Computational models articles within Nature

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  • Article
    | Open Access

    Quantitative time-resolved microscopy analysis of SHR and SCR dynamics in single cells of living Arabidopsis roots shows that these transcription factors coordinate formative and proliferative cell divisions early in the cell cycle.

    • Cara M. Winter
    • , Pablo Szekely
    •  & Philip N. Benfey

  • Article
    | Open Access

    EVEscape, a flexible framework using deep learning and biophysical structural information, enables early identification of concerning mutations in viruses with pandemic potential, facilitating the development of vaccines and therapeutics.

    • Nicole N. Thadani
    • , Sarah Gurev
    •  & Debora S. Marks

  • Article
    | Open Access

    We uncover the mechanism underlying the restriction point phenomenon, suggest a role for cyclin-dependent kinase 4 and 6 activity in S and G2 phases, and explain the behaviour of cells following loss of mitogen signalling.

    • James A. Cornwell
    • , Adrijana Crncec
    •  & Steven D. Cappell

  • Article |

    A context-aware, attention-based deep learning model pretrained on single-cell transcriptomes enables predictions in settings with limited data in network biology and could accelerate discovery of key network regulators and candidate therapeutic targets.

    • Christina V. Theodoris
    • , Ling Xiao
    •  & Patrick T. Ellinor

  • Article |

    Using data from a single time point, passenger-approximated clonal expansion rate (PACER) estimates the fitness of common driver mutations that lead to clonal haematopoiesis and identifies TCL1A activation as a mediator of clonal expansion.

    • Joshua S. Weinstock
    • , Jayakrishnan Gopakumar
    •  & Siddhartha Jaiswal

  • Article
    | Open Access

    Intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer, with most genetic intratumour variation having no detected phenotypic consequence and transcriptional plasticity being widespread within a tumour.

    • Jacob Househam
    • , Timon Heide
    •  & Trevor A. Graham

  • Article |

    An approach called cell state transition assessment and regulation uses diverse multiomics data to map cell states, model their transitions, and understand the signalling networks that control them.

    • Oleksii S. Rukhlenko
    • , Melinda Halasz
    •  & Boris N. Kholodenko

  • Article |

    A framework for studying and engineering gene regulatory DNA sequences, based on deep neural sequence-to-expression models trained on large-scale libraries of random DNA, provides insight into the evolution, evolvability and fitness landscapes of regulatory DNA.

    • Eeshit Dhaval Vaishnav
    • , Carl G. de Boer
    •  & Aviv Regev

  • Article |

    A genome-wide association meta-analysis study of blood lipid levels in roughly 1.6 million individuals demonstrates the gain of power attained when diverse ancestries are included to improve fine-mapping and polygenic score generation, with gains in locus discovery related to sample size.

    • Sarah E. Graham
    • , Shoa L. Clarke
    •  & Cristen J. Willer

  • Article |

    Serial femtosecond crystallography (SFX) has provided significant understanding of time-resolved processes of various systems in biology, for example, rhodopsin, which underlies our vision. The approach involves femtosecond-length X-ray pulses directed at protein crystals and has been used to study various photoactive proteins. However, the function of proteins such as rhodopsin requires trans–cis isomerization of a chromophore, which involves crossing of a conical intersection—a funnel separating potential energy surfaces—at timescales faster than what can be achieved experimentally. Here, Ourmazd and colleagues report a machine learning analysis of SFX data of photoactive yellow protein, which resolves the protein passing through a conical intersection, providing information about the potential energy surfaces involved and achieving time resolution of less than 10 fs. This approach offers an opportunity to understand some of the fastest processes in biology by extracting even more information from SFX datasets.

    • A. Hosseinizadeh
    • , N. Breckwoldt
    •  & A. Ourmazd

  • Article |

    High-performance hydrodynamic simulations show that the skeletal structure of the deep-sea sponge Euplectella aspergillum reduces the hydrodynamic stresses on it, while possibly being beneficial for feeding and reproduction.

    • Giacomo Falcucci
    • , Giorgio Amati
    •  & Sauro Succi

  • Article |

    The building blocks of the nanostructures observed on Drosophila corneas are determined, and then used to create artificial nanostructures with anti-reflective and anti-adhesive properties.

