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Volumn 8, Issue SUPPL. 6, 2007, Pages

Current approaches to gene regulatory network modelling

Author keywords

[No Author keywords available]

Indexed keywords

CONTINUOUS APPROACH; GENE REGULATORY NETWORK MODEL; GENE REGULATORY NETWORKS; NETWORK CONTROL; NETWORK DYNAMICS; NETWORK MODELLING; NETWORK TOPOLOGY; TRANSCRIPTION FACTOR BINDING;

EID: 45149101194     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S6-S9     Document Type: Review
Times cited : (243)

References (113)
  • 1
    • 14844307659 scopus 로고    scopus 로고
    • Modelling gene networks at different organisational levels
    • 10.1016/j.febslet.2005.01.073 15763564
    • Schlitt T Brazma A Modelling gene networks at different organisational levels FEBS Lett 2005, 579(8):1859-1866 10.1016/j.febslet.2005.01.073 15763564
    • (2005) FEBS Lett , vol.579 , Issue.8 , pp. 1859-1866
    • Schlitt, T.1    Brazma, A.2
  • 2
    • 33646360604 scopus 로고    scopus 로고
    • Modelling in molecular biology: Describing transcription regulatory networks at different scales
    • 10.1098/rstb.2005.1806 16524837
    • Schlitt T Brazma A Modelling in molecular biology: Describing transcription regulatory networks at different scales Philos Trans R Soc Lond B Biol Sci 2006, 361(1467):483-494 10.1098/rstb.2005.1806 16524837
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , Issue.1467 , pp. 483-494
    • Schlitt, T.1    Brazma, A.2
  • 4
    • 0033215210 scopus 로고    scopus 로고
    • Pathway alignment: Application to the comparative analysis of glycolytic enzymes
    • 1220531 10493919 10.1042/0264-6021:3430115
    • Dandekar T Schuster S Snel B Huynen M Bork P Pathway alignment: application to the comparative analysis of glycolytic enzymes Biochem J 1999, 343(Pt 1):115-124 1220531 10493919 10.1042/0264-6021:3430115
    • (1999) Biochem J , vol.343 , Issue.PART 1 , pp. 115-124
    • Dandekar, T.1    Schuster, S.2    Snel, B.3    Huynen, M.4    Bork, P.5
  • 7
    • 0032413411 scopus 로고    scopus 로고
    • Predicting gene regulatory elements in silico on a genomic scale
    • 310790 9847082
    • Brazma A Jonassen I Vilo J Ukkonen E Predicting gene regulatory elements in silico on a genomic scale Genome Res 1998, 8(11):1202-1215 310790 9847082
    • (1998) Genome Res , vol.8 , Issue.11 , pp. 1202-1215
    • Brazma, A.1    Jonassen, I.2    Vilo, J.3    Ukkonen, E.4
  • 10
    • 0037785111 scopus 로고    scopus 로고
    • Computer modeling of promoter organization as a tool to study transcriptional coregulation
    • 10.1096/fj.02-0955rev
    • Werner T Fessele S Maier H Nelson PJ Computer modeling of promoter organization as a tool to study transcriptional coregulation Faseb J 2003, 17(10):1228-1237 10.1096/fj.02-0955rev 12832287
    • (2003) Faseb J , vol.17 , Issue.10 , pp. 1228-1237
    • Werner, T.1    Fessele, S.2    Maier, H.3    Nelson, P.J.4
  • 11
    • 16344369891 scopus 로고    scopus 로고
    • The identification and functional characterisation of conserved regulatory elements in developmental genes
    • 10.1093/bfgp/3.4.332 15814024
    • Dickmeis T Muller F The identification and functional characterisation of conserved regulatory elements in developmental genes Brief Funct Genomic Proteomic 2005, 3(4):332-350 10.1093/bfgp/3.4.332 15814024
    • (2005) Brief Funct Genomic Proteomic , vol.3 , Issue.4 , pp. 332-350
    • Dickmeis, T.1    Muller, F.2
  • 12
    • 32544446322 scopus 로고    scopus 로고
    • Evaluating phylogenetic footprinting for human-rodent comparisons
    • (Oxford, England) 10.1093/bioinformatics/bti819 16332706
