Approaches to Modeling Gene Regulatory Networks: A Gentle Introduction

Methods in Molecular Biology

Volumn 1021, Issue , 2013, Pages 13-35

  Schlitt, Thomas ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

SPACER DNA; TRANSCRIPTION FACTOR;

BACTERIOPHAGE LAMBDA; BINDING SITE; BIOINFORMATICS; CELL DIFFERENTIATION; DELETION MUTANT; DROSOPHILA MELANOGASTER; GEL MOBILITY SHIFT ASSAY; GENE ACTIVATION; GENE ACTIVITY; GENE DELETION; GENE REGULATORY NETWORK; GENETIC MODEL; GENETIC REGULATION; METABOLISM; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; REVIEW; STATISTICAL MODEL; STOCHASTIC MODEL; TRANSLATION INITIATION;

EID: 84883214800     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-450-0_2     Document Type: Review

References (113)

1. SchlittT,BrazmaA(2005)Modelling gene networks at different organisational levels. FEBS Lett 579(8):1859-1866. doi:S0014-5793(05) 00186-9[pii]10.1016/j. febslet.2005.01.073
2. Schlitt T, Brazma A (2006) Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos Trans R Soc Lond B Biol Sci 361 (1467):483-494. doi:E686M06225352114 [pii]10.1098/rstb.2005.1806
3. Schlitt T, Brazma A (2007) Current approaches to gene regulatory network modelling. BMC Bioinformatics 8(suppl 6):S9. doi:1471-2105-8-S6-S9[pii]10.1186/ 1471-2105-8-S6-S9
4. Krebs JE (2009) Lewin's genes X, 10th edn. Jones and Bartlett, Burlington, MA
5. Ptashne M (1992) A genetic switch-phage lambda and higher organisms, 2nd edn. Cell Press & Blackwell Science, Oxford
6. Lederberg EM, Lederberg J (1953) Genetic studies of lysogenicity in Escherichia Coli. Genetics 38(1):51-64
7. Johnson AD, Poteete AR, Lauer G, Sauer RT, Ackers GK, PtashneM(1981) Lambda repressor and cro-components of an efficient molecular switch. Nature 294(5838):217-223
8. St-Pierre F, Endy D (2008) Determination of cell fate selection during phage lambda infection. Proc Natl Acad Sci USA 105 (52):20705-20710. doi:0808831105[pii] 10.1073/pnas.0808831105
9. Brazma A, Schlitt T (2003) Reverse engineering of gene regulatory networks: a finite state linear model. Genome Biol 4(6):P5
10. Ruklisa D, Brazma A, Viksna J (2005) Reconstruction of gene regulatory networks under the Finite State Linear Model. Genome Inform 16(2):225-236
11. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33(17):5691-5702
12. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14(3):283-291
13. Madan Babu M, Teichmann SA (2003) Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. Trends Genet 19(2):75-79
14. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S,Wolf YI, Yin JJ, Natale DA (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5(2):R7
15. Bornholdt S, Schuster HG (eds) (2003) Handbook of graphs and networks, 1st edn. Willey-VCH, Weinheim
16. Saris CG, Horvath S, vanVught PW, vanEs MA, Blauw HM, Fuller TF, Langfelder P, DeYoung J, Wokke JH, Veldink JH, van denBerg LH, Ophoff RA (2009) Weighted gene co-expression network analysis of the peripheral blood from amyotrophic lateral sclerosis patients. BMC Genomics 10:405. doi:doi:1471-2164-10-405 [pii]10.1186/1471-2164-10-405
17. Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4: Article17. doi:10.2202/1544-6115.1128
18. Langfelder P,Horvath S (2008)WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559. doi:1471-2105-9-559[pii]10.1186/ 1471-2105-9-559
19. Suderman M, Hallett M (2007) Tools for visually exploring biological networks. Bioinformatics 23(20):2651-2659. doi:btm401 [pii]10.1093/ bioinformatics/btm401
20. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang P-L, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2 (10):2366-2382
21. Galas DJ, Schmitz A (1978) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5(9):3157-3170
22. Garner MM, Revzin A (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res 9(13):3047-3060
23. Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25(3):99-104
24. Deonier RC, Tavaré S, Waterman MS (2005) Computational genome analysis: an introduction. Springer, Heidelberg
25. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31 (1):374-378
26. Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36(Database issue): D102-D106. doi:gkm955[pii]10.1093/nar/ gkm955
