NetExplore: A web server for modeling small network motifs

Bioinformatics

Volumn 31, Issue 11, 2015, Pages 1860-1862

  Papatsenko, Dmitri ^a   Lemischka, Ihor R ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; GENE REGULATORY NETWORK; INTERNET; SOFTWARE;

ALGORITHMS; GENE REGULATORY NETWORKS; INTERNET; MODELS, GENETIC; SOFTWARE;

EID: 84941712501     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv058     Document Type: Conference Paper

References (17)

1. Berg, O. G. and von Hippel, P. H. (1988) Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol. , 200, 709-723.
2. Bintu, L. et al. (2005) Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. , 15, 116-124.
3. Goentoro, L. et al. (2009) The incoherent feedforward loop can provide foldchange detection in gene regulation. Mol Cell. , 36, 894-899.
4. Heinaniemi, M. et al. (2013) Gene-pair expression signatures reveal lineage control. Nat. Methods, 10, 577-583.
5. Ivanova, N. et al. (2006) Dissecting self-renewal in stem cells with RNA interference. Nature, 442, 533-538.
6. Janssens, H. et al. (2006). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet. , 38, 1159-1165.
7. Lu, R. et al. (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature, 462, 358-362.
8. Mangan, S. and Alon, U. (2003) Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA, 100, 11980-11985.
9. Milo, R. et al. (2002) Network motifs: simple building blocks of complex networks. Science. 298, 824-827.
10. Papatsenko, D. and Levine, M. (2011) The Drosophila gap gene network is composed of two parallel toggle switches. PLoS 6, e21145.
11. Papatsenko, D. et al. (2011) Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS 9, e1000584.
12. Papatsenko, D. et al. (2013). Quantitative Approaches to Model Pluripotency and Differentiation in Stem Cells. In: Sell, S. (ed.) Stem Cell Handbook. Springer Science, New York, pp. 59-74.
13. Shen, Y. et al. (2012) A map of the cis-regulatory sequences in the mouse genome. Nature, 488, 116-120.
14. Stricker, J. et al. (2008). A fast, robust and tunable synthetic gene oscillator. Nature, 456, 516-519.
15. Warmflash, A. et al. (2012) Pareto evolution of gene networks: An algorithm to optimize multiple fitness objectives. Phys. Biol. 9, 1478-3975.
16. Zinzen, R. P. and Papatsenko, D. (2007) Enhancer responses to similarly distributed antagonistic gradients in development. PLoS Comput. Biol. , 3, e84.
17. Zinzen, R. P. et al. (2006) Computational models for neurogenic gene expression in the Drosophila embryo. Curr. Biol. 16, 1358-1365.