"Antelope": A hybrid-logic model checker for branching-time Boolean GRN analysis

BMC Bioinformatics

Volumn 12, Issue 1, 2011, Pages

  Arellano, Gustavo ^d   Argil, Julián ^d   Azpeitia, Eugenio ^a,b   Benítez, Mariana ^a,c   Carrillo, Miguel ^d   Góngora, Pedro ^d   Rosenblueth, David A ^a,d   Alvarez Buylla, Elena R ^a,b  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b INSTITUTO DE ECOLOGÍA   (Mexico)

^c MASARYK UNIVERSITY   (Czech Republic)

^d Ciudad Universitaria   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA; BRANCHING TIME; DIRECT APPROACH; GENE REGULATORY NETWORKS; INCOMPLETE NETWORKS; POSSIBLE FUTURES; SOFTWARE SYSTEMS; USEFULNESS OF MODELS;

STEM CELLS;

MODEL CHECKING;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ANIMAL; ARABIDOPSIS; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; CYTOLOGY; GENE REGULATORY NETWORK; HUMAN; LOGIC; METABOLISM;

ANIMALS; ARABIDOPSIS; GENE REGULATORY NETWORKS; HUMANS; LOGIC; MODELS, GENETIC; SOFTWARE;

EID: 84055213967     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-490     Document Type: Article

References (76)

