Literature DB >> 17689240

Logic of gene regulatory networks.

Stefan C Materna1, Eric H Davidson.   

Abstract

Regulatory networks of transcription factors and signaling molecules lie at the heart of development. Their architecture implements logic functions whose execution propels cells from one regulatory state to the next, thus driving development forward. As an example of a subcircuit that translates transcriptional input into developmental output, we consider a particularly simple case, the regulatory processes underlying pigment cell formation in sea urchin embryos. The regulatory events in this process can be represented as elementary logic functions.

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Year:  2007        PMID: 17689240      PMCID: PMC2031216          DOI: 10.1016/j.copbio.2007.07.008

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  18 in total

1.  A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.

Authors:  Eric H Davidson; Jonathan P Rast; Paola Oliveri; Andrew Ransick; Cristina Calestani; Chiou-Hwa Yuh; Takuya Minokawa; Gabriele Amore; Veronica Hinman; César Arenas-Mena; Ochan Otim; C Titus Brown; Carolina B Livi; Pei Yun Lee; Roger Revilla; Maria J Schilstra; Peter J C Clarke; Alistair G Rust; Zhengjun Pan; Maria I Arnone; Lee Rowen; R Andrew Cameron; David R McClay; Leroy Hood; Hamid Bolouri
Journal:  Dev Biol       Date:  2002-06-01       Impact factor: 3.582

Review 2.  Notch signaling: control of cell communication and cell fate.

Authors:  Eric C Lai
Journal:  Development       Date:  2004-03       Impact factor: 6.868

Review 3.  Logic functions of the genomic cis-regulatory code.

Authors:  Sorin Istrail; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-23       Impact factor: 11.205

4.  LvGroucho and nuclear beta-catenin functionally compete for Tcf binding to influence activation of the endomesoderm gene regulatory network in the sea urchin embryo.

Authors:  Ryan C Range; Judith M Venuti; David R McClay
Journal:  Dev Biol       Date:  2005-03-01       Impact factor: 3.582

Review 5.  Genomic regulatory networks and animal development.

Authors:  Angelike Stathopoulos; Michael Levine
Journal:  Dev Cell       Date:  2005-10       Impact factor: 12.270

Review 6.  Computational representation of developmental genetic regulatory networks.

Authors:  William J R Longabaugh; Eric H Davidson; Hamid Bolouri
Journal:  Dev Biol       Date:  2005-07-01       Impact factor: 3.582

Review 7.  Gene regulation: gene control network in development.

Authors:  Smadar Ben-Tabou de-Leon; Eric H Davidson
Journal:  Annu Rev Biophys Biomol Struct       Date:  2007

8.  LvNotch signaling mediates secondary mesenchyme specification in the sea urchin embryo.

Authors:  D R Sherwood; D R McClay
Journal:  Development       Date:  1999-04       Impact factor: 6.868

Review 9.  Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms.

Authors:  E H Davidson; R A Cameron; A Ransick
Journal:  Development       Date:  1998-09       Impact factor: 6.868

10.  A fate map of the vegetal plate of the sea urchin (Lytechinus variegatus) mesenchyme blastula.

Authors:  S W Ruffins; C A Ettensohn
Journal:  Development       Date:  1996-01       Impact factor: 6.868

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  12 in total

Review 1.  Structure of developmental gene regulatory networks from the perspective of cell fate-determining genes.

Authors:  Mercedes Martín; María F Organista; Jose F de Celis
Journal:  Transcription       Date:  2016

2.  A synthetic genetic edge detection program.

Authors:  Jeffrey J Tabor; Howard M Salis; Zachary Booth Simpson; Aaron A Chevalier; Anselm Levskaya; Edward M Marcotte; Christopher A Voigt; Andrew D Ellington
Journal:  Cell       Date:  2009-06-26       Impact factor: 41.582

3.  Design specifications for cellular regulation.

Authors:  David C Krakauer; Lydia Müller; Sonja J Prohaska; Peter F Stadler
Journal:  Theory Biosci       Date:  2016-11-18       Impact factor: 1.919

4.  Single-cell transcriptomic signatures and gene regulatory networks modulated by Wls in mammalian midline facial formation and clefts.

Authors:  Ran Gu; Shuwen Zhang; Subbroto Kumar Saha; Yu Ji; Kurt Reynolds; Moira McMahon; Bo Sun; Mohammad Islam; Paul A Trainor; YiPing Chen; Ying Xu; Yang Chai; Diana Burkart-Waco; Chengji J Zhou
Journal:  Development       Date:  2022-07-22       Impact factor: 6.862

5.  The sea urchin genome as a window on function.

Authors:  Stefan C Materna; R Andrew Cameron
Journal:  Biol Bull       Date:  2008-06       Impact factor: 1.818

Review 6.  Geometric control of tissue morphogenesis.

Authors:  Celeste M Nelson
Journal:  Biochim Biophys Acta       Date:  2009-01-02

7.  Eric Davidson: Steps to a gene regulatory network for development.

Authors:  Ellen V Rothenberg
Journal:  Dev Biol       Date:  2016-01-26       Impact factor: 3.582

8.  Protein networks as logic functions in development and cancer.

Authors:  Janusz Dutkowski; Trey Ideker
Journal:  PLoS Comput Biol       Date:  2011-09-29       Impact factor: 4.475

9.  The Comet Cometh: Evolving Developmental Systems.

Authors:  Johannes Jaeger; Manfred Laubichler; Werner Callebaut
Journal:  Biol Theory       Date:  2015-02-17

10.  Gene expression and regulation of higher plants under soil water stress.

Authors:  Fu-Tai Ni; Li-Ye Chu; Hong-Bo Shao; Zeng-Hui Liu
Journal:  Curr Genomics       Date:  2009-06       Impact factor: 2.236

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