Dynamic networks articles within Nature Communications

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  • Article
    | Open Access

    Kinetic modeling of in vitro enzymatic reaction networks (ERNs) is severely hampered by the lack of training data. Here, authors introduce a methodology that combines an active learning-like approach and flow chemistry to create optimized datasets for an intricate ERN.

    • Bob van Sluijs
    • , Tao Zhou
    •  & Wilhelm T. S. Huck

  • Article
    | Open Access

    Here, the authors simulate COVID-19 outbreaks on an empirical contact network derived from digital contact data collected on cruise ships. They model impacts of different control measures and find that combinations of measures, particularly vaccination and rapid antigen testing, are important for mitigating outbreaks.

    • Rachael Pung
    • , Josh A. Firth
    •  & Adam J. Kucharski

  • Article
    | Open Access

    Boolean networks allow a simplified representation of interactions. Here, the authors systematically analyze regulation in dozens of biological Boolean networks, finding mathematical regularities that suggest biological systems could be controlled through a relatively small number of components.

    • Enrico Borriello
    •  & Bryan C. Daniels

  • Article
    | Open Access

    The formation of large-scale brain networks represents crucial developmental processes that can drive individual differences in cognition and which are associated with multiple neurodevelopmental conditions. Here, the authors use generative network modelling to provide a computational framework for understanding neurodevelopmental diversity.

    • Danyal Akarca
    • , Petra E. Vértes
    •  & Duncan E. Astle

  • Article
    | Open Access

    Robustness is a prominent feature of most biological systems, but most of the current efforts have been focused on studying homogeneous molecular networks. Here the authors propose a comprehensive framework for understanding how the interactions between genes, proteins, and metabolites contribute to the determinants of robustness.

    • Xueming Liu
    • , Enrico Maiorino
    •  & Amitabh Sharma

  • Article
    | Open Access

    Boolean Networks are a well-established model of biological networks, but usual interpretations can preclude the prediction of behaviours observed in quantitative systems. The authors introduce Most Permissive Boolean Networks, which are shown not to miss any behaviour achievable by the corresponding quantitative model.

    • Loïc Paulevé
    • , Juri Kolčák
    •  & Stefan Haar

  • Article
    | Open Access

    Synthetic circuits based on CRISPRi have not achieved multistable and dynamic behaviors. Here the authors build an oscillator, a toggle switch and an incoherent feed-forward loop using CRISPRi, and provide a mathematical model suggesting that unspecific binding in CRISPRi enables multistability.

    • Javier Santos-Moreno
    • , Eve Tasiudi
    •  & Yolanda Schaerli

  • Article
    | Open Access

    Conventional methods cannot reveal transient transcription factors (TFs) and targets interactions. Here, Alvarez et al. capture both stable and transient TF-target interactions by time-series ChIP-seq and/or DamID-seq in a cell-based TF perturbation system and show NLP7 as a master TF to initiate a rapid nitrogen-response cascade.

    • José M. Alvarez
    • , Anna-Lena Schinke
    •  & Gloria M. Coruzzi

  • Article
    | Open Access

    How heterogeneities arise in stem cell populations remains unclear. Here, Glen et al. find that in ESC colonies cell cycle asynchronies modulate gap junctions, causing variation in intracellular signalling molecule diffusion between cells, and ultimately in spatial heterogeneity in differentiation.

    • Chad M. Glen
    • , Todd C. McDevitt
    •  & Melissa L. Kemp

  • Article
    | Open Access

    Biomarkers of the tipping point before metastasis in hepatocellular carcinoma (HCC) could help stratify patient treatment. Here, the authors study dynamic network biomarkers to identify CALM3 as a potential suppressor of metastasis, the level of which can predict overall survival and relapse-free survival in postoperative HCC.

    • Biwei Yang
    • , Meiyi Li
    •  & Jinglin Xia

  • Article
    | Open Access

    The evolutionary rationale behind the extensive crosstalk between Metazoan signalling pathways remains elusive. Here the authors provide evidence that crosstalk in the human signalling network evolves as a means to allow efficient diversification of cellular responses to the same signals between different cell types.

    • Michael A. Rowland
    • , Joseph M. Greenbaum
    •  & Eric J. Deeds

  • Article
    | Open Access

    The R2TP/Prefoldin-like cochaperone complex is involved in the assembly of a number of protein complexes. Here the authors provide evidence that RUVBL1/RUVBL2, subunits of that cochaperone complex, directly interact with ZNHIT2 to regulate assembly of U5 small ribonucleoprotein.

    • Philippe Cloutier
    • , Christian Poitras
    •  & Benoit Coulombe

  • Article
    | Open Access

    In biological systems, timing is often critical to the interpretation of signals that determine cell fate. Here the authors demonstrate how single cells and cellular populations respond dynamically to pulsatile stimulation by TNFα and IL-1β, and suggest a mechanism by which the two cytokines can synergistically modulate inflammation.

    • Antony Adamson
    • , Christopher Boddington
    •  & Pawel Paszek

  • Article
    | Open Access

    Large-scale, multimodal phenotypic characterisation is a valuable tool to explore brain function. Poldrack et al. collect and relate MRI, psychological, physiological, metabolic and gene expression data from a single human over an 18 month period, providing a rich resource for future studies.

    • Russell A. Poldrack
    • , Timothy O. Laumann
    •  & Jeanette A. Mumford

  • Article
    | Open Access

    Cognitive control is fundamental to human intelligence, yet the principles constraining the neural dynamics of cognitive control remain elusive. Here, the authors use network control theory to demonstrate that the structure of brain networks dictates their functional role in controlling dynamics.

    • Shi Gu
    • , Fabio Pasqualetti
    •  & Danielle S. Bassett

  • Article
    | Open Access

    The effect of the rate of forming and breaking social ties on cooperative behaviour is not clear. Here the authors experimentally test the effect of rewiring the connections between individuals, and find that optimal levels of cooperation are achieved at intermediate levels of change in ties.

    • Hirokazu Shirado
    • , Feng Fu
    •  & Nicholas A. Christakis

  • Article |

    Nonlinearity is a hallmark of complex networks, but has generally been regarded as an obstacle to controlling their behaviour. Here Cornelius et al.show how nonlinear dynamics can be harnessed to control a network and drive it to desired states.

    • Sean P. Cornelius
    • , William L. Kath
    •  & Adilson E. Motter

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