Evidence map›Paper›PMID 40748213›Full record

ReviewDevelopment (Cambridge, England)2025

From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms.

Usha Kadiyala, David Sprinzak, Nicholas A M Monk, Shannon E Taylor, Berta Verd, Katharina F Sonnen, Lauren Moon, Adrienne H K Roeder, Ruben Perez-Carrasco, Pau Formosa-Jordan

Abstract readReview
In one paragraph

Review in Development (Cambridge, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Review
  5. Article
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Usha KadiyalaDepartment of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0002-5437-3123
David SprinzakSchool of Neurobiology, Biochemistry, and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 69978, Israel.ORCID 0000-0001-6776-6957
Nicholas A M MonkSchool of Mathematical and Physical Sciences, University of Sheffield, Sheffield S3 7RH, UK.ORCID 0000-0002-5465-4857
Shannon E TaylorBiology Department, University of Oxford, Oxford OX1 3RB, UK.ORCID 0000-0003-3490-3307
Berta VerdBiology Department, University of Oxford, Oxford OX1 3RB, UK.ORCID 0000-0001-9835-009X
Katharina F SonnenHubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 GR Utrecht, The Netherlands.ORCID 0000-0002-2902-9419
Lauren MoonDepartment of Physiology, Development and Neuroscience, University of Cambridge, 4, 7 Downing Pl, Cambridge CB2 3EL, UK.ORCID 0000-0003-3075-5968
Adrienne H K RoederWeill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0001-6685-2984
Ruben Perez-CarrascoDepartment of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.ORCID 0000-0001-5348-8829
Pau Formosa-JordanPolyploidy Integration and Innovation Institute.ORCID 0000-0003-3005-597X

Funding

Alexander von Humboldt-StiftungBiotechnology and Biological Sciences Research Council BB/Y002709/1Bundesministerium für Bildung und ForschungClarendon FundDeutsche Forschungsgemeinschaft 390686111European Research Council 101163722 / COUNTSHubrecht Institute 850554Imperial College LondonIsrael Science Foundation 1343/22Leverhulme Trust RPG-2023-085Max-Planck-GesellschaftNational Science Foundation 2020260279National Science Foundation DBI-232051National Science Foundation EF-2222434University of MichiganUniversity of OxfordWellcome TrustWellcome Trust 222274/Z/20/Z
6 · The paper itself

Abstract

Developmental biology seeks to unravel the intricate regulatory mechanisms orchestrating the transformation of a single cell into a complex, multicellular organism. Dynamical systems theory provides a powerful quantitative, visual and intuitive framework for understanding this complexity. This Primer examines five core dynamical systems theory concepts and their applications to pattern formation during development: (1) analysis of phase portraits, (2) bistable switches, (3) stochasticity, (4) response to time-dependent signals, and (5) oscillations. We explore how these concepts shed light onto cell fate decision making and provide insights into the dynamic nature of developmental processes driven by signals and gradients, as well as the role of noise in shaping developmental outcomes. Selected examples highlight how integrating dynamical systems with experimental approaches has significantly advanced our understanding of the regulatory logic underlying development across scales, from molecular networks to tissue-level dynamics.

Indexed as

Body PatterningGene Expression Regulation, DevelopmentalAnimalsDevelopmental BiologyGene Regulatory NetworksHumansModels, BiologicalSignal TransductionStochastic ProcessesDevelopmental dynamicsDynamical systemsModellingSignallingWaddington landscape

Identifiers

PMID40748213
PMCPMC12377817

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

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.