BioFNet: Biological functional network database for analysis and synthesis of biological systems

Briefings in Bioinformatics

Volumn 15, Issue 5, 2013, Pages 699-709

  Kurata, Hiroyuki ^a   Maeda, Kazuhiro ^a   Onaka, Toshikazu ^a   Takata, Takenori ^a  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Biological database; Functional network; Network motif; Rational design; Simulator

Indexed keywords

DATA BASE; THEORETICAL MODEL;

DATABASE MANAGEMENT SYSTEMS; MODELS, THEORETICAL;

EID: 84906947160     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbt048     Document Type: Article

References (65)

1. Ball P. Synthetic biology: designs for life. Nature 2007;448:32-3.
2. Drubin DA, Way JC, Silver PA. Designing biological systems. Genes Dev 2007;21:242-54.
3. Elowitz M, Lim WA. Build life to understand it. Nature 2010;468:889-90.
4. Kitano H. Systems biology: a brief overview. Science 2002; 295:1662-4.
5. Stelling J, Sauer U, Szallasi Z, et al. Robustness of cellular functions. Cell 2004;118:675-85.
6. Sneppen K, Krishna S, Semsey S. Simplified models of biological networks. AnnuRev Biophys 2010;39:43-59.
7. Li C, Courtot M, Le Novere N, et al. BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform 2010;11:270-7.
8. Milo R, Shen-Orr S, Itzkovitz S, et al. Network motifs:simple building blocks of complex networks. Science 2002; 298:824-7.
9. Alon U. Network motifs: theory and experimental approaches. Nat RevGenet 2007;8:450-61.
10. Kurata H, El-Samad H, Iwasaki R, et al. Module-based analysis of robustness tradeoffs in the heat shock response system. PLoSComput Biol 2006;2:e59.
11. Nishio Y, Usuda Y, Matsui K, et al. Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol Syst Biol 2008;4:160.
12. El-Samad H, Kurata H, Doyle JC, et al. Surviving heat shock: control strategies for robustness and performance. ProcNatl Acad SciUSA 2005;102:2736-41.
13. Shen-Orr SS, Milo R, Mangan S, et al. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002;31:64-8.
14. Fraser JS, Gross JD, Krogan NJ. From systems to structure:bridging networks and mechanism. Mol Cell 2013;49:222-31.
15. Lim WA, Lee CM, Tang C. Design principles of regulatory networks: searching for the molecular algorithms of the cell. Mol Cell 2013;49:202-12.
16. Tyson JJ, Chen KC, Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr OpinCell Biol 2003;15:221-31.
17. Tyson JJ, Novak B. Functional motifs in biochemical reaction networks. Annu Rev Phys Chem 2010;61:219-40.
18. Yeger-Lotem E, Sattath S, Kashtan N, et al. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA 2004;101:5934-9.
19. Ma W, Trusina A, El-Samad H, et al. Defining network topologies that can achieve biochemical adaptation. Cell 2009;138:760-73.
20. Cotterell J, Sharpe J. An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients. Mol Syst Biol 2010;6:425.
21. Prill RJ, Iglesias PA, Levchenko A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 2005;3:e343.
22. Cooling MT, Rouilly V, Misirli G, et al. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010;26:925-31.
23. Rodrigo G, Carrera J, Jaramillo A. Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors. Nucleic Acids Res 2011;39:e138.
24. Kurata H, Matoba N, Shimizu N. CADLIVE for constructing a large-scale biochemical network based on a simulation- directed notation and its application to yeast cell cycle. Nucleic Acids Res 2003;31:4071-84.
25. Kurata H, Masaki K, Sumida Y., et al. CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models. Genome Res 2005;15:590-600.
26. Siegal-Gaskins D, Mejia-Guerra MK, Smith GD, et al. Emergence of switch-like behavior in a large family of simple biochemical networks. PLoS Comput Biol 2011;7:e1002039.
27. Alon U, Camarena L, Surette MG, et al. Response regulator output in bacterial chemotaxis. EMBOJ 1998;17:4238-48.
28. Alon U, Surette MG, Barkai N, et al. Robustness in bacterial chemotaxis. Nature 1999;397:168-71.
29. Yi TM, Huang Y, Simon MI, et al. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci USA 2000;97:4649-53.
30. Qiao L, Nachbar RB, Kevrekidis IG, et al. Bistability and oscillations in the Huang-Ferrell model of MAPK signaling. PLoSComput Biol 2007;3:1819-26.
31. Shinar G, Milo R, Martinez MR, et al. Input output robustness in simple bacterial signaling systems. Proc Natl Acad Sci USA 2007;104:19931-5.
32. Guantes R, Poyatos JF. Dynamical principles of two-component genetic oscillators. PLoSComput Biol 2006;2:e30.