27. Brazma A, Jonassen I, Vilo J, Ukkonen E (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res 8 (11):1202-1215
28. Rustici G, Mata J, Kivinen K, Lio P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bahler J (2004) Periodic gene expression program of the fission yeast cell cycle. Nat Genet 36(8):809-817
29. Werner T, Fessele S, Maier H, Nelson PJ (2003) Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J 17(10):1228-1237
30. Dickmeis T, Muller F (2005) The identification and functional characterisation of conserved regulatory elements in developmental genes. Brief Funct Genomic Proteomic 3 (4):332-350
31. Sauer T, Shelest E,Wingender E (2006) Evaluating phylogenetic footprinting for humanrodent comparisons. Bioinformatics 22 (4):430-437
32. Bansal M, Califano A (2012) Genome-wide dissection of posttranscriptional and posttranslational interactions. Methods Mol Biol 786:131-149. doi:10.1007/978-1-61779-292-2-8
33. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA,Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pal C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C (2010) The genetic landscape of a cell. Science 327 (5964):425-431. doi:327/5964/425[pii] 10.1126/science.1180823
34. Guelzim N, Bottani S, Bourgine P, Kepes F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31(1):60-63
35. Erdös P, Rényi A (1960) On the evolution of random graphs. Publications of the Mathematical Institute of the Hungarian Academy of Sciences 17-61
36. de Silva E, Stumpf MP (2005) Complex networks and simple models in biology. J R Soc Interface 2(5):419-430
37. Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406(6794):378-382. doi:10.1038/35019019
38. Albert R, Jeong H, Barabasi AL (2001) Correction: error and attack tolerance of complex networks. Nature 409(6819):542
39. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402(6761 suppl):C47-C52
40. Schlosser G, Wagner GP (2004) Modularity in development and evolution, 1st edn. University of Chicago Press, Chicago
41. Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30(7):1575-1584
42. Frey BJ, Dueck D (2007) Clustering by passing messages between data points. Science 315(5814):972-976. doi:1136800[pii] 10.1126/science.1136800
43. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298(5594):824-827
44. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430(6995):88-93
45. ParkD, Park J, Park SG, ParkT,Choi SS (2008) Analysis of human disease genes in the context of gene essentiality. Genomics 92(6):414-418. doi:10.1016/j.ygeno.2008.08.001
46. Zotenko E, Mestre J, O'Leary DP, Przytycka TM (2008) Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol 4(8):e1000140
47. He X, Zhang J (2006)Why do hubs tend to be essential in protein networks? PLoS Genet 2 (6):e88. doi:10.1371/journal.pgen.0020088
48. Batada NN, Hurst LD, Tyers M (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2(7):e88. doi:06-PLCB-RA- 0076R2[pii]10.1371/journal.pcbi.0020088
49. Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22(4):803-806. doi: msi072[pii]10.1093/molbev/msi072
50. Yu H, Greenbaum D, Xin Lu H, Zhu X, GersteinM( 2004) Genomic analysis of essentiality within protein networks. Trends Genet 20 (6):227-231. doi:10.1016/j.tig.2004.04.008 S0168952504001015[pii]
51. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411(6833):41-42
52. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431 (7004):99-104
53. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-312
54. Yuh CH, Bolouri H, Davidson EH (1998) Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279(5358):1896-1902
55. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Rust AG, Pan Z, Schilstra MJ, Clarke PJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H (2002) A genomic regulatory network for development. Science 295 (5560):1669-1678
56. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Schilstra MJ, Clarke PJ, Rust AG, Pan Z, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H (2002) A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol 246 (1):162-190
57. Longabaugh WJ, Davidson EH, Bolouri H (2009) Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. Biochim Biophys Acta 1789 (4):363-374. doi:S1874-9399(08)00162-4 [pii]10.1016/j.bbagrm.2008.07.014
58. Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK (2009) Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol 5:331. doi: msb200987[pii]10.1038/msb.2009.87
59. Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S (2009) The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol 5(8):e1000438. doi:10.1371/journal.pcbi. 1000438
60. Klamt S, Saez-Rodriguez J, Gilles ED (2007) Structural and functional analysis of cellular networks with Cell NetAnalyzer. BMC Syst Biol 1:2. doi:1752-0509-1-2[pii]10.1186/1752-0509-1-2
61. de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9(1):67-103
62. Kauffman S (1969) Homeostasis and differentiation in random genetic control networks. Nature 224(215):177-178
63. Kauffman SA (1993) The origins of order, self-organization and selection in evolution. Oxford University Press, New York
64. Akutsu T, Miyano S, Kuhara S (2000) Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics 16 (8):727-734
65. Albert R, Barabasi AL (2000) Dynamics of complex systems: scaling laws for the period of Boolean networks. Phys Rev Lett 84 (24):5660-5663
66. D'Haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from coexpression clustering to reverse engineering. Bioinformatics 16(8):707-726
67. Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED (2006) A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7:56
68. Pandey S, Wang RS, Wilson L, Li S, Zhao Z, Gookin TE, Assmann SM, Albert R (2010) Boolean modeling of transcriptome data reveals novel modes of heterotrimeric Gprotein action. Mol Syst Biol 6:372. doi: msb201028[pii]10.1038/ msb.2010.28
69. Kauffman S, PetersonC, Samuelsson B, TroeinC (2003) RandomBooleannetworkmodels andthe yeast transcriptional network. Proc Natl Acad Sci USA 100(25):14796-14799. doi:10.1073/pnas.2036429100 2036429100[pii]
70. Kauffman S, Peterson C, Samuelsson B, Troein C (2004) Genetic networks with canalyzing Boolean rules are always stable. Proc Natl Acad Sci USA 101(49):17102-17107. doi:0407783101[pii]10.1073/pnas.0407783101
71. Albert I, Thakar J, Li S, Zhang R, Albert R (2008) Boolean network simulations for life scientists. Source Code Biol Med 3:16. doi:1751-0473-3- 16[pii]10.1186/1751-0473-3-16
72. Saadatpour A, Albert I, Albert R (2010) Attractor analysis of asynchronous Boolean models of signal transduction networks. J Theor Biol 266(4):641-656. doi:S0022-5193(10)00379-6[pii]10.1016/j. jtbi.2010.07.022
73. Thomas R (1973) Boolean formalization of genetic control circuits. J Theor Biol 42 (3):563-585
74. Thomas R (1991) Regulatory networks seen as asynchronous automata: a logical description. J Theor Biol 153:1-23
75. Naldi A, Carneiro J, Chaouiya C, Thieffry D (2010) Diversity and plasticity of Th cell types predicted from regulatory network modelling. PLoS Comput Biol 6(9):e1000912. doi:e1000912[pii]10.1371/journal. pcbi.1000912
76. Naldi A, Berenguier D, Faure A, Lopez F, Thieffry D, Chaouiya C (2009) Logical modelling of regulatory networkswithGINsim 2.3. Biosystems 97(2):134-139. doi: S0303-2647(09)00066-5[pii]10.1016/j. biosystems.2009.04.008
77. Petri CA, Reisig W (2008) Petri net. Scholarpedia 3(4):6477
78. Koch I, Reisig W, Schreiber F (eds) (2011) Modeling in systems biology: the Petri net approach. Computational biology, 1st edn. Springer, London. doi:10.1007/978-1-84996-474-6
79. Banks R, Khomenko V, Steggles LJ (2011) Modeling genetic regulatory networks. In: Koch I, Reisig W, Schreiber F (eds) Modeling in systems biology: the Petri net approach, 1st edn. Springer, London. doi:10.1007/978-1-84996-474-6
80. D'Haeseleer P, Wen X, Fuhrman S, Somogyi R (1999) Linear modeling of mRNA expression levels during CNS development and injury. Pac Symp Biocomput 41-52 http://www.ncbi.nlm.nih.gov/pubmed/10380184
81. van Someren EP, Wessels LF, Reinders MJ (2000) Linear modeling of genetic networks from experimental data. Proc Int Conf Intell Syst Mol Biol 8:355-366
82. von Dassow G, Meir E, Munro EM, Odell GM (2000) The segment polarity network is a robust developmental module. Nature 406 (6792):188-192
