population density and release genetically encoded therapeutics; treatment of mice with these bacteria slowed the growth of tumours.

    • M. Omar Din
    • , Tal Danino
    •  & Jeff Hasty

  • Outlook |

    Cities are complex environments. Planning interventions that borrow principles from theoretical physics could help to improve peoples' lives.

    • Kevin Pollock

  • Letter |

    A diverse range of molecular and genetic manipulations all alter lifespan distributions of Caenorhabditis elegans by an apparent stretching or shrinking of time.

    • Nicholas Stroustrup
    • , Winston E. Anthony
    •  & Walter Fontana

  • Books & Arts |

    Barbara Kiser reviews five of the week's best science picks.

    • Barbara Kiser

  • News & Views |

    Plots of survival against time for nematode worms in different conditions can be superimposed by rescaling the time axis. This observation has far-reaching implications for our understanding of the nature of ageing. See Letter p.103

    • Zachary Pincus

  • Article |

    In-depth analyses of protein expression studies are used to derive a new codon-influence metric that correlates with global protein levels, mRNA levels and mRNA lifetimes in vivo, indicating tight coupling between translation efficiency and mRNA stability; genes redesigned based on these analyses consistently yield high protein expression levels both in vivo and in vitro.

    • Grégory Boël
    • , Reka Letso
    •  & John F. Hunt

  • Article |

    Using experimental proteomics and modelling in E. coli, the amount of protein needed to run respiration (per ATP produced) is shown to be twice as much as that needed to run fermentation; results demonstrate that overflow metabolism (known as the Warburg effect in cancer cells) is a necessary outcome of optimal bacterial growth, governed by a global resource allocation program, and that the methodology is directly applicable to synthetic biology and cancer research.

    • Markus Basan
    • , Sheng Hui
    •  & Terence Hwa

  • Article |

    A new deep proteomic analysis method is used to identify proteins that interact with wild-type cystic fibrosis transmembrane conductance regulator (CFTR) and its mutant version that is the major cause of cystic fibrosis.

    • Sandra Pankow
    • , Casimir Bamberger
    •  & John R. Yates III

  • Outlook |

    Precision medicine demands precise matching of deep genomic and phenotypic models — and the deeper you go, the more you know.

    • Cathryn M. Delude

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