1. von Dassow G, Meir E, Munro E, Odell G. The segment polarity network is a robust developmental module. Nature 2000, 406:188-192. 10.1038/35018085, 10910359.
2. Espinosa-Soto C, Padilla-Longoria P, Alvarez-Buylla E. A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. The Plant Cell 2004, 16:2923-2939. 10.1105/tpc.104.021725, 527189, 15486106.
3. Li S, Assmann SM, Albert R. Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biology 2006, 4(10):1732-1748.
4. Albert R. Boolean modeling of genetic regulatory networks. Complex Networks 2004, 459-481. Springer, Ben-Naim E, Frauenfelder H, Toroczkai Z, [Lecture Notes in Physics Vol. 650].
5. de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. Journal of Computational Biology 2002, 9:67-103. 10.1089/10665270252833208, 11911796.
6. Fisher J, Henzinger TA. Executable cell biology. Nature Biotechnology 2007, 25(11):1239-1249. 10.1038/nbt1356, 17989686.
7. Bornholdt S. Boolean network models of cellular regulation: prospects and limitations. J R Soc Interface 2008, 5:S85-S94. 10.1098/rsif.2008.0132.focus, 2386560, 18508746.
8. Albert R, Othmer HG. 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, 12782112.
9. Alvarez-Buylla ER, Benítez M, Corvera-Poiré A, Candor AC, de Folter S, de Buen AG, Garay-Arroyo A, García-Ponce B, Jaimes-Miranda F, Pérez-Ruiz RV, Pineiro-Nelson A, Sánchez-Corrales YE. Flower development. The Arabidopsis Book 2010, 8:e0999. [Doi:10.1199/tab.0999].
10. Fauré A, Naldi A, Chaouiya C, Thieffry D. Dynamical analysis of a genetic Boolean model for the control of the mammalian cell cycle. Bioinformatics 2006, 22(14):e124-e131. 10.1093/bioinformatics/btl210, 16873462.
11. Li F, Long T, Lu Y, Ouyang Q, Tang C. The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA 2004, 101(14):4781-4786. 10.1073/pnas.0305937101, 387325, 15037758.
12. Davidich MI, Bornholdt S. Boolean network model predicts cell cycle sequence of fission yeast. PLoS One 2008, 3(2):e1672. [Doi:10.1371/journal.pone.0001672], 10.1371/journal.pone.0001672, 2243020, 18301750.
13. Thomas R, D'Ari R. Biological Feedback 1990, CRC Press.
14. Thomas R. Regulatory networks seen as asynchronous automata. J Theor Biol 1991, 1-23.
15. 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(2):247-276.
16. Albert I, Thakar J, Li S, Zhang R, Albert R. Boolean networks simulations for life scientists. Source Code Biol Med 2008, 3(16). [Doi: 10.1186/1751-0473-3-16].
17. Müssel C, Hopfensitz M, Kestler HA. BoolNet--an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 2010, 26(10):1378-1380. [Applications Note], 10.1093/bioinformatics/btq124, 20378558.
18. Chaouiya C, Remy E, Mossé B, Thieffry D. Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework. Positive Systems, LNCIS 2003, 294:119-126.
19. Gonzalez AG, Naldia A, Sánchez L, Thieffry D, Chaouiya C. GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks. BioSystems 2006, 84:91-100. 10.1016/j.biosystems.2005.10.003, 16434137.
20. Naldi A, Berenguier D, Fauré A, Lopez F, Thieffry D, Chaouiya C. Logical modelling of regulatory networks with GINsim 2.3. BioSystems 2009, 97:134-139. 10.1016/j.biosystems.2009.04.008, 19426782.
21. Corblin F, Tripodi S, Fanchon E, Ropers D, Trilling L. A declarative constraint-based method for analyzing discrete genetic regulatory networks. BioSystems 2009, 98:91-104. 10.1016/j.biosystems.2009.07.007, 19664681.
22. Corblin F, Fanchon E, Trilling L. Applications of a formal approach to decipher discrete genetic networks. BMC Bioinfomatics 2010, 11:385.
23. Bernot G, Comet JP, Richard A, Guespin J. Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. Journal of Theoretical Biology 2004, 229:339-347. 10.1016/j.jtbi.2004.04.003, 15234201.
24. Khalis Z, Comet JP, Richard A, Bernot G. The SMBioNet method for discovering models of gene regulatory networks. Genes, Genomes and Genomics 2009, 3:15-22.
25. Mendoza L, Xenarios I. A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theoretical Biology and Medical Modelling 2006, 3:13. 10.1186/1742-4682-3-13, 1440308, 16542429.
26. Cara AD, Garg A, Micheli BD, Xenarios I, Mendoza L. Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics 2007, 8:462. 10.1186/1471-2105-8-462, 2238325, 18039375.
