ArticleCurrent opinion in systems biology2022
Eukaryotic gene regulation at equilibrium, or non?
Article in Current opinion in systems biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Exchange dynamics and kinetic control of gene regulation complexes.Nature reviews. Molecular cell biology · 2026Review
- Stable epigenetic states set single-cell activation thresholds in mammalian expression systems.bioRxiv : the preprint server for biology · 2026Article
- Invariant nonequilibrium dynamics in gene regulation optimize information flow.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis.bioRxiv : the preprint server for biology · 2026Article
- Decoupling between activation time and steady-state level in input-output responses.PLoS computational biology · 2026Article
- A model of transcriptional bursting dynamics based on coupling between chromatin and enhancer states.bioRxiv : the preprint server for biology · 2025Article
- Emergence of activation or repression in transcriptional control under a fixed molecular context.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Timing is everything: transcription bursting in development.Genes & development · 2025Review
- Quantification and potential functional relevance of binding cooperativity of adjacent transcription factors on DNA.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Article
- A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits.bioRxiv : the preprint server for biology · 2025Article
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deriving a genetic regulatory network from an optimization principle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Flexibility and sensitivity in gene regulation out of equilibrium.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Energy Aware Technology Mapping of Genetic Logic Circuits.ACS synthetic biology · 2024Article
- Energy Aware Technology Mapping of Genetic Logic Circuits.bioRxiv : the preprint server for biology · 2024Article
- Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.Nature communications · 2024Article
- Time will tell: comparing timescales to gain insight into transcriptional bursting.Trends in genetics : TIG · 2024Review
- Size limits the sensitivity of kinetic schemes.Nature communications · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 3 countries.
Funding
Abstract
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory-theory that prescribes rather than just describes-in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.