    • Sauer T Shelest E Wingender E Evaluating phylogenetic footprinting for human-rodent comparisons Bioinformatics (Oxford, England) 2006, 22(4):430-437 10.1093/bioinformatics/bti819 16332706
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 430-437
    • Sauer, T.1    Shelest, E.2    Wingender, E.3
  • 13
    • 20844434817 scopus 로고    scopus 로고
    • Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites
    • 1150811 15937122 10.1073/pnas.0409638102
    • Balhoff JP Wray GA Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites Proc Natl Acad Sci USA 2005, 102(24):8591-8596 1150811 15937122 10.1073/ pnas.0409638102
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.24 , pp. 8591-8596
    • Balhoff, J.P.1    Wray, G.A.2
  • 14
    • 0018199224 scopus 로고
    • DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
    • 342238 212715 10.1093/nar/5.9.3157
    • Galas DJ Schmitz A DNAse footprinting: A simple method for the detection of protein-DNA binding specificity Nucleic Acids Res 1978, 5(9):3157-3170 342238 212715 10.1093/nar/5.9.3157
    • (1978) Nucleic Acids Res , vol.5 , Issue.9 , pp. 3157-3170
    • Galas, D.J.1    Schmitz, A.2
  • 15
    • 0019878376 scopus 로고
    • Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis
    • 327619 6275366 10.1093/nar/9.23.6505
    • Fried M Crothers DM Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis Nucleic Acids Res 1981, 9(23):6505-6525 327619 6275366 10.1093/nar/9.23.6505
    • (1981) Nucleic Acids Res , vol.9 , Issue.23 , pp. 6505-6525
    • Fried, M.1    Crothers, D.M.2
  • 16
    • 0019877067 scopus 로고
    • 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
    • 327330 6269071 10.1093/nar/9.13.3047
    • Garner MM Revzin A 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 1981, 9(13):3047-3060 327330 6269071 10.1093/nar/9.13.3047
    • (1981) Nucleic Acids Res , vol.9 , Issue.13 , pp. 3047-3060
    • Garner, M.M.1    Revzin, A.2
  • 17
    • 0036940469 scopus 로고    scopus 로고
    • Learning about gene regulatory networks from gene deletion experiments
    • 10.1002/cfg.220
    • Schlitt T Brazma A Learning about gene regulatory networks from gene deletion experiments Comp Funct Genom 2002, 3:499-503 10.1002/cfg.220
    • (2002) Comp Funct Genom , vol.3 , pp. 499-503
    • Schlitt, T.1    Brazma, A.2
  • 22
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • 10.1038/82360 11101803
    • Schwikowski B Uetz P Fields S A network of protein-protein interactions in yeast Nat Biotechnol 2000, 18(12):1257-1261 10.1038/82360 11101803
    • (2000) Nat Biotechnol , vol.18 , Issue.12 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 26
    • 0345928693 scopus 로고    scopus 로고
    • Building and analysing genome-wide gene disruption networks
    • (Oxford, England) 12386004
    • Rung J Schlitt T Brazma A Freivalds K Vilo J Building and analysing genome-wide gene disruption networks Bioinformatics (Oxford, England) 2002, 18(Suppl 2):S202-210 12386004
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2
    • Rung, J.1    Schlitt, T.2    Brazma, A.3    Freivalds, K.4    Vilo, J.5
  • 27
    • 0141792394 scopus 로고    scopus 로고
    • Correlating protein-DNA and protein-protein interaction networks
    • 10.1016/j.jmb.2003.08.004 14516744
    • Manke T Bringas R Vingron M Correlating protein-DNA and protein-protein interaction networks Journal of molecular biology 2003, 333(1):75-85 10.1016/j.jmb.2003.08.004 14516744
    • (2003) Journal of Molecular Biology , vol.333 , Issue.1 , pp. 75-85
