Introduction to Focus Issue: Quantitative Approaches to Genetic Networks

Chaos

Volumn 23, Issue 2, 2013, Pages

  Albert, Réka ^a   Collins, James J ^b   Glass, Leon ^c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b BOSTON UNIVERSITY   (United States)

^c MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; NONLINEAR SYSTEM; EDITORIAL;

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; MODELS, GENETIC; NONLINEAR DYNAMICS;

EID: 84880351136     PISSN: 10541500     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4810923     Document Type: Article

References (111)

1. Monod J. Jacob F. General conclusions: Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harbor Symp. Quantum Biol. 1961, 26:389-401. 10.1101/SQB.1961.026.01.048, and ",".
2. Hartwell L.H. Hopfield J.J. Leibler S. Murray A.W. From molecular to modular cell biology. Nature 1999, 402:C47-C52. 10.1038/35011540, and ",".
3. Gerstein M.B. Kundaje A. Hariharan M. Landt S.G. Yan K.-K. Cheng C. Mu X.J. Khurana E. Rozowsky J. Alexander R. Architecture of the human regulatory network derived from ENCODE data. Nature 2012, 489:91-100. 10.1038/nature11245, ",".
4. Sugita M. The idea of a molecular automaton. J. Theor. Biol. 1963, 4:179-192. 10.1016/0022-5193(63)90027-4, ",".
5. Thomas R. Boolean formalization of genetic control circuits. J. Theor. Biol. 1973, 42:563-585. 10.1016/0022-5193(73)90247-6, ",".
6. Thomas R. Logical analysis of systems comprising feedback loops. J. Theor. Biol. 1978, 73:631-656. 10.1016/0022-5193(78)90127-3, ",".
7. Kauffman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 1969, 22:437-467. 10.1016/0022-5193(69)90015-0, ",".
8. Glass L. Kauffman S.A. The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol. 1973, 39:103-129. 10.1016/0022-5193(73)90208-7, and ",".
9. De Jong H. Modeling and simulation of genetic regulatory systems: A literature review. J. Comp. Biol. 2002, 9:67-103. 10.1089/10665270252833208, ",".
10. Wang R.-S. Saadatpour A. Albert R. Boolean modeling in systems biology: An overview of methodology and applications. Phys. Biol. 2012, 9:055001. 10.1088/1478-3975/9/5/055001, and ",".
11. Elowitz M.B. Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338. 10.1038/35002125, and ",".
12. Gardner T.S. Cantor C.R. Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342. 10.1038/35002131, and ",".
13. Newman M. Networks: An Introduction 2009, (Oxford University Press, New York, ).
14. Watts D.J. Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442. 10.1038/30918, and ",".
15. Barabási A.-L. Albert R. Emergence of scaling in random networks. Science 1999, 286:509-512. 10.1126/science.286.5439.509, and ",".
16. Thieffry D. Huerta A.M. Pérez-Rueda E. Collado-Vides J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 1998, 20:433-440. 10.1002/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3.0.CO;2-2, and ",".
17. Ravasi T. Suzuki H. Cannistraci C.V. Katayama S. Bajic V.B. Tan K. Akalin A. Schmeier S. Kanamori-Katayama M. Bertin N. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 2010, 140:744-752. 10.1016/j.cell.2010.01.044, ",".
18. Giot L. Bader J.S. Brouwer C. Chaudhuri A. Kuang B. Li Y. Hao Y.L. Ooi C.E. Godwin B. Vitols E. A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736. 10.1126/science.1090289, ",".
19. Yook S.-H. Oltvai Z.N. Barabási A.-L. Functional and topological characterization of protein interaction networks. Proteomics 2004, 4:928-942. 10.1002/pmic.200300636, and ",".
20. Maayan A. Blitzer R.D. Iyengar R. Toward predictive models of mammalian cells. Annu. Rev. Biophys. Biomol. Struct. 2005, 34:319-349. 10.1146/annurev.biophys.34.040204.144415, and ",".
21. Guelzim N. Bottani S. Bourgine P. Képès F. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 2002, 31:60-63. 10.1038/ng873, and ",".
22. Lee T.I. Rinaldi N.J. Robert F. Odom D.T. Bar-Joseph Z. Gerber G.K. Hannett N.M. Harbison C.T. Thompson C.M. Simon I. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804. 10.1126/science.1075090, ",".
23. Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits 2007, (Chapman and Hall, London, ).
24. 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 ",".
25. Balazsi G. Barabási A.-L. Oltvai Z.N. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:7841-7846. 10.1073/pnas.0500365102, and ",".
26. Wuchty S. Oltvai Z.N. Barabási A.-L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 2003, 35:176-179. 10.1038/ng1242, and ",".
27. Prill R.J. Iglesias P.A. Levchenko A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol. 2005, 3:e343. 10.1371/journal.pbio.0030343, and ",".
28. Phenix H. Perkins T. Kaern M. Identifiability and inference of pathway motifs by epistasis analysis. Chaos 2013, 23:025103. 10.1063/1.4807483, and ",".
29. Kadelka C. Murrugarra D. Laubenbacher R. Stabilizing gene regulatory networks through feed-forward loops. Chaos 2013, 23:025107. 10.1063/1.4808248, and ",".
30. Kauffman S.A. The Origins of Order: Self-Organization and Selection in Evolution 1993, (Oxford University Press, New York, ).
31. Samuelsson B. Troein C. Superpolynomial growth in the number of attractors in Kauffman networks. Phys. Rev. Lett. 2003, 90:098701. 10.1103/PhysRevLett.90.098701, and ",".
32. Derrida B. Pomeau Y. Random networks of automata: A simple annealed approximation. Europhys. Lett. 1986, 1:45-49. 10.1209/0295-5075/1/2/001, and ",".
33. Bastolla U. Parisi G. The modular structure of Kauffman networks. Physica D 1998, 115:219-233. 10.1016/S0167-2789(97)00242-X, and ",".
34. Aldana M. Coppersmith S. Kadanoff L.P. Boolean dynamics with random couplings. Perspectives and Problems in Nonlinear Science 2003, 23-89. and "," in (Springer, New York, )
35. Socolar J.E. S. Kauffman S.A. Scaling in ordered and critical random Boolean networks. Phys. Rev. Lett. 2003, 90:068702. 10.1103/PhysRevLett.90.068702, and ",".
36. Drossel B. Greil F. Critical Boolean networks with scale-free in-degree distribution. Phys. Rev. E: Stat. Nonlinear Soft Matter Phys. 2009, 80:026102. 10.1103/PhysRevE.80.026102, and ",".
37. Ghil M. Mullhaupt A. Boolean delay equations. II. Periodic and aperiodic solutions. J. Stat. Phys. 1985, 41:125-173. 10.1007/BF01020607, and ",".
38. Zhang R. Cavalcante H.L. D. Gao Z. Gauthier D.J. Socolar J.E. S. Adams M.M. Lathrop D.P. Boolean chaos. Phys. Rev. E: Stat. Nonlinear Soft Matter Phys. 2009, 80:045202. 10.1103/PhysRevE.80.045202, and ",".
39. Sun M. Cheng X. Socolar J.E. S. Causal structure of oscillations in gene regulatory networks: Boolean analysis of ODE attractors. Chaos 2013, 23:025104. 10.1063/1.4807733, and ",".
40. Rosin D.P. Rontani D. Gauthier D.J. Schöll E. Experiments on autonomous Boolean networks. Chaos 2013, 23:025102. 10.1063/1.4807481, and ",".
41. Glass L. Classification of biological networks by their qualitative dynamics. J. Theor. Biol. 1975, 54:85-107. 10.1016/S0022-5193(75)80056-7, ",".
42. Thomas R. Regulatory networks seen as asynchronous automata: A logical description. J. Theor. Biol. 1991, 153:1-23. 10.1016/S0022-5193(05)80350-9, ",".
43. Thomas R. On the relation between the logical structure of systems and their ability to generate multiple steady states or sustained oscillations. Numerical Methods in the Study of Critical Phenomena 1981, 180-193. "," in (Springer, New York, )
44. Thomas R. Thieffry D. Kaufman M. Dynamical behaviour of biological regulatory networks. I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Math. Biol. 1995, 57:247-276. and ",".
45. Snoussi E.H. Necessary conditions for multistationarity and stable periodicity. J. Biol. Syst. 1998, 6:3-9. 10.1142/S0218339098000042, ",".