83. Lequieu J, Chakrabarti A, Nayak S, Varner JD (2011)Computationalmodeling andanalysis of insulin induced eukaryotic translation initiation. PLoS Comput Biol 7(11):e1002263. doi:10.1371/journal.pcbi.1002263 PCOMPBIOL-D-11-00832[pii]
84. Weisse AY, Middleton RH, Huisinga W (2010) Quantifying uncertainty, variability and likelihood for ordinary differential equation models. BMC Syst Biol 4:144. doi:1752-0509-4-144[pii]10.1186/1752-0509-4-144
85. Mendes P, Kell DB (2001) MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinformatics 17(3):288-289
86. Mendes P (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi. Trends Biochem Sci 22 (9):361-363. doi: S0968000497011031[pii]
87. Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H (2008) Cell Designer 3.5: a versatile modeling tool for biochemical networks. Proc IEEE 96 (8):1254-1265
88. Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M (2003) E-Cell 2: multi-platform E-Cell simulation system. Bioinformatics 19 (13):1727-1729
89. McAdams HH, Shapiro L (1995) Circuit simulation of genetic networks. Science 269 (5224):650-656
90. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. J Comput Biol 7 (3-4):601-620
91. Murphy K, Mian S (1999) Modelling gene expression data using dynamic Bayesian networks. Technical report, U.C. Berkeley, Department of Computer Science
92. Pournara I, Wernisch L (2004) Reconstruction of gene networks using Bayesian learning and manipulation experiments. Bioinformatics 20(17):2934-2942
93. Titsias MK, Honkela A, Lawrence ND, Rattray M (2012) Identifying targets of multiple coregulating transcription factors from expression time-series by Bayesian model comparison. BMC Syst Biol 6(1):53.doi:1752-0509-6-53 [pii]10.1186/1752-0509-6-53
94. Pe'er D (2005) Bayesian network analysis of signaling networks: a primer. Sci STKE 2005 (281):pl4
95. Shmulevich I,Dougherty ER, KimS, ZhangW (2002) Probabilistic BooleanNetworks: a rulebased uncertainty model for gene regulatory networks. Bioinformatics 18(2):261-274
96. Matsuno H, Doi A, Nagasaki M, Miyano S (2000) Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput 341-352 http://www.ncbi.nlm.nih.gov/pubmed/?term=10902182
97. Goss PJ, Peccoud J (1998) Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc Natl Acad Sci USA 95(12):6750-6755
98. RuthsD,MullerM, Tseng JT,Nakhleh L, Ram PT(2008)The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks. PLoS Comput Biol 4(2):e1000005. doi:10.1371/journal.pcbi.1000005
99. Arkin A, Ross J, McAdams HH (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149 (4):1633-1648
100. McAdams HH, Arkin A (1997) Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA 94(3):814-819
101. McAdams HH, Arkin A (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 15(2):65-69
102. Theocharidis A, van Dongen S, Enright AJ, Freeman TC (2009) Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc 4 (10):1535-1550. doi:nprot.2009.177[pii] 10.1038/nprot.2009.177
103. Albert R, Barabasi AL (2002) Statistical mechanics of complex networks. Rev Mod Phys 74(1):47-97
104. Barabasi A-L (2007) Network medicine-from obesity to the "diseasome". N Engl J Med 357(4):404-407. doi:10.1056/NEJMe078114
105. Dewey TG (2002) From microarrays to networks: mining expression time series. Drug Discov Today 7(20 Suppl):S170-S175
106. Friedman N (2004) Inferring cellular networks using probabilistic graphical models. Science 303(5659):799-805
107. Huber W, Carrey VJ, Long L, Falcon S, Gentleman R (2007) Graphs in molecular biology. BMC Bioinformatics 8(suppl 6):S8
108. Kitano H (2002) Computational systems biology. Nature 420(6912):206-210
109. Moore JH, Boczko EM, Summar ML (2005) Connecting the dots between genes, biochemistry, and disease susceptibility: systems biology modeling in human genetics. Mol Genet Metab 84(2):104-111
110. van Someren EP, Wessels LF, Backer E, Reinders MJ (2002) Genetic network modeling. Pharmacogenomics 3(4):507-525
111. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524-531
112. Levine M, Tjian R (2003) Transcription regulation and animal diversity. Nature 424 (6945):147-151. doi:10.1038/nature01763 nature01763[pii]
113. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (5594):799-804