    • Manke, T.1    Bringas, R.2    Vingron, M.3
  • 28
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • 10.1038/nature750
    • von Mering C Krause R Snel B Cornell M Oliver SG Fields S Bork P Comparative assessment of large-scale data sets of protein-protein interactions Nature 2002, 417(6887:399-403 10.1038/nature750 12000970
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 29
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • 10.1038/35019019 10935628
    • Albert R Jeong H Barabasi AL Error and attack tolerance of complex networks Nature 2000, 406(6794):378-382 10.1038/35019019 10935628
    • (2000) Nature , vol.406 , Issue.6794 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.L.3
  • 30
    • 0035945558 scopus 로고    scopus 로고
    • Correction: Error and attack tolerance of complex networks
    • Albert R Jeong H Barabasi AL correction: Error and attack tolerance of complex networks Nature 2001, 409(6819):542
    • (2001) Nature , vol.409 , Issue.6819 , pp. 542
    • Albert, R.1    Jeong, H.2    Barabasi, A.L.3
  • 32
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • 10.1038/nature02782 15372033
    • Luscombe NM Babu MM Yu H Snyder M Teichmann SA Gerstein M Genomic analysis of regulatory network dynamics reveals large topological changes Nature 2004, 431(7006):308-312 10.1038/nature02782 15372033
    • (2004) Nature , vol.431 , Issue.7006 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 33
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • 10.1126/science.298.5594.824 12399590
    • Milo R Shen-Orr S Itzkovitz S Kashtan N Chklovskii D Alon U Network motifs: Simple building blocks of complex networks Science 2002, 298(5594):824-827 10.1126/science.298.5594.824 12399590
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 34
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • 10.1038/ng1340 15107850
    • Teichmann SA Babu MM Gene regulatory network growth by duplication Nat Genet 2004, 36(5):492-496 10.1038/ng1340 15107850
    • (2004) Nat Genet , vol.36 , Issue.5 , pp. 492-496
    • Teichmann, S.A.1    Babu, M.M.2
  • 35
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • 10.1038/35011540 10591225
    • Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999, 402(6761 Suppl):C47- 52 10.1038/35011540 10591225
    • (1999) Nature , vol.402 , Issue.6761 SUPPL.
    • Hartwell, L.H.1    Hopfield, J.J.2    Leibler, S.3    Murray, A.W.4
  • 37
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • 12740579
    • Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data Nat Genet 2003, 34(2):166-176 12740579
    • (2003) Nat Genet , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 38
    • 0036699526 scopus 로고    scopus 로고
    • Revealing modular organization in the yeast transcriptional network
    • 12134151
    • Ihmels J Friedlander G Bergmann S Sarig O Ziv Y Barkai N Revealing modular organization in the yeast transcriptional network Nat Genet 2002, 31(4):370-377 12134151
    • (2002) Nat Genet , vol.31 , Issue.4 , pp. 370-377
    • Ihmels, J.1    Friedlander, G.2    Bergmann, S.3    Sarig, O.4    Ziv, Y.5    Barkai, N.6
  • 39
    • 0037676107 scopus 로고    scopus 로고
    • Motifs, modules and games in bacteria
    • 10.1016/S1369-5274(03)00033-X 12732301
    • Wolf DM Arkin AP Motifs, modules and games in bacteria Curr Opin Microbiol 2003, 6(2):125-134 10.1016/S1369-5274(03)00033-X 12732301
    • (2003) Curr Opin Microbiol , vol.6 , Issue.2 , pp. 125-134
    • Wolf, D.M.1    Arkin, A.P.2
  • 40
    • 1542286745 scopus 로고    scopus 로고
    • Quantifying modularity in the evolution of biomolecular systems
