The DOI matches its Crossref record; 102 of the 106 references it cites were found in a registry or an index.
Modeling the dynamics of transcriptional gene regulatory networks for animal development
Open accessAbstract
The dynamic process of cell fate specification is regulated by networks of regulatory genes. The architecture of the network defines the temporal order of specification events. To understand the dynamic control of the developmental process, the kinetics of mRNA and protein synthesis and the response of the cis-regulatory modules to transcription factor concentration must be considered. Here we review mathematical models for mRNA and protein synthesis kinetics which are based on experimental measurements of the rates of the relevant processes. The model comprises the response functions of cis-regulatory modules to their transcription factor inputs, by incorporating binding site occupancy and its dependence on biologically measurable quantities. We use this model to simulate gene expression, to distinguish between cis-regulatory execution of "AND" and "OR" logic functions, rationalize the oscillatory behavior of certain transcriptional auto-repressors and to show how linked subcircuits can be dealt with. Model simulations display the effects of mutation of binding sites, or perturbation of upstream gene expression. The model is a generally useful tool for understanding gene regulation and the dynamics of cell fate specification.
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“Based on Davidson and co-workers the estimated maximal translation rate constant in sea urchin embryos is 140 copies / (mRNA*h) 1 which is surprisingly close to the prediction of our model for mouse fibroblasts.”
From Global quantification of mammalian gene expression control (2011) · cites this paper as [1]
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Structure and function of the feed-forward loop network motif
Mangan, S., & Alon, U. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2133841100 · Cited by 1,827
Gene Activity in Early Development
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Self-citationFelsenfeld, G., & Groudine, M. T. (2003) · Nature · doi:10.1038/nature01411 · Cited by 1,252
Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell
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The Regulatory Genome: Gene Regulatory Networks In Development And Evolution
Davidson, E. H. (2006) · Thammasat University Digital Collections · Cited by 1,048
Self-citationVirus induction of human IFNβ gene expression requires the assembly of an enhanceosome
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Items 101–109 of 109
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26074114
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736741
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736720
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736714
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26074264
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736744
Zhuravskaya, A., Yap, K., Hamid, F., & Makeyev, E. V. (2024) · Figshare · doi:10.6084/m9.figshare.26736738
Bougioukos, K. (2010) · UEA Digital Repository (University of East Anglia)
Modeling Oncogenic Signaling Networks from Gene Expression Dynamics
Bollig-Fischer, A. B. (2012) · Springer eBooks · doi:10.1007/978-94-007-4819-4_3
Metadata
- Authors
- Ben-Tabou de-Leon, S., & Davidson, E. H.
- Affiliations
- California Institute of Technology (US)
- Corresponding author
- Davidson, Eric H.
- Venue
- Developmental Biology
- Publisher
- Elsevier BV
- Published
- 2009-01
- Volume
- 325
- Issue
- 2
- Pages
- 317-328
- ISSN
- 0012-1606 (ISSN-L)
- PMC
- PMC4100934
- OpenAlex
- W2120009112
- Cited by
- 99
- References
- 106
- Citations by year
- 2025: 1 · 2024: 8 · 2023: 3 · 2022: 3 · 2021: 5 · 2020: 5 · 2019: 5 · 2018: 4 · 2017: 9 · 2016: 6 · 2015: 10 · 2014: 3 · 2013: 6 · 2012: 6
- FWCI
- 0.64
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 1694 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Developmental Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM 61005, R01GM061005)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- cell fate specification, animal development, protein synthesis kinetics, cis-regulatory modules, response functions, gene expression oscillations, binding site mutations, mathematical modeling of gene regulation
- MeSH terms
- Animals, Binding Sites, Biological Clocks, DNA-Binding Proteins, Genes, Regulator, Kinetics, Models, Genetic, RNA, Messenger, Transcription Factors, Transcription, Genetic, Protein Biosynthesis, Gene Expression Regulation, Developmental, Gene Regulatory Networks
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