Stabilizing gene regulatory networks through feedforward loops

Chaos

Volumn 23, Issue 2, 2013, Pages

  Kadelka, C ^a,b   Murrugarra, D ^c   Laubenbacher, R ^a,b  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR;

ANIMAL; FEEDBACK SYSTEM; GENE REGULATORY NETWORK; GENETICS; METABOLISM; STATISTICS; ARTICLE;

ANIMALS; FEEDBACK, PHYSIOLOGICAL; GENE REGULATORY NETWORKS; MICRORNAS; STOCHASTIC PROCESSES; TRANSCRIPTION FACTORS;

EID: 84880345811     PISSN: 10541500     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4808248     Document Type: Article

References (28)

1. Waddington C.H. Canalisation of development and the inheritance of acquired characters. Nature 1942, 150:563-564. 10.1038/150563a0, ",".
2. Avigdor E. Elowitz M. Functional roles for noise in genetic circuits. Nature 2010, 467:167-173. 10.1038/nature09326, and ",".
3. Ambros V. The functions of animal microRNAs. Nature 2004, 431:350-355. 10.1038/nature02871, ",".
4. Bartel D. MicroRNAs: Target recognition and regulatory functions. Cell 2009, 136:215-233. 10.1016/j.cell.2009.01.002, ",".
5. Stark A. Brennecke J. Bushati N. Russell R. Cohen S. Animal microRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 2005, 123:1133-1146. 10.1016/j.cell.2005.11.023, and ",".
6. Hornstein E. Shomron N. Canalization of development by microRNAs. Nat. Genet. 2006, 38:S20-24. 10.1038/ng1803, and ",".
7. MacNeil L. Walhout A. Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res. 2011, 21:645-657. 10.1101/gr.097378.109, and ",".
8. Mangan S. Alon U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:11980-11985. 10.1073/pnas.2133841100, and ",".
9. von Dassow M. Davidson L. Physics and the canalization of morphogenesis: A grand challenge in organismal biology. Phys. Biol. 2011, 8:045002. 10.1088/1478-3975/8/4/045002, and "," (4).
10. Huang S. Tumor progression: Chance and necessity in Darwinian and Lamarckian somatic (mutationless) evolution. Prog. Biophys. Mol. Biol. 2012, 110:69-86. 10.1016/j.pbiomolbio.2012.05.001, ",".
11. Kaneko K. Characterization of stem cells and cancer cells on the basis of gene expression profile stability, plasticity, and robustness. Bioessays 2011, 33:403-413. 10.1002/bies.201000153, ",".
12. Capp J.-P. Stochastic gene expression is the driving force of cancer. Bioessays 2011, 33:781-782. 10.1002/bies.201100092, ",".
13. Laforge B. Guez D. Martinez M. Kupiec J. Modeling embryogenesis and cancer: An approach based on an equilibrium between autostabilization of stochastic gene expression and the interdependence of cells for proliferation. Prog. Biophys. Mol. Biol. 2005, 89:93-120. 10.1016/j.pbiomolbio.2004.11.004, and ",".
14. Kauffman S. Differentiation of malignant to benign cells. J. Theor. Biol. 1971, 31:429-451. 10.1016/0022-5193(71)90020-8, ",".
15. Bassler K. Lee C. Lee Y. Evolution of developmental canalization in networks of competing boolean nodes. Phys. Rev. Lett. 2004, 93:038101. 10.1103/PhysRevLett.93.038101, and "," (3).
16. Huerta-Sanchez E. Durrett R. Wagner's canalization model. Theor. Popul. Biol. 2007, 71:121-130. 10.1016/j.tpb.2006.10.006, and ",".
17. Jia T. Kulkarni R. Post-transcriptional regulation of noise in protein distributions during gene expression. Phys. Rev. Lett. 2010, 105:018101. 10.1103/PhysRevLett.105.018101, and "," (1).
18. Osella M. Bosia C. Cora D. Caselle M. The role of incoherent microrna-mediated feedforward loops in noise buffering. PLoS Comput. Biol. 2011, 7:e1001101. 10.1371/journal.pcbi.1001101, and "," (3).
19. Valencia-Sanchez M.A. Liu J. Hannon G.J. Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 2006, 20:515-524. 10.1101/gad.1399806, and ",".
20. Murrugarra D. Veliz-Cuba A. Aguilar B. Arat S. Laubenbacher R. Modeling stochasticity and variability in gene regulatory networks. EURASIP J. Bioinform. Syst. Biol. 2012, 2012:5. 10.1186/1687-4153-2012-5, and ",".
21. Albert I. Thakar J. Li S. Zhang R. Albert R. Boolean network simulations for life scientists. Source Code Biol. Med. 2008, 3:16. 10.1186/1751-0473-3-16, and ",".
22. Aldana M. Balleza E. Kauffman S. Resendiz O. Robustness and evolvability in genetic regulatory networks. J. Theor. Biol. 2007, 245:433-448. 10.1016/j.jtbi.2006.10.027, and ",".
23. Kim J. Inoue K. Ishii J. Vanti W.B. Voronov S.V. Murchison E. Hannon G. Abeliovich A. A MicroRNA feedback circuit in midbrain dopamine neurons. Science 2007, 317:1220-1224. 10.1126/science.1140481, and ",".
24. Derrida B. Weisbuch G. Evolution of overlaps between configurations in random boolean networks. J. Phys. 1986, 47:1297-1303. 10.1051/jphys:019860047080129700, and ",".
25. Kauffman S. Peterson C. Samuelsson B. Troein C. Random Boolean network models and the yeast transcriptional network. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:14796-14799. 10.1073/pnas.2036429100, and ",".
26. Shen-Orr S.S. Milo R. Mangan S. Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 2002, 31:64-68. 10.1038/ng881, and ",".
27. Milo R. Shen-Orr S. Itzkovitz S. Kashtan N. Chklovskii D. Alon U. Network motifs: Simple building blocks of complex networks. Science 2002, 298:824-827. 10.1126/science.298.5594.824, and ",".
28. Ishihara S. Fujimoto K. Shibata T. Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes Cells 2005, 10:1025-1038. 10.1111/j.1365-2443.2005.00897.x, and ",".