    • 353226 14993205 10.1101/gr.1969504
    • Snel B Huynen MA Quantifying modularity in the evolution of biomolecular systems Genome Res 2004, 14(3):391-397 353226 14993205 10.1101/gr.1969504
    • (2004) Genome Res , vol.14 , Issue.3 , pp. 391-397
    • Snel, B.1    Huynen, M.A.2
  • 43
    • 17044444207 scopus 로고    scopus 로고
    • Binary and graded responses in gene networks
    • 12149512
    • Louis M Becskei A Binary and graded responses in gene networks Sci STKE 2002 2002, 143:PE33 12149512
    • (2002) Sci STKE , vol.2002
    • Louis, M.1    Becskei, A.2
  • 44
    • 0032549745 scopus 로고    scopus 로고
    • Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
    • 10.1126/science.279.5358.1896 9506933
    • Yuh CH Bolouri H Davidson EH Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene Science 1998, 279(5358):1896-1902 10.1126/science.279.5358.1896 9506933
    • (1998) Science , vol.279 , Issue.5358 , pp. 1896-1902
    • Yuh, C.H.1    Bolouri, H.2    Davidson, E.H.3
  • 46
    • 33646337667 scopus 로고    scopus 로고
    • A methodology for the structural and functional analysis of signaling and regulatory networks
    • 1458363 16464248 10.1186/1471-2105-7-56
    • Klamt S Saez-Rodriguez J Lindquist JA Simeoni L Gilles ED A methodology for the structural and functional analysis of signaling and regulatory networks BMC Bioinformatics 2006, 7:56 1458363 16464248 10.1186/ 1471-2105-7-56
    • (2006) BMC Bioinformatics , vol.7 , pp. 56
    • Klamt, S.1    Saez-Rodriguez, J.2    Lindquist, J.A.3    Simeoni, L.4    Gilles, E.D.5
  • 47
    • 0037270514 scopus 로고    scopus 로고
    • Towards reconstruction of gene networks from expression data by supervised learning
    • 151290 12540298 10.1186/gb-2003-4-1-r6
    • Soinov LA Krestyaninova MA Brazma A Towards reconstruction of gene networks from expression data by supervised learning Genome Biol 2003, 4(1):R6 151290 12540298 10.1186/gb-2003-4-1-r6
    • (2003) Genome Biol , vol.4 , Issue.1
    • Soinov, L.A.1    Krestyaninova, M.A.2    Brazma, A.3
  • 48
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • 10.1089/106652700750050961 11108481
    • Friedman N Linial M Nachman I Pe'er D Using Bayesian networks to analyze expression data J Comput Biol 2000, 7(3-4):601-620 10.1089/ 106652700750050961 11108481
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Pe'er, D.4
  • 49
    • 18144442687 scopus 로고    scopus 로고
    • Inferring subnetworks from perturbed expression profiles
    • (Oxford, England)
    • Pe'er D Regev A Elidan G Friedman N Inferring subnetworks from perturbed expression profiles Bioinformatics (Oxford, England) 2001, 17(Suppl1): S215-224 11473012
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pe'er, D.1    Regev, A.2    Elidan, G.3    Friedman, N.4
  • 50
    • 10244230983 scopus 로고    scopus 로고
    • Reconstruction of gene networks using Bayesian learning and manipulation experiments
    • (Oxford, England) 10.1093/bioinformatics/bth337
    • Pournara I Wernisch L Reconstruction of gene networks using Bayesian learning and manipulation experiments Bioinformatics (Oxford, England) 2004, 20(17):2934-2942 10.1093/bioinformatics/bth337 15180938
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 2934-2942
    • Pournara, I.1    Wernisch, L.2
  • 51
    • 17644412264 scopus 로고    scopus 로고
    • Bayesian network analysis of signaling networks: A primer
    • 10.1126/stke.2812005pl4 15855409
    • Pe'er D Bayesian network analysis of signaling networks: A primer Sci STKE 2005 2005, 281:pL4 10.1126/stke.2812005pl4 15855409