27. Garg A, Xenarios I, Mendoza L, DeMicheli G. An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments. Proc Research in Computational Molecular Biology 2007, 62-76. [Lecture Notes in Computer Science No. 4453].
28. Feinendegen LE. Significance of basic and clinical research in radiation medicine: challenges for the future. British Institute of Radiology supplement 2005, 27:185-195.
29. Poole DL, Mackworth AK. Artificial Intelligence. Foundations of Computational Agents 2010, Cambridge University Press.
30. Cohen J. Constraint logic programming languages. Communications of the ACM 1990, 33(7):52-68.
31. Clarke EM, Emerson EA. Design and synthesis of synchronization skeletons using branching time temporal logic. Proc Workshop on Logics of Programs 1981, 52-71. IBM Watson Research Center, [Lecture Notes in Computer Science No. 131].
32. Quielle JP, Sifakis J. Specification and verification of concurrent systems in CESAR. Proc 5th International Symposium on Programming 1981, 337-350.
33. Emerson EA. The beginning of model checking: a personal perspective. 25 Years of Model Checking 2008, 27-45. Springer, [Lecture Notes in Computer Science No. 5000, DOI: 10.1007/978-3-540-69850-0_2].
34. Eker S, Knapp M, Laderoute K, Lincoln P, Meseguer J, Sonmez K. Pathway logic: symbolic analysis of biological signaling. Proc Pacific Symposium on Biocomputing 2002, 400-412.
35. Calder M, Vyshemirsky V, Gilbert D, Orton R. Analysis of signalling pathways using the PRISM model checker. Proc Computational Methods in Systems Biology 2005, 179-190. [Lecture Notes in Computer Science No. 4416].
36. Ahmad J, Bernot G, Comet JP, Lime D, Roux O. Hybrid modelling and dynamical analysis of gene regulatory networks with delays. Complexus 2006, 3:231-251.
37. Heath J, Kwiatkowska M, Norman G, Parker D, Tymchyshyn O. Probabilistic model checking of complex biological pathways. Theoretical Computer Science 2008, 391(3):239-257.
38. Ciocchetta F, Gilmore S, Guerriero ML, Hillston J. Integrated simulation and model-checking for the analysis of biochemical systems. Electronic Notes in Theoretical Computer Science 2009, 232:17-38.
39. Mateus D, Gallois JP, Comet JP, Gall PL. Symbolic modeling of genetic regulatory networks. Journal of Bioinformatics and Computational Biology 2007, 5(2b):627-640. 10.1142/S0219720007002850, 17636866.
40. Batt G, Ropers D, de Jong H, Geiselmann J, Mateescu R, Page M, Schneider D. Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli. Bioinformatics 2005, 21(Suppl 1):i19-i28. 10.1093/bioinformatics/bti1048, 15961457.
41. Calzone L, Fages F, Soliman S. BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 2006, 22(14):1805-1807. 10.1093/bioinformatics/btl172, 16672256.
42. Li C, Nagasaki M, Ueno K, Miyano S. Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Systems Biology 2009, 3(42). [Doi:10.1186/1752-0509-3-42].
43. Fisher J, Piterman N, Hajnal A, Henzinger TA. Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Computational Biology 2007, 3(5):e92. [Doi:10.1371/journal.pcbi.0030092], 10.1371/journal.pcbi.0030092, 1868774, 17511512.
44. Prior A. Past, Present and Future. Clarendon 1967,
45. Blackburn P, Seligman J. Hybrid languages. Journal of Logic, Language and Information 1995, 4:251-272.
46. Clarke EM, Emerson EA, Sistla AP. Automatic verification of finite-state concurrent systems using temporal logic specifications. ACM Transactions of Programming Languages and Systems 1986, 8(2):244-263.
47. Clarke EM, Grumberg O, Peled DA. Model Checking 1999, MIT Press.
48. Bérard B, Bidoit M, Finkel A, Laroussinie F, Petit A, Petrucci L, Schnoebelen P, McKenzie P. Systems and Software Verification. Model-Checking Techniques and Tools 2001, Springer.
49. Huth MRA, Ryan MD. Logic in Computer Science. Modelling and reasoning about systems 2004, Cambridge University Press, 2.
50. Baier C, Katoen JP. Principles of Model Checking 2008, MIT Press.
51. Chabrier-Rivier N, Chiaverini M, Danos V, Fages F, Schächter V. Modeling and querying biomolecular interaction networks. Theoretical Computer Science 2004, 325:25-44.
52. Franceschet M, de Rijke M. Model checking hybrid logics (with an application to semistructured data). Journal of Applied Logic 2006, 4(3):279-304.