46. Soulé C. Graphic requirements for multistationarity. ComPlexUs 2004, 1:123-133. ",".
47. Remy E. Ruet P. Thieffry D. Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Adv. Appl. Math. 2008, 41:335-350. 10.1016/j.aam.2007.11.003, and ",".
48. Zañudo J.G. T. Albert R. An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks. Chaos 2013, 23:025111. 10.1063/1.4809777, and ",".
49. Keister W. Ritchie A.E. Washburn S.H. The Design of Switching Circuits 1951, and (Van Nostrand, New York, ).
50. Edwards R. Farcot E. Foxall E. Explicit construction of chaotic attractors in Glass networks. Chaos, Solitons Fractals 2012, 45:666-680. 10.1016/j.chaos.2012.02.018, and ",".
51. Edwards R. Glass L. Combinatorial explosion in model gene networks. Chaos 2000, 10:691-704. 10.1063/1.1286997, and ",".
52. Bérenguier D. Chaouiya C. Monteiro P. T. Naldi A. Remy E. Thieffry D. Tichit L. Dynamical modeling and analysis of large cellular regulatory networks. Chaos 2013, 23:025114. 10.1063/1.4809783, and ",".
53. Chaves M. Albert R. Sontag E.D. Robustness and fragility of Boolean models for genetic regulatory networks. J. Theor. Biol. 2005, 235:431-449. 10.1016/j.jtbi.2005.01.023, and ",".
54. Edwards R. Siegelmann H.T. Aziza K. Glass L. Symbolic dynamics and computation in model gene networks. Chaos 2001, 11:160-169. 10.1063/1.1336498, and ",".
55. Farcot E. Geometric properties of a class of piecewise affine biological network models. J. Math. Biol. 2006, 52:373-418. 10.1007/s00285-005-0360-4, ",".
56. Glass L. Pasternack J.S. Stable oscillations in mathematical models of biological control systems. J. Math. Biol. 1978, 6:207-223. 10.1007/BF02547797, and ",".
57. Perkins T.J. Hallett M. Glass L. Inferring models of gene expression dynamics. J. Theor. Biol. 2004, 230:289-299. 10.1016/j.jtbi.2004.05.022, and ",".
58. Glass L. Pasternack J.S. Prediction of limit cycles in mathematical models of biological oscillations. Bull. Math. Biol. 1978, 40:27-44. and ",".
59. Mestl T. Plahte E. Omholt S.W. Periodic solutions in systems of piecewise-linear differential equations. Dyn. Syst. 1995, 10:179-193. 10.1080/02681119508806202, and ",".
60. Edwards R. Analysis of continuous-time switching networks. Physica D 2000, 146:165-199. 10.1016/S0167-2789(00)00130-5, ",".
61. Farcot E. Gouzé J.-L. Limit cycles in piecewise-affine gene network models with multiple interaction loops. Int. J. Control 2010, 41:119-130. and ",".
62. Mestl T. Lemay C. Glass L. Chaos in high-dimensional neural and gene networks. Physica D 1996, 98:33-52. 10.1016/0167-2789(96)00086-3, and ",".
63. Edwards R. Chaos in neural and gene networks with hard switching. Diff. Eq. Dyn. Syst. 2001, 9:187-220. ",".
64. Glass L. Hill C. Ordered and disordered dynamics in random networks. Europhys. Lett. 1998, 41:599-604. 10.1209/epl/i1998-00199-0, and ",".
65. Plahte E. Kjøglum S. Analysis and generic properties of gene regulatory networks with graded response functions. Physica D 2005, 201:150-176. 10.1016/j.physd.2004.11.014, and ",".
66. Filippov A.F. Differential Equation with Discontinuous Right-Hand Sides 1998, (Nauka, Moscow, ); English translation (Kluwer, Dordecht, ).
67. Bernardo M. Budd C. Champneys A.R. Kowalczyk P. Piecewise-Smooth Dynamical Systems: Theory and Applications. Applied Mathematical Sciences 2007, 163. and Vol. (Springer, New York, ).
68. Casey R. De Jong H. Gouzé J.-L. Piecewise-linear models of genetic regulatory networks: Equilibria and their stability. J. Math. Biol. 2006, 52:27-56. 10.1007/s00285-005-0338-2, and ",".
