Monte carlo analysis of an ode model of the sea urchin endomesoderm network

BMC Systems Biology

Volumn 3, Issue , 2009, Pages 83-

  Kühn, Clemens ^a,b   Wierling, Christoph ^a   Kühn, Alexander ^a   Klipp, Edda ^b   Panopoulou, Georgia ^a   Lehrach, Hans ^a   Poustka, Albert J ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ECHINOIDEA;

ANIMAL; ARTICLE; COMPUTER SIMULATION; GENE REGULATORY NETWORK; GENETICS; KINETICS; MESODERM; METABOLISM; MONTE CARLO METHOD; PRENATAL DEVELOPMENT; REPRODUCIBILITY; SEA URCHIN;

ANIMALS; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; KINETICS; MESODERM; MONTE CARLO METHOD; REPRODUCIBILITY OF RESULTS; SEA URCHINS;

EID: 70349574614     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-83     Document Type: Article

References (34)

1. Ideker T, Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol 2003, 21(6):255-262.
2. Davidson EH. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Developmental Biology 2002, 246:162-190.
3. Davidson E. Gene activity in early development 1986, Academic Press New York, 3.
4. Endomesoderm and Ectoderm Models. , http://sugp.caltech.edu/endomes/
5. Howard E, Newman L, Oleksyn D, Angerer R, Angerer L. SpKrl: a direct target of β-catenin regulation required for endoderm differentiation in sea urchin embryos. Development 2001, 128:365-375.
6. Smith J. A protocol describing the principles of cis-regulatory analysis in the sea urchin. Nat Protoc 2008, 3(4):710-718.
7. Livi CB, Davidson EH. Expression ad function of blimp1/krox, an alternatively transcribed regulatory gene of the sea urchin edomesoderm network. Developmental Biology 2006, 293:513-525.
8. Yuh CH, Dorman ER, Davidson EH. Brn1/2/4, the predicted midgut regulator of the endo16 gene of the sea urchin embryo. Developmental Biology 2005, 281:286-298.
9. Oliveri P, Walton KD, Davidson EH, McClay DR. Repression of mesodermal fate by FoxA, a key endoderm regulator of the sea urchin embryo. Development 2006, 133:4173-4181.
10. Lee PY, Davidson EH. Expression of SpGataE, the Strongylocentrotus purpuratus ortholog of vertebrate GATA4/5/6 factors. Gene Expression Patterns 2004, 5:161-165.
11. Howard-Ashby M, Materna SC, Brown CT, Chen L, Cameron RA, Davidson EH. Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and theor expression in embryonic development. Developmental Biology 2006, 300:74-89.
12. Oliveri P, Carrick DM, Davidson EH. A regulatory Gene Network that directs micromere specification in the sea urchin embryo. Developmental Biology 2002, 246:209-228.
13. Li X, Chuang CK, Mao CA, Angerer LM, Klein WH. Two Otx proteins generated from multiple transcripts of a single gene in strongylocentrotus purpuratus. Developmental Biology 1997, 187:253-266.
14. Wikramanayake AH, Peterson R, Chen J, Huanf L, Bince JM, McClay DR, Klein WH. Nuclear β-catenin dependent Wnt8 signaling in vegetal cells of the early sea urchin embryo regulates gastrulation and differentiation of endoderm and mesoderma cell lineages. Genesis 2004, 39:194-205.
15. Nijhout HF. The nature of robustness in development. BioEssays 2002, 24:553-563.
16. Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 2006, (34 Database):D689. 1347454, 16381960.
17. Karlebach G, Shamir R. Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 2008, 9(10):770-780.
18. Kühn C, Kühn A, Poustka AJ, Klipp E. Modeling development: spikes of the sea urchin. Genome Inform 2007, 18:75-84.
19. Joachimczak M, Wróbel B. Evo-devo in silico: a model of a gene network regulating multicellular development in 3D space with artificial physics. Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems 2008, 297-304. MIT Press, Cambridge, MA, Bullock S, Noble J, Watson R, Bedau MA.
20. Walker D, Wood S, Southgate J, Holcombe M, Smallwood R. An integrated agent-mathematical model of the effect of intercellular signalling via the epidermal growth factor receptor on cell proliferation. J Theor Biol 2006, 242(3):774-789.
21. Bolouri H, Davidson E. The gene regulatory network basis of the "community effect", and analysis of a sea urchin embryo example. Dev Biol 2009,
22. Yuh C, Bolouri H, Davidson E. Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control. Development 2001, 128(5):617-629.
23. Longabaugh W, Davidson E, Bolouri H. Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. BBA-Gene Regulatory Mechanisms 2009, 1789(4):363-374.
24. QPCR Data Relevant to Endomesoderm Network. , http://sugp.caltech.edu/endomes/qpcr.html
25. Revilla-i-Domingo R, Oliveri P, Davidson EH. A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres. Proc Natl Acad Sci USA 2007, 104(30):12383-12388. 1941478, 17636127.
26. Oliveri P, Tu Q, Davidson EH. Global regulatory logic for specification of an embryonic cell lineage. Proc Natl Acad Sci USA 2008, 105(16):5955-5962. 2329687, 18413610.
27. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U. Superfamilies of evolved and designed networks. Science 2004, 303(5663):1538-1542.
28. Stelling J, Sauer U, Szallasi Z, Doyle FJ, Doyle J. Robustness of cellular functions. Cell 2004, 118:675-685.
29. de Leon SBT, Davidson EH. Modeling the dynamics of transcriptional gene regulatory networks for animal development. Dev Biol 2009, 325(2):317-328.
30. Kim HD, O'Shea EK. A quantitative model of transcription factor-activated gene expression. Nat Struct Mol Biol 2008, 15(11):1192-1198. 2696132, 18849996.
31. Schilstra MJ, Bolouri H. The logic of gene regulation. 3rd Int Conf on Systems Biology 2002,
32. The NetBuilder Homepage. , http://strc.herts.ac.uk/bio/maria/NetBuilder
33. Klipp E, Herwig R, Kowald A, Wierling C, Lehrach H. Systems Biology in Practice 2005, Weinheim: Wiley-VCH.
34. Wierling C, Herwig R, Lehrach H. Resources, standards and tools for systems biology. Brief Funct Genomic Proteomic 2007, elm027., http://bfgp.oxfordjournals.org/cgi/content/abstract/elm027v1