Imperfect molecular detection can renormalize apparent kinetic rates in stochastic gene regulatory networks

Quantitative Biology > Molecular Networks [Submitted on 2 Dec 2025 (v1), last revised 18 Jun 2026 (this version, v2)] Title:Imperfect molecular detection can renormalize apparent kinetic rates in stochastic gene regulatory networks View PDF HTML (experimental)Abstract:Imperfect molecular detection in single-cell experiments introduces technical noise that obscures the true stochastic dynamics of gene regulatory networks. While binomial models of molecular capture provide a principled description of imperfect detection, they have so far been analyzed only for simple gene-expression models that do not explicitly account for regulation. Here, we extend binomial models of capture to general gene regulatory networks to understand how imperfect capture reshapes the observed time-dependent statistics of molecular counts. Our results reveal when capture effects correspond to a renormalization of a subset of the kinetic rates and when they cannot be absorbed into effective rates, providing a systematic basis for interpreting noisy single-cell measurements. In particular, we show that rate renormalization depends on the level of regulatory detail in the model. For implicit regulatory models based on promoter state transitions, it arises whenever gene product synthesis does not trigger a promoter state change, as in the absence of promoter-proximal pausing or when pausing is short-lived. For models with explicit transcription factor binding, the same condition holds, together with sufficiently high transcription factor abundance, which in practice requires only a few tens of molecules per cell. In these cases, technical noise reduces the apparent mean burst size of synthesized gene products and accelerates the apparent rates of transcription factor binding reactions. This acceleration becomes stronger as the number of protein species and/or molecules involved in promoter switching increases. These effects hold for gene regulatory networks of arbitrary connectivity and remain valid under time-dependent kinetic rates. Submission history From: Ramon Grima [view email][v1] Tue, 2 Dec 2025 16:25:05 UTC (556 KB) [v2] Thu, 18 Jun 2026 12:16:17 UTC (1,160 KB) Current browse context: q-bio.MN References & Citations Loading... Bibliographic and Citation Tools Bibliographic Explorer (What is the Explorer?) Connected Papers (What is Connected Papers?) Litmaps (What is Litmaps?) scite Smart Citations (What are Smart Citations?) Code, Data and Media Associated with this Article alphaXiv (What is alphaXiv?) CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub (What is DagsHub?) Gotit.pub (What is GotitPub?) Hugging Face (What is Huggingface?) ScienceCast (What is ScienceCast?) Demos Recommenders and Search Tools Influence Flower (What are Influence Flowers?) CORE Recommender (What is CORE?) arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.