Stochastic networks articles within Nature Communications

Featured

• Article
  25 July 2022 | Open Access

  Frequency spectra and the color of cellular noise

  The invention of the Fourier integral in the 19th century laid the foundation for modern spectral analysis methods. Here the authors develop frequency-based methods for analyzing the reaction mechanisms within living cells from distinctively noisy single-cell output trajectories and present forward engineering of synthetic oscillators and controllers.

  • Ankit Gupta
  •  & Mustafa Khammash

• Article
  21 June 2022 | Open Access

  A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

  Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. Here the authors develop a scalable, open-source pipeline for constructing and simulating large-scale, single-cell mechanistic models, an important building block for clinically-predictive mechanistic models and interpretable big data integration.

  • Cemal Erdem
  • , Arnab Mutsuddy
  •  & Marc R. Birtwistle

• Article
  01 June 2017 | Open Access

  Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome

  Robust quantification of the differentiation potential of single cells is a task of great importance. Here the authors integrate single-cell RNA-Seq profiles with a cellular interaction network to compute the signaling entropy, and show that it can identify normal and cancer stem-cell phenotypes.

  • Andrew E. Teschendorff
  •  & Tariq Enver

• Article
  25 May 2016 | Open Access

  Cox process representation and inference for stochastic reaction–diffusion processes

  Stochastic reaction-diffusion systems are used for modelling spatial dynamics in many disciplines, but parameter inference and model selection remain challenging. Here the authors offer a solution enabled by a connection between reaction-diffusion and the well-studied spatio-temporal Cox processes.

  • David Schnoerr
  • , Ramon Grima
  •  & Guido Sanguinetti

• Article | 09 August 2011

  Delay-induced anomalous fluctuations in intracellular regulation

  Direct negative feedback decreases fluctuations in homoeostatic control, but intracellular regulatory systems are indirect. Here, an analytical expression is derived to show that indirect feedback in transcription and translation leads to more fluctuations for intermediate delays but not for long delays.

  • Andreas Grönlund
  • , Per Lötstedt
  •  & Johan Elf