    • (2005) Sci STKE , vol.2005
    • Pe'er, D.1
  • 52
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • 10.1126/science.1094068 14764868
    • Friedman N Inferring cellular networks using probabilistic graphical models Science 2004, 303(5659):799-805 10.1126/science.1094068 14764868
    • (2004) Science , vol.303 , Issue.5659 , pp. 799-805
    • Friedman, N.1
  • 53
    • 0842309161 scopus 로고    scopus 로고
    • Discovering molecular pathways from protein interaction and gene expression data
    • (Oxford, England) 10.1093/bioinformatics/btg1037
    • Segal E Wang H Koller D Discovering molecular pathways from protein interaction and gene expression data Bioinformatics (Oxford, England) 2003, 19(Suppl 1):I264-I272 10.1093/bioinformatics/btg1037 12855469
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Segal, E.1    Wang, H.2    Koller, D.3
  • 55
    • 0036842375 scopus 로고    scopus 로고
    • Reverse engineers map the molecular switching yards
    • 10.1016/S0167-7799(02)02051-6 124138110
    • Greller LD Somogyi R Reverse engineers map the molecular switching yards Trends Biotechnol 2002, 20(11):445-447 10.1016/S0167-7799(02)02051-6 124138110
    • (2002) Trends Biotechnol , vol.20 , Issue.11 , pp. 445-447
    • Greller, L.D.1    Somogyi, R.2
  • 56
    • 0031635563 scopus 로고    scopus 로고
    • Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": Their application for understanding carcinogenesis and assessing therapeutic strategies
    • 9697172
    • Szallasi Z Liang S Modeling the normal and neoplastic cell cycle with "realistic Boolean genetic networks": Their application for understanding carcinogenesis and assessing therapeutic strategies Pac Symp Biocomput 1998, 66-76 9697172
    • (1998) Pac Symp Biocomput , pp. 66-76
    • Szallasi, Z.1    Liang, S.2
  • 57
    • 0032616683 scopus 로고    scopus 로고
    • Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
    • 10380182
    • Akutsu T Miyano S Kuhara S Identification of genetic networks from a small number of gene expression patterns under the Boolean network model Pac Symp Biocomput 1999, 17-28 10380182
    • (1999) Pac Symp Biocomput , pp. 17-28
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 58
    • 0031616241 scopus 로고    scopus 로고
    • Reveal, a general reverse engineering algorithm for inference of genetic network architectures
    • 9697168
    • Liang S Fuhrman S Somogyi R Reveal, a general reverse engineering algorithm for inference of genetic network architectures Pac Symp Biocomput 1998, 18-29 9697168
    • (1998) Pac Symp Biocomput , pp. 18-29
    • Liang, S.1    Fuhrman, S.2    Somogyi, R.3
  • 59
    • 0346158342 scopus 로고    scopus 로고
    • Petri Net representations in systems biology
    • 14641101
    • Pinney JW Westhead DR McConkey GA Petri Net representations in systems biology Biochem Soc Trans 2003, 31(Pt 6):1513-1515 14641101
    • (2003) Biochem Soc Trans , vol.31 , Issue.PART 6 , pp. 1513-1515
    • Pinney, J.W.1    Westhead, D.R.2    McConkey, G.A.3
  • 60
    • 21644439156 scopus 로고    scopus 로고
    • Modeling and simulation of molecular biology systems using petri nets: Modeling goals of various approaches
    • 10.1142/S0219720004000764 15617157
    • Hardy S Robillard PN Modeling and simulation of molecular biology systems using petri nets: Modeling goals of various approaches J Bioinform Comput Biol 2004, 2(4):595-613 10.1142/S0219720004000764 15617157
    • (2004) J Bioinform Comput Biol , vol.2 , Issue.4 , pp. 595-613
    • Hardy, S.1    Robillard, P.N.2
  • 61
