dorsal/arxiv
View SchemaOscillation patterns in negative feedback loops
| Authors | Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611038 |
| URL | https://arxiv.org/abs/q-bio/0611038 |
| DOI | 10.1073/pnas.0610759104 |
Abstract
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein concentrations or gene expression levels are related to the presence of at least one negative feedback loop in the regulatory network. Here we study the dynamics of a very general class of negative feedback loops. Our main result is that in these systems the sequence of maxima and minima of the concentrations is uniquely determined by the topology of the loop and the activating/repressing nature of the interaction between pairs of variables. This allows us to devise an algorithm to reconstruct the topology of oscillating negative feedback loops from their time series; this method applies even when some variables are missing from the data set, or if the time series shows transients, like damped oscillations. We illustrate the relevance and the limits of validity of our method with three examples: p53-Mdm2 oscillations, circadian gene expression in cyanobacteria, and cyclic binding of cofactors at the estrogen-sensitive pS2 promoter.
{
"annotation_id": "654a10b6-267f-47ae-847c-fd2c1c3ea26c",
"date_created": "2026-03-02T18:01:35.541000Z",
"date_modified": "2026-03-02T18:01:35.541000Z",
"file_hash": "be758c05a1bfe4e3afa192f39bc480f895b68a050caa9ce414ea9e2b246bc836",
"private": false,
"record": {
"abstract": "Organisms are equipped with regulatory systems that display a variety of\ndynamical behaviours ranging from simple stable steady states, to switching and\nmultistability, to oscillations. Earlier work has shown that oscillations in\nprotein concentrations or gene expression levels are related to the presence of\nat least one negative feedback loop in the regulatory network. Here we study\nthe dynamics of a very general class of negative feedback loops. Our main\nresult is that in these systems the sequence of maxima and minima of the\nconcentrations is uniquely determined by the topology of the loop and the\nactivating/repressing nature of the interaction between pairs of variables.\nThis allows us to devise an algorithm to reconstruct the topology of\noscillating negative feedback loops from their time series; this method applies\neven when some variables are missing from the data set, or if the time series\nshows transients, like damped oscillations. We illustrate the relevance and the\nlimits of validity of our method with three examples: p53-Mdm2 oscillations,\ncircadian gene expression in cyanobacteria, and cyclic binding of cofactors at\nthe estrogen-sensitive pS2 promoter.",
"arxiv_id": "q-bio/0611038",
"authors": [
"Simone Pigolotti",
"Sandeep Krishna",
"Mogens H. Jensen"
],
"categories": [
"q-bio.MN"
],
"doi": "10.1073/pnas.0610759104",
"title": "Oscillation patterns in negative feedback loops",
"url": "https://arxiv.org/abs/q-bio/0611038"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "3db20dbb-1a1a-4cb9-b991-08cba8cc0a66",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}