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Cited by 434Developmental Biology and Gene RegulationGene Regulatory Network AnalysisPhilosophy of Biology and Scientific Explanation

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

Mjolsness, Eric, Sharp, David H., Reinitz, John·1991·Journal of Theoretical Biology
DOI 10.1016/s0022-5193(05)80391-1
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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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Citations

Cites

Show all 1 references

Research works printed but not linked: 20

  1. Akam, 1987, The molecular basis for metameric pattern in the Drosophila embryo, Development, 101, 1, 10.1242/dev.101.1.1 · DOI
  2. Baum, 1989, What size net gives valid generalization?, Vol. 1, 81
  3. Carroll, 1988, Expression, function, and regulation of the hairy segmentation protein in the Drosophila embryo, Genes and Development, 2, 883, 10.1101/gad.2.7.883 · DOI
  4. Carroll, 1986, Zygotically active genes that affect the spatial expression of the fushi tarazu segmentation gene during early Drosophila embryogenesis, Cell, 45, 113, 10.1016/0092-8674(86)90543-X · DOI
  5. Edgar, 1989, A genetic switch, based on negative regulation, sharpens stripes in Drosophila embryos, Dev. Gen., 10, 124, 10.1002/dvg.1020100303 · DOI
  6. Foe, 1983, Studies of nuclear and cytoplasmic behaviour during the five mitotic cycles that precede gastrulation in Drosophila embryogenesis, J. Cell Sci., 61, 31, 10.1242/jcs.61.1.31 · DOI
  7. Frasch, 1987, Complementary patterns of even-skipped and fushi tarazu expression involve their differential regulation by a common set of segmentation genes in Drosophila, Genes Dev., 1, 981, 10.1101/gad.1.9.981 · DOI
  8. Goodwin, 1990, Spatial harmonics and pattern specification in early Drosophila development. Bifurcation sequences and gene expression, J. theor. Biol., 144, 303, 10.1016/S0022-5193(05)80078-5 · DOI
  9. Ingham, 1988, The molecular genetics of embryonic pattern formation in Drosophila, Nature Lond., 335, 25, 10.1038/335025a0 · DOI
  10. Jackle, 1986, Cross-regulatory interactions among the gap genes of Drosophila, Nature, Lond., 324, 668, 10.1038/324668a0 · DOI
  11. Lacalli, 1988, Theoretical aspects of stripe formation in relation to Drosophila segmentation, Development, 104, 105, 10.1242/dev.104.1.105 · DOI
  12. Lindenmayer, 1986, Mathematical models for cellular interaction in development, parts I and II, J. theor. Biol., 18, 280, 10.1016/0022-5193(68)90079-9 · DOI
  13. Meinhardt, 1986, Hierarchical inductions of cell states: a model for segmentation in Drosophila, J. Cell Sci. (Suppl.), 4, 357, 10.1242/jcs.1986.Supplement_4.20 · DOI
  14. Mjolsness, 1989, Scaling, machine learning, and genetic neural nets, Advan. appl. Math., 10, 137, 10.1016/0196-8858(89)90008-0 · DOI
  15. Muller, 1932, Further studies on the nature and causes of gene mutations, Vol. 1, 213
  16. O'Farrell, 1989, Directing cell division during development, Science, 246, 635, 10.1126/science.2683080 · DOI
  17. Pankratz, 1989, Kruppel requirement for knirps enhancement reflects overlapping gap gene activities in the Drosophila embryo, Nature, Lond., 341, 337, 10.1038/341337a0 · DOI
  18. Pearmutter, 1989, Learning state space trajectories in recurrent neural networks, Neural Computation, 1, 263, 10.1162/neco.1989.1.2.263 · DOI
  19. Reinitz, 1990, Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila, Dev. Biol., 140, 57, 10.1016/0012-1606(90)90053-L · DOI
  20. Smith, 1987, A mesoderm-inducing factor is produced by a Xenopus cell line, Development, 99, 3, 10.1242/dev.99.1.3 · DOI

Cited by

Metadata

Authors
Mjolsness, E., Sharp, D. H., & Reinitz, J.
Affiliations
  • Yale University (US)
  • Los Alamos National Laboratory (US)
ORCID
Venue
Journal of Theoretical Biology
Publisher
Elsevier BV
Published
1991-10
Volume
152
Issue
4
Pages
429-453
ISSN
0022-5193 (ISSN-L)
DOI
10.1016/s0022-5193(05)80391-1
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
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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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