69. Plahte E. Mestl T. Omholt S.W. A methodological basis for description and analysis of systems with complex switch-like interactions. J. Math. Biol. 1998, 36:321-348. 10.1007/s002850050103, and ",".
70. Ironi L. Panzeri L. Plahte E. Simoncini V. Dynamics of actively regulated gene networks. Physica D 2011, 240:779-794. 10.1016/j.physd.2010.12.010, and ",".
71. Machina A. Edwards R. van den Driessche P. Sensitive dependence on initial conditions in gene networks. Chaos 2013, 23:025101. 10.1063/1.4807480, and ",".
72. de Jong H. Geiselmann J. Hernandez C. Page M. Genetic network analyzer: Qualitative simulation of genetic regulatory networks. Bioinformatics 2003, 19:336-344. 10.1093/bioinformatics/btf851, and ",".
73. Chaouiya C. Remy E. Mossé B. Thieffry D. Qualitative analysis of regulatory graphs: A computational tool based on a discrete formal framework. Positive Systems 2003, 119-126. and "," in (Springer, Rome, )
74. Chaves M. Preto M. Hierarchy of models: From qualitative to quantitative analysis of circadian rhythms in cyanobacteria. Chaos 2013, 23:025113. 10.1063/1.4810922, and ",".
75. Robinson-Mosher A. Shinar T. Silver P. Way J. Dynamics simulations for engineering macromolecular interactions. Chaos 2013, 23:025110. 10.1063/1.4810915, and ",".
76. Thieffry D. Thomas R. Dynamical behaviour of biological regulatory networks. II. Immunity control in bacteriophage lambda. Bull. Math. Biol. 1995, 57:277-297. and ",".
77. Mendoza L. Alvarez-Buylla E.R. Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis. J. Theor. Biol. 1998, 193:307-319. 10.1006/jtbi.1998.0701, and ",".
78. Yuh C.-H. Bolouri H. Davidson E.H. Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science 1998, 279:1896-1902. 10.1126/science.279.5358.1896, and ",".
79. Istrail S. Davidson E.H. Logic functions of the genomic cis-regulatory code. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:4954-4959. 10.1073/pnas.0409624102, and ",".
80. Meinhardt H. Hierarchical inductions of cell states: A model for segmentation in Drosophila. J. Cell Sci. 1986, 4:357-381. ",".
81. Von Dassow G. Meir E. Munro E.M. Odell G.M. The segment polarity network is a robust developmental module. Nature 2000, 406:188-192. 10.1038/35018085, and ",".
82. Sanchez L. Thieffry D. A logical analysis of the Drosophila gap-gene system. J. Theor. Biol. 2001, 211:115-141. 10.1006/jtbi.2001.2335, and ",".
83. Albert R. Othmer H.G. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol. 2003, 223:1-18. 10.1016/S0022-5193(03)00035-3, and ",".
84. Sánchez L. Chaouiya C. Thieffry D. Segmenting the fly embryo: Logical analysis of the role of the segment polarity cross-regulatory module. Int. J. Dev. Biol. 2008, 52:1059-1075. 10.1387/ijdb.072439ls, and ",".
85. Mjolsness E. Sharp D.H. Reinitz J. A connectionist model of development. J. Theor. Biol. 1991, 152:429-453. 10.1016/S0022-5193(05)80391-1, and ",".
86. Janssens H. Hou S. Jaeger J. Kim A.-R. Myasnikova E. Sharp D. Reinitz J. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat. Genet. 2006, 38:1159-1165. 10.1038/ng1886, and ",".
87. Perkins T.J. Jaeger J. Reinitz J. Glass L. Reverse engineering the gap gene network of Drosophila melanogaster. PLOS Comput. Biol. 2006, 2:e51. 10.1371/journal.pcbi.0020051, and ",".
88. Kim Y. Iagovitina A. Ishihara K. Fitzgerald K.M. Deplancke B. Papatsenko D. Shvartsman S.Y. Context-dependent transcriptional interpretation of MAPK signaling in the Drosophila embryo. Chaos 2013, 23:025105. 10.1063/1.4808157, and ",".
89. Khalil A.S. Collins J.J. Synthetic biology: Applications come of age. Nat. Rev. Genet. 2010, 11:367-379. 10.1038/nrg2775, and ",".
