The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
A connectionist model of development
Abstract
We present a phenomenological modeling framework for development. Our purpose is to provide a systematic method for discovering and expressing correlations in experimental data on gene expression and other developmental processes. The modeling framework is based on a connectionist or "neural net" dynamics for biochemical regulators, coupled to "grammatical rules" which describe certain features of the birth, growth, and death of cells, synapses and other biological entities. We outline how spatial geometry can be included, although this part of the model is not complete. As an example of the application of our results to a specific biological system, we show in detail how to derive a rigorously testable model of the network of segmentation genes operating in the blastoderm of Drosophila. To further illustrate our methods, we sketch how they could be applied to two other important developmental processes: cell cycle control and cell-cell induction. We also present a simple biochemical model leading to our assumed connectionist dynamics which shows that the dynamics used is at least compatible with known chemical mechanisms.
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“expression levels of transcription factors (TFs), to be indicated as [Ti] (intracellular concentration) of different TF (Ti in figure 7d) change following a dynamical model [271]”
From Fundamental constraints to the logic of living systems (2024) · cites this paper as [271]
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Cites
Hopfield, J. J. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.10.3088 · Cited by 6,918
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Cited by
Robustness can evolve gradually in complex regulatory gene networks with varying topology
Ciliberti, S., Martin, O. C., & Wagner, A. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030015 · Cited by 390
Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster
Jaeger, J., Blagov, M., Kosman, D., Kozlov, K. N., Manu, Myasnikova, E., Surkova, S., Vanario-Alonso, C. E., Samsonova, M., Sharp, D. H., et al. (2004) · Genetics · doi:10.1534/genetics.104.027334 · Cited by 248
Self-citationEfficient reverse-engineering of a developmental gene regulatory network
Crombach, A., Wotton, K. R., Cicin-Sain, D., Ashyraliyev, M., & Jaeger, J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002589 · Cited by 83
“The particular reverse-engineering approach we use to investigate the gap gene network is called the gene circuit method [1,38,39] (Figure 1).”
BackgroundMethodFundamental constraints to the logic of living systems
Solé, R., Kempes, C. P., Corominas-Murtra, B., De Domenico, M., Kolchinsky, A., Lachmann, M., Libby, E., Saavedra, S., Smith, E., & Wolpert, D. (2024) · Interface Focus · doi:10.1098/rsfs.2024.0010 · Cited by 34
Metadata
- Authors
- Mjolsness, E., Sharp, D. H., & Reinitz, J.
- Affiliations
- Yale University (US)
- Los Alamos National Laboratory (US)
- Venue
- Journal of Theoretical Biology
- Publisher
- Elsevier BV
- Published
- 1991-10
- Volume
- 152
- Issue
- 4
- Pages
- 429-453
- ISSN
- 0022-5193 (ISSN-L)
- OpenAlex
- W2036338631
- Cited by
- 434
- References
- 1
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 9 · 2023: 11 · 2022: 11 · 2021: 19 · 2020: 9 · 2019: 7 · 2018: 15 · 2017: 19 · 2016: 15 · 2015: 11 · 2014: 14 · 2013: 16 · 2012: 26
- FWCI
- 0.93
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Theoretical Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. National Library of Medicine (5-T15-LM07056, T15LM007056)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Philosophy of Biology and Scientific Explanation
- Keywords
- connectionist models, developmental biology, gene expression, neural network dynamics, segmentation genes, cell cycle regulation, spatial geometry, phenomenological model
- MeSH terms
- Animals, Blastoderm, Cell Cycle, Cell Division, Drosophila melanogaster, Embryonic Induction, Genes, Growth, Mathematics, Models, Genetic, Gene Expression, Neural Networks, Computer
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- Mjolsness, E., Sharp, D. H., & Reinitz, J. (1991). A connectionist model of development. Journal of Theoretical Biology. https://doi.org/10.1016/s0022-5193(05)80391-1
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