    • Mikhail Kryuchkov
    • , Oleksii Bilousov
    •  & Vladimir L. Katanaev

  • Article |

    The authors find that slow plant growth at low temperatures during winter reduces dilution of the transcription factor NTL8, which allows slow accumulation of NTL8 and thus the gradual increase in transcription of VIN3—a gene involved in memory of cold exposure.

    • Yusheng Zhao
    • , Rea L. Antoniou-Kourounioti
    •  & Martin Howard

  • Article |

    A new computational framework, novoSpaRc, leverages single-cell data to reconstruct spatial context for cells and spatial expression across tissues and organisms, on the basis of an organization principle for gene expression.

    • Mor Nitzan
    • , Nikos Karaiskos
    •  & Nikolaus Rajewsky

  • Letter |

    An algorithm that allows rare cell type identification in a complex population of single cells, based on single-cell mRNA-sequencing, is applied to mouse intestinal cells, revealing novel subtypes of enteroendocrine cells and showing that the Lgr5-expressing population consists of a homogenous stem cell population with a few rare secretory cells, including Paneth cells.

    • Dominic Grün
    • , Anna Lyubimova
    •  & Alexander van Oudenaarden

  • Letter |

    An efficient protein disaggregation system uncovered in metazoan cells requires transient interactions between J-protein co-chaperones of classes A and B, which synergistically boost HSP70-dependent disaggregation activity, providing a flexible further level of regulation for metazoan protein quality control, with direct relevance to human diseases such as age-related neurodegeneration.

    • Nadinath B. Nillegoda
    • , Janine Kirstein
    •  & Bernd Bukau

  • Letter |

    The analysis of more than 9,000 haemagglutinin sequences of human seasonal influenza viruses over a 12-year time period shows that the global circulation patterns of A/H1N1 and B viruses are different from those of the well characterised A/H3N2 viruses; in particular the A/H1N1 and B viruses are shown to persist locally across several seasons and do not display the same degree of global movement as the H3N2 viruses.

    • Trevor Bedford
    • , Steven Riley
    •  & Colin A. Russell

  • Letter |

    Through a combination of experimental and computational approaches, the interplay between the plant hormone auxin and the auxin-induced PLETHORA transcription factors is shown to control zonation and gravity-prompted growth movements in plants.

    • Ari Pekka Mähönen
    • , Kirsten ten Tusscher
    •  & Ben Scheres

  • Letter |

    Bovine tuberculosis is a major economic burden on the cattle industry, and attempts to control it have been politically controversial; here farm movement and bovine tuberculosis incidence data are used to construct a mechanistic model and tease apart the factors contributing to epidemic bovine tuberculosis spread.

    • Ellen Brooks-Pollock
    • , Gareth O. Roberts
    •  & Matt J. Keeling

  • Letter |

    Phosphoinositides are important regulators of intracellular membrane traffic, and although the role of PI(4,5)P2 has been well characterised, the function of PI(3,4)P2 remains unclear; here the formation of PI(3,4)P2 by the class II phosphatidylinositol-3-kinase C2α enzyme is shown to control clathrin-mediated endocytosis.

    • York Posor
    • , Marielle Eichhorn-Gruenig
    •  & Volker Haucke

  • News & Views Forum |

    Many scientists now use the power of computer models to advance their subjects. But there is a choice: to simplify complex systems or to include more detail. Modelling the intricate processes of sedimentary geology is a case in point.

    • Chris Paola
    •  & Mike Leeder

  • News |

    The Deepwater Horizon oil spill puts ocean-current modelling to the test.

    • Janet Fang

  • Letter |

    Genotype and phenotype cannot be connected simply by one-to-one mapping; instead they are linked by the nonlinear process of development. Here, a computational model is described — based on real data about the development of seal teeth — that attempts to combine the three. The results show that a few genetic parameters regulating signalling during cusp development may explain variation among individuals. But a cellular parameter regulating epithelial growth may explain tooth-to-tooth variation along the jaw.

    • Isaac Salazar-Ciudad
    •  & Jukka Jernvall

  • Article |

    A defining focus of synthetic biology is the engineering of genetic circuits with predictive functionality in living cells. Here, a decade after the first synthesized genetic toggle switch and oscillator, an engineered gene network with global intercellular coupling is designed that is capable of generating synchronized oscillations in a growing population of cells.

    • Tal Danino
    • , Octavio Mondragón-Palomino
    •  & Jeff Hasty

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