90. Cheng A.A. Lu T.K. Synthetic biology: An emerging engineering discipline. Annu. Rev. Biomed. Eng. 2012, 14:155-178. 10.1146/annurev-bioeng-071811-150118, and ",".
91. Slusarczyk A.L. Lin A. Weiss R. Foundations for the design and implementation of synthetic genetic circuits. Nat. Rev. Genet. 2012, 13:406-420. 10.1038/nrg3227, and ",".
92. Becskei A. Serrano L. Engineering stability in gene networks by autoregulation. Nature 2000, 405:590-593. 10.1038/35014651, and ",".
93. Stricker J. Cookson S. Bennett M.R. Mather W.H. Tsimring L.S. Hasty J. A fast, robust and tunable synthetic gene oscillator. Nature 2008, 456:516-519. 10.1038/nature07389, and ",".
94. Tigges M. Marquez-Lago T.T. Stelling J. Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009, 457:309-312. 10.1038/nature07616, and ",".
95. Deans T.L. Cantor C.R. Collins J.J. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 2007, 130:363-372. 10.1016/j.cell.2007.05.045, and ",".
96. Tabor J.J. Salis H. Simpson Z.B. Chevalier A.A. Levskaya A. Marcotte E.M. Voigt C.A. Ellington A.D. A synthetic genetic edge detection program. Cell 2009, 137:1272-1281. 10.1016/j.cell.2009.04.048, and ",".
97. Friedland A.E. Lu T.K. Wang X. Shi D. Church G. Collins J.J. Synthetic gene networks that count. Science 2009, 324:1199-1202. 10.1126/science.1172005, and ",".
98. Burrill D.R. Inniss M.C. Boyle P.M. Silver P.A. Synthetic memory circuits for tracking human cell fate. Genes Dev. 2012, 26:1486-1497. 10.1101/gad.189035.112, and ",".
99. Kim J. White K.S. Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2006, 2:68. 10.1038/msb4100099, and ",".
100. Kim J. Winfree E. Synthetic in vitro transcriptional oscillators. Mol. Syst. Biol. 2011, 7:468. and ",".
101. Ellis T. Wang X. Collins J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol. 2009, 27:465-471. 10.1038/nbt.1536, and ",".
102. Moon T.S. Lou C. Tamsir A. Stanton B.C. Voigt C.A. Genetic programs constructed from layered logic gates in single cells. Nature 2012, 491:249-253. 10.1038/nature11516, and ",".
103. Lu T.K. Khalil A.S. Collins J.J. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27:1139-1150. 10.1038/nbt.1591, and ",".
104. Khalil A.S. Lu T.K. Bashor C.J. Ramirez C.L. Pyenson N.C. Joung J.K. Collins J.J. A synthetic biology framework for programming eukaryotic transcription functions. Cell 2012, 150:647-658. 10.1016/j.cell.2012.05.045, and ",".
105. Purcell O. Jain B. Karr J. Lu T. Towards a whole-cell modeling approach for synthetic biology. Chaos 2013, 23:025112. 10.1063/1.4811182, and ",".
106. Mettetal J.T. Muzzey D. Gómez-Uribe C. van Oudenaarden A. The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Sci. 2008, 319:482-484. 10.1126/science.1151582, and ",".
107. Fiore G. Menolascina F. di Bernardo M. di Bernardo D. An experimental approach to identify dynamical models of transcriptional regulation in living cells. Chaos 2013, 23:025106. 10.1063/1.4808247, and ",".
108. Mondragón-Palomino O. Danino T. Selimkhanov J. Tsimring L. Hasty J. Entrainment of a population of synthetic genetic oscillators. Science 2011, 333:1315-1319. 10.1126/science.1205369, and ",".
109. Rodrigo G. Kirov B. Shen S. Jaramillo A. Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model. Chaos 2013, 23:025109. 10.1063/1.4809786, and ",".
110. Lomnitz J.G. Savageau M.A. Analysis of synthetic genetic circuitry in system design space. Chaos 2013, 23:025108. 10.1063/1.4809776, and ",".
111. Wilds R. Kauffman S.A. Glass L. Evolution of complex dynamics. Chaos 2008, 18:033109. 10.1063/1.2962223, and ",".