53. Areces C, ten Cate B. Hybrid logics. Handbook of Modal Logics 2006, 821-868. Elsevier, Blackburn P, Wolter F, van Benthem J.
54. Burch J, Clarke E, McMillan K, Dill DL, Hwang LJ. Symbolic model checking: 1020 states and beyond. Information and Computation 1992, 98:142-170.
55. Bryant RE. Graph-based algorithms for Boolean function manipulation. IEEE Transactions on Computers 1986, C-35(8):1035-1044.
56. Whaley J. JavaBDD 1.0b2. 2007, , http://javabdd.sourceforge.net/
57. Lind-Nielsen J. BuDDy 2.4. 2004, , http://sourceforge.net/projects/buddy/
58. Scheres B. Stem-cell niches: nursery rhymes across kingdoms. Nat Rev Mol Cell Biol 2007, 8(5):345-354. 10.1038/nrm2164, 17450175.
59. Dolan L, Janmaat K, Willemsen V, Linstead P, Poethig S, Roberts K, Scheres B. Cellular organisation of the Arabidopsis thaliana root. Development 1993, 119:71-84.
60. Sarkar AK, Luijten M, Miyashima S, Lenhard M, Hashimoto T, Nakajima K, Scheres B, Heidstra R, Laux T. Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers. Nature 2007, 446(7137):811-814. 10.1038/nature05703, 17429400.
61. Azpeitia E, Benítez M, Vega I, Villarreal C, Alvarez-Buylla ER. Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche. BMC Syst Biol 2010, 4(135).
62. Levesque M, Vernoux T, Busch W, Cui H, Wang J, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann J, Scheres B, Benfey P. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol 2006, 4(5):e143. 10.1371/journal.pbio.0040143, 1450008, 16640459.
63. Cui H, Levesque M, Vernoux T, Jung J, Paquette A, Gallagher K, Wang J, Blilou I, Scheres B, Benfey P. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 2007, 316(5823):421-425. 10.1126/science.1139531, 17446396.
64. Welch D, Hassan H, Blilou I, Immink R, Heidstra R, Scheres B. Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action. Genes Dev 2007, 21(17):2196-2204. 10.1101/gad.440307, 1950858, 17785527.
65. Sabatini S, Heidstra R, Wildwater M, Scheres B. SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem. Genes Dev 2003, 17(3):354-358. 10.1101/gad.252503, 195985, 12569126.
66. Ogasawara H, Kaimi R, Colasanti J, Kozaki A. Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT. Plant Mol Biol 2011,
67. Kaya H, Shibahara K, Taoka K, Iwabuchi M, Stillman B, Araki T. FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems. Cell 2001, 104:131-142. 10.1016/S0092-8674(01)00197-0, 11163246.
68. Inagaki S, Suzuki T, Ohto M, Urawa H, Horiuchi T, Nakamura K, Morikami A. Arabidopsis TEBICHI, with helicase and DNA polymerase domains, is required for regulated cell division and differentiation in meristems. Plant Cell 2006, 18(4):879-892. 10.1105/tpc.105.036798, 1425847, 16517762.
69. de Jong H, Geiselmann J, Hernández C, Page M. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 2003, 19(3):336-344. 10.1093/bioinformatics/btf851, 12584118.
70. Batt G, Ropers D, de Jong H, Geiselmann J, Mateescu R, Page M, Schneider D. Analysis and verification of qualitative models of genetic regulatory networks: a model-checking approach. IJCAI 2005, 370-375.
71. Ropers D, de Jong H, Page M, Schneider D, Geiselmann J. Qualitative simulation of the carbon starvation response in Escherichia coli. BioSystems 2006, 84:124-152. 10.1016/j.biosystems.2005.10.005, 16325332.
72. Monteiro PT, Dumas E, Besson B, Mateescu R, Page M, Freitas AT, de Jong H. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. BMC Bioinformatics 2009, 10(450)., http://www.biomedcentral.com/1471-2105/10/450
73. Batt G, de Jong H, Page M, Geiselmann J. Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. Automatica 2008, 44:982-989.
74. Mateescu R, Monteiro PT, Dumas E, de Jong H. Computation Tree Regular Logic for genetic regulatory networks. Proc Automated Technology for Verification and Analysis (ATVA) 2008, 48-63. Cha SS, Choi JY, Kim M, Lee I, Viswanathan M, [Lecture Notes in Computer Science No. 5311, Seoul, Korea].
75. Clarke E, Grumberg O, Jha S, Lu Y, Veith H. Counterexample-guided abstraction refinement for symbolic model checking. Journal of the ACM 2003, 50(5):752-794.
76. Mosca A, Manzoni L, Codecasa D. HyLMoC a model checker for hybrid logic. Proc 24th Italian Congress on Computational Logic (CILC-09) 2009,