    • 12844277447 scopus 로고    scopus 로고
    • Connecting the dots between genes, biochemistry, and disease susceptibility: Systems biology modeling in human genetics
    • 10.1016/j.ymgme.2004.10.006 15670716
    • Moore JH Boczko EM Summar ML Connecting the dots between genes, biochemistry, and disease susceptibility: Systems biology modeling in human genetics Mol Genet Metab 2005, 84(2):104-111 10.1016/ j.ymgme.2004.10.006 15670716
    • (2005) Mol Genet Metab , vol.84 , Issue.2 , pp. 104-111
    • Moore, J.H.1    Boczko, E.M.2    Summar, M.L.3
  • 62
    • 33847304166 scopus 로고    scopus 로고
    • Qualitatively modelling and analysing genetic regulatory networks: A Petri net approach
    • 10.1093/bioinformatics/btl596 17121774
    • Steggles LJ Banks R Shaw O Wipat A Qualitatively modelling and analysing genetic regulatory networks: A Petri net approach Bioinformatics (Oxford, England) 2007, 23(3):336-343 10.1093/bioinformatics/btl596 17121774
    • (2007) Bioinformatics (Oxford, England) , vol.23 , Issue.3 , pp. 336-343
    • Steggles, L.J.1    Banks, R.2    Shaw, O.3    Wipat, A.4
  • 63
    • 0032611513 scopus 로고    scopus 로고
    • Modeling gene expression with differential equations
    • 10380183
    • Chen T He HL Church GM Modeling gene expression with differential equations Pac Symp Biocomput 1999, 29-40 10380183
    • (1999) Pac Symp Biocomput , pp. 29-40
    • Chen, T.1    He, H.L.2    Church, G.M.3
  • 64
    • 0032612220 scopus 로고    scopus 로고
    • Linear modeling of mRNA expression levels during CNS development and injury
    • 10380184
    • D'Haeseleer P Wen X Fuhrman S Somogyi R Linear modeling of mRNA expression levels during CNS development and injury Pac Symp Biocomput 1999, 41-52 10380184
    • (1999) Pac Symp Biocomput , pp. 41-52
    • D'Haeseleer, P.1    Wen, X.2    Fuhrman, S.3    Somogyi, R.4
  • 65
    • 0036905483 scopus 로고    scopus 로고
    • The dynamics of cell cycle regulation
    • 10.1002/bies.10191 12447975
    • Tyson JJ Csikasz-Nagy A Novak B The dynamics of cell cycle regulation Bioessays 2002, 24(12):1095-1109 10.1002/bies.10191 12447975
    • (2002) Bioessays , vol.24 , Issue.12 , pp. 1095-1109
    • Tyson, J.J.1    Csikasz-Nagy, A.2    Novak, B.3
  • 66
    • 0033782304 scopus 로고    scopus 로고
    • Modeling transcriptional control in gene networks-methods, recent results, and future directions
    • 10.1006/bulm.1999.0155 10824430
    • Smolen P Baxter DA Byrne JH Modeling transcriptional control in gene networks-methods, recent results, and future directions Bull Math Biol 2000, 62(2):247-292 10.1006/bulm.1999.0155 10824430
    • (2000) Bull Math Biol , vol.62 , Issue.2 , pp. 247-292
    • Smolen, P.1    Baxter, D.A.2    Byrne, J.H.3
  • 67
    • 0033642487 scopus 로고    scopus 로고
    • Algorithms for inferring qualitative models of biological networks
    • 10902178
    • Akutsu T Miyano S Kuhara S Algorithms for inferring qualitative models of biological networks Pac Symp Biocomput 2000, 293-304 10902178
    • (2000) Pac Symp Biocomput , pp. 293-304
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 68
    • 0032879544 scopus 로고    scopus 로고
    • Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis
    • (Oxford, England) 10.1093/bioinformatics/15.7.593 10487867
    • Mendoza L Thieffry D Alvarez-Buylla ER Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis Bioinformatics (Oxford, England) 1999, 15(7-8):593-606 10.1093/bioinformatics/15.7.593 10487867
    • (1999) Bioinformatics , vol.15 , Issue.7-8 , pp. 593-606
    • Mendoza, L.1    Thieffry, D.2    Alvarez-Buylla, E.R.3
