Computer modelling articles within Nature Communications

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  • Article
    | Open Access

    The intractability of most stochastic models of gene regulatory networks (GRNs) limits their utility. Here, the authors present a linear-mapping approximation mapping models onto simpler ones, giving approximate but accurate analytic or semi- analytic solutions for a wide range of model GRNs.

    • Zhixing Cao
    •  & Ramon Grima

  • Article
    | Open Access

    Normal adult tissue fibroblasts can be activated during wound healing, pathologic fibrosis and in cancer stroma, but the regulatory network that controls its dynamics is unknown. Here the authors show that fibroblasts are activated by a positive feedback loop formed by Twist1, Prrx1, and Tenascin-C bi-stably.

    • So-Young Yeo
    • , Keun-Woo Lee
    •  & Seok-Hyung Kim

  • Article
    | Open Access

    Sign epistasis clearly constrains evolution, but its causes are difficult to decipher. Here, the authors study epistasis in a signalling cascade, and arrive at a general criterion and understanding of sign epistasis as arising from the inherent hierarchy between signalling cascade components.

    • Philippe Nghe
    • , Manjunatha Kogenaru
    •  & Sander J. Tans

  • Article
    | Open Access

    Two-component systems are a major family of signal transduction pathways and a rich source of sensors for biotechnology. Here, the authors develop a general method for rationally tuning two-component system input detection thresholds via specific point mutations in sensor histidine kinase proteins.

    • Brian P. Landry
    • , Rohan Palanki
    •  & Jeffrey J. Tabor

  • Article
    | Open Access

    Existing transcriptional regulatory networks models fall short of deciphering the cooperation between multiple transcription factors on dynamic gene expression. Here the authors develop an integrative method that combines gene expression and transcription factor-DNA binding data to decode transcription regulatory logics.

    • Bin Yan
    • , Daogang Guan
    •  & Hailong Zhu

  • Article
    | Open Access

    Genetic drift can reduce fitness in small populations by counteracting selection against deleterious mutations. Here, LaBar and Adami demonstrate through a mathematical model and simulations that small populations tend to evolve to drift-robust fitness peaks, which have a low likelihood of slightly-deleterious mutations.

    • Thomas LaBar
    •  & Christoph Adami

  • Article
    | Open Access

    The quiescence-exit process is noisy even in genetically identical cells under the same environmental conditions. Here the authors show that the heterogeneity of quiescence exit reflects a memory of preceding cell growth at quiescence induction and immediate division history prior to quiescence entry.

    • Xia Wang
    • , Kotaro Fujimaki
    •  & Guang Yao

  • Article
    | Open Access

    Kinetic models of microbial metabolism have great potential to aid metabolic engineering efforts, but the challenge of parameterization has so far limited them to core metabolism. Here, the authors introduce a genome-scale metabolic model of E. colimetabolism that satisfies fluxomic data for a wild-type and 25 mutant strains in various growth conditions.

    • Ali Khodayari
    •  & Costas D. Maranas

  • Article
    | Open Access

    Translating omics data sets into biological insight is one of the great challenges of our time. Here, the authors make headway by synchronising pairs of omics data types via invariants across conditions and by integrating datasets into a genome-scale model of E. coli metabolism and gene expression.

    • Ali Ebrahim
    • , Elizabeth Brunk
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    Glycolytic regulator PFKFB3 is a key player in vessel sprouting. Here the authors develop a computational model predicting that PFKFB3 drives endothelial cell rearrangement during vessel sprouting by promoting filopodia formation and reducing intercellular adhesion, and empirically validate this prediction.

    • Bert Cruys
    • , Brian W. Wong
    •  & Peter Carmeliet

  • Article
    | Open Access

    Mouse digit patterning is controlled by a Turing network of Bmp, Sox9, and Wnt. Here, Onimaru et al. show that fin patterning in the catshark, Scyliorhinus canicula, is controlled by the same network with a different spatial organization; thus, the Turing network is deeply conserved in limb development.

    • Koh Onimaru
    • , Luciano Marcon
    •  & James Sharpe

  • Article
    | Open Access

    A fundamental question in evolutionary biology is how complex innovations requiring multiple genetic changes arise. Here the authors provide lines of evidence that changing environments facilitate the adaptive evolution of complex metabolic innovations via stepwise acquisition of single reactions.

    • Balázs Szappanos
    • , Jonathan Fritzemeier
    •  & Balázs Papp

  • Article
    | Open Access

    Hes1 is an important regulator of progenitor maintenance and timed differentiation, which shows oscillatory expression. Here, the authors combine experimental data and mathematical modelling to show that the interaction between miRNA-9 and Hes1 can predict progenitor transition from one cell state to another, as well as the timing of this transition.

    • Marc Goodfellow
    • , Nicholas E. Phillips
    •  & Nancy Papalopulu

  • Article |

    Alterations in hepatocyte metabolism can lead to disorders such as non-alcoholic steatohepatitis (NASH). Here the authors create a comprehensive model of hepatocyte metabolism and use it to identify metabolic pathways altered in disease, revealing that serine levels are reduced in patients with NASH.

    • Adil Mardinoglu
    • , Rasmus Agren
    •  & Jens Nielsen

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