Differential equations articles within Nature Communications

Featured

• Article
  20 October 2023 | Open Access

  CD8⁺ T cells control SIV infection using both cytolytic effects and non-cytolytic suppression of virus production

  Control of HIV and SIV infection is largely thought to be achieved through direct lysis of target cells. Here, using mathematical modelling of viral load data from rhesus macaques, the authors propose that virus control is best explained by the combination of cytolytic and non-cytolytic effects.

  • Benjamin B. Policicchio
  • , Erwing Fabian Cardozo-Ojeda
  •  & Ruy M. Ribeiro

• Article
  14 September 2023 | Open Access

  Activator-blocker model of transcriptional regulation by pioneer-like factors

  How gene expression timing is regulated during development remains a key area of research. Here they show that zebrafish genome activators Pou5f3 and Nanog block each other’s activity on the enhancers of differentiation genes, preventing their premature expression.

  • Aileen Julia Riesle
  • , Meijiang Gao
  •  & Daria Onichtchouk

• Article
  29 April 2023 | Open Access

  Positive feedback induces switch between distributive and processive phosphorylation of Hog1

  How cells shape signalling dynamics in MAPK cascades remains unclear. Here the authors combine mathematical modelling with in vivo validation to uncover a novel feedback mechanism that increases processivity and robustness of the yeast Hog1 module.

  • Maximilian Mosbacher
  • , Sung Sik Lee
  •  & Manfred Claassen

• Article
  23 November 2022 | Open Access

  Kinetics of mRNA nuclear export regulate innate immune response gene expression

  The UCLA Ribonomics group reports that the nuclear export efficiency of innate immune mRNAs varies over a hundred-fold range such that for many genes only a small fraction of the newly synthesized premRNA reaches the cytoplasm. They show that nuclear export and cytoplasmic decay rates are correlated thereby ensuring similar expression levels of short-lived and long-lived mRNAs.

  • Diane Lefaudeux
  • , Supriya Sen
  •  & Sri Kosuri

• Article
  25 January 2022 | Open Access

  A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host

  The herpesvirus protein ORF45 can bind the two host kinases ERK and RSK but how this affects cell signalling is unclear. Here, the authors show that ORF45 hijacks the ERK-RSK complex by binding to the two kinases with optimized linear motifs and interfering with the host kinase docking systems.

  • Anita Alexa
  • , Péter Sok
  •  & Attila Reményi

• Article
  10 January 2022 | Open Access

  Mini-batch optimization enables training of ODE models on large-scale datasets

  Ordinary differential equation (ODE) models are widely used to understand multiple processes. Here the authors show how the concept of mini-batch optimization can be transferred from the field of Deep Learning to ODE modelling.

  • Paul Stapor
  • , Leonard Schmiester
  •  & Jan Hasenauer

• Article
  19 March 2021 | Open Access

  Nonlinear delay differential equations and their application to modeling biological network motifs

  Network motif models focus on small sub-networks in biological systems to quantitatively describe overall behavior but they often overlook time delays. Here, the authors systematically examine the most common network motifs via delay differential equations (DDE), often leading to more concise descriptions.

  • David S. Glass
  • , Xiaofan Jin
  •  & Ingmar H. Riedel-Kruse

• Article
  08 December 2020 | Open Access

  Design of efficacious somatic cell genome editing strategies for recessive and polygenic diseases

  Gene correction of multiple alleles is a promising therapeutic strategy. Here the authors present bi-allelic correction of Pompe disease and provide an in silico model for predicting in vivo somatic editing outcomes.

  • Jared Carlson-Stevermer
  • , Amritava Das
  •  & Krishanu Saha

• Article
  13 July 2020 | Open Access

  Gene regulatory network inference from sparsely sampled noisy data

  Gene regulatory network inference is a topical problem in systems biology. Here, the authors presents BINGO, a powerful method for network inference from time series data.

  • Atte Aalto
  • , Lauri Viitasaari
  •  & Jorge Gonçalves

• Article
  13 February 2020 | Open Access

  Macrophages employ quorum licensing to regulate collective activation

  Macrophage activation is tightly regulated to maintain immune homeostasis, yet activation is also heterogeneous. Here, the authors show that macrophages coordinate activation by partitioning into two phenotypes that can nonlinearly amplify collective inflammatory cytokine production as a function of cell density.

  • Joseph J. Muldoon
  • , Yishan Chuang
  •  & Joshua N. Leonard

• Article
  21 March 2019 | Open Access

  Mitochondrial origins of fractional control in regulated cell death

  Phenotypic cell-to-cell variability contributes to fractional killing, but the mechanisms are incompletely understood. Here the authors show that mitochondrial density correlates with cell survival in response to TRAIL, and that variable effective concentrations of Bax/Bak contribute to the effect.

  • Luís C. Santos
  • , Robert Vogel
  •  & Pablo Meyer

• Article
  26 November 2018 | Open Access

  Quantifying post-transcriptional regulation in the development of Drosophila melanogaster

  Proteome and transcriptome often show poor correlation, hindering the system-wide analysis of post-transcriptional regulation. Here, the authors study proteome and transcriptome dynamics during Drosophila embryogenesis and present basic mathematical models describing the temporal regulation of most protein-RNA pairs.

  • Kolja Becker
  • , Alina Bluhm
  •  & Stefan Legewie