  • 69
    • 0014671878 scopus 로고
    • Homeostasis and differentiation in random genetic control networks
    • 10.1038/224177a0 5343519
    • Kauffman S Homeostasis and differentiation in random genetic control networks Nature 1969, 224(215):177-178 10.1038/224177a0 5343519
    • (1969) Nature , vol.224 , Issue.215 , pp. 177-178
    • Kauffman, S.1
  • 70
  • 71
    • 33344474684 scopus 로고    scopus 로고
    • Properties of attractors of canalyzing random Boolean networks
    • 16605409
    • Paul U Kaufman V Drossel B Properties of attractors of canalyzing random Boolean networks Phys Rev E Stat Nonlin Soft Matter Phys 2006, 73(2 Pt 2):026118 16605409
    • (2006) Phys Rev E Stat Nonlin Soft Matter Phys , vol.73 , Issue.2 PART 2 , pp. 026118
    • Paul, U.1    Kaufman, V.2    Drossel, B.3
  • 72
    • 0033737840 scopus 로고    scopus 로고
    • Inferring qualitative relations in genetic networks and metabolic pathways
    • (Oxford, England) 10.1093/bioinformatics/16.8.727 11099258
    • Akutsu T Miyano S Kuhara S Inferring qualitative relations in genetic networks and metabolic pathways Bioinformatics (Oxford, England) 2000, 16(8):727-734 10.1093/bioinformatics/16.8.727 11099258
    • (2000) Bioinformatics , vol.16 , Issue.8 , pp. 727-734
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 73
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean Networks: A rule-based uncertainty model for gene regulatory networks
    • (Oxford, England) 10.1093/bioinformatics/18.2.261 11847074
    • Shmulevich I Dougherty ER Kim S Zhang W Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks Bioinformatics (Oxford, England) 2002, 18(2):261-274 10.1093/ bioinformatics/18.2.261 11847074
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.R.2    Kim, S.3    Zhang, W.4
  • 74
    • 0029267491 scopus 로고
    • Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop- characteristic state
    • 7703920
    • 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 7703920
    • (1995) Bull Math Biol , vol.57 , Issue.2 , pp. 247-276
    • Thomas, R.1    Thieffry, D.2    Kaufman, M.3
  • 75
    • 16344381707 scopus 로고    scopus 로고
    • Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
    • (Oxford, England) 10.1093/bioinformatics/bti145 15546934
    • Koch I Junker BH Heiner M Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber Bioinformatics (Oxford, England) 2005, 21(7):1219-1226 10.1093/ bioinformatics/bti145 15546934
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 1219-1226
    • Koch, I.1    Junker, B.H.2    Heiner, M.3
  • 76
    • 0033670135 scopus 로고    scopus 로고
    • Pathway analysis in metabolic databases via differential metabolic display (DMD)
    • (Oxford, England) 10.1093/bioinformatics/16.9.825 11108705
    • Kuffner R Zimmer R Lengauer T Pathway analysis in metabolic databases via differential metabolic display (DMD) Bioinformatics (Oxford, England) 2000, 16(9):825-836 10.1093/bioinformatics/16.9.825 11108705
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 825-836
    • Kuffner, R.1    Zimmer, R.2    Lengauer, T.3
  • 77
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
    • (Oxford, England) 10.1093/bioinformatics/18.2.351 11847093
    • Schuster S Pfeiffer T Moldenhauer F Koch I Dandekar T Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae Bioinformatics (Oxford, England) 2002, 18(2):351-361 10.1093/bioinformatics/18.2.351 11847093
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 351-361
    • Schuster, S.1    Pfeiffer, T.2    Moldenhauer, F.3    Koch, I.4    Dandekar, T