33. Eldar A, Rosin D, Shilo BZ, et al. Self-enhanced ligand degradation underlies robustness of morphogen gradients. Dev Cell 2003;5:635-46.
34. Eldar A, Shilo BZ, Barkai N. Elucidating mechanisms underlying robustness of morphogen gradients. Curr Opin Genet Dev 2004;14:435-9.
35. Ben-Zvi D, Barkai N. Scaling of morphogen gradients by an expansion-repression integral feedback control. ProcNatl Acad SciUSA 2010;107:6924-9.
36. White MA, Parker DS, Barolo S, et al. A model of spatially restricted transcription in opposing gradients of activators and repressors. Mol Syst Biol 2012;8:614.
37. Kohn KW. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell 1999;10:2703-34.
38. Kurata H, Inoue K, Maeda K, et al. Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res 2007;35:e134.
39. Kalir S, Mangan S, Alon U. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol 2005;1:2005.0006.
40. Shoval O, Goentoro L, Hart Y, et al. Fold-change detection and scalar symmetry of sensory input fields. ProcNatlAcadSci USA 2010;107:15995-6000.
41. Brandman O, Meyer T. Feedback loops shape cellular signals in space and time. Science 2008;322:390-5.
42. Krishna S, Semsey S, Sneppen K. Combinatorics of feedback in cellular uptake and metabolism of small molecules. ProcNatl Acad SciUSA 2007;104:20815-9.
43. Ferrell JEJr. Self-perpetuating states in signal transduction:positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 2002;14:140-8.
44. Craciun G, Tang Y, Feinberg M. Understanding bistability in complex enzyme-driven reaction networks. Proc Natl Acad SciUSA 2006;103:8697-702.
45. Ferrell JE Jr. Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses. Curr Biol 2008; 18:R244-5.
46. Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 2000;403:339-42.
47. Brandman O, Ferrell JEJr, Li R, et al. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 2005;310:496-8.
48. Eichenberger P, Fujita M, Jensen ST, et al. The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol 2004;2:e328.
49. Alon U. An introduction of systems biology: Design principles of biological circuits. London: Chapman & Hall/CRC Mathematical & Computational Biology, 2006.
50. Masaki K, Maeda K, Kurata H. Biological design principles of complex feedback modules in the E. coli ammonia assimilation system. Artif Life 2012;18:53-90.
51. Mitrophanov AY, Hadley TJ, Groisman EA. Positive autoregulation shapes response timing and intensity in twocomponent signal transduction systems. J Mol Biol 2010; 401:671-80.
52. Hsia J, Holtz WJ, Huang DC, et al. A feedback quenched oscillator produces turing patterning with one diffuser. PLoSComput Biol 2012;8:e1002331.
53. Lipshtat A, Jayaraman G, He JC, et al. Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues. Proc Natl Acad Sci USA 2010;107:1247-52.
54. Ozbudak EM, Thattai M, Kurtser I, et al. Regulation of noise in the expression of a single gene. Nat Genet 2002; 31:69-73.
55. Paszek P, Ryan S, Ashall L, et al. Population robustness arising from cellular heterogeneity. Proc Natl Acad Sci USA 2010;107:11644-9.
56. Hasty J, Pradines J, Dolnik M, et al. Noise-based switches and amplifiers for gene expression. Proc Natl Acad Sci USA 2000;97:2075-80.
57. Warmflash A, Adamson DN, Dinner AR. How noise statistics impact models of enzyme cycles. J Chem Phys 2008; 128:225101.
58. Samoilov M, Plyasunov S, Arkin AP. Stochastic amplification and signaling in enzymatic futile cycles through noiseinduced bistability with oscillations. Proc Natl Acad Sci USA 2005;102:2310-5.
59. Miller CA, Beard DA. The effects of reversibility and noise on stochastic phosphorylation cycles and cascades. BiophysJ 2008;95:2183-92.
60. Artyomov MN, Mathur M, Samoilov MS, et al. Stochastic bimodalities in deterministically monostable reversible chemical networks due to network topology reduction. JChemPhys 2009;131:195103.
61. Ochab-Marcinek A, Tabaka M. Bimodal gene expression in noncooperative regulatory systems. Proc Natl Acad Sci USA 2010;107:22096-101.
62. Maeda K, Fukano Y, Yamamichi S, et al. An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks. Bioprocess BiosystEng 2011;34:433-46.
63. Maeda K, Minamida H, Yoshida K, et al. Flux module decomposition for parameter estimation in a multiplefeedback loop model of biochemical networks. Bioprocess Biosyst Eng 2013;36:333-44.
64. Arkin A. Setting the standard in synthetic biology. Nat Biotechnol 2008;26:771-4.
65. Vilar JM, Kueh HY, Barkai N, et al. Mechanisms of noiseresistance in genetic oscillators. ProcNatlAcad SciUSA 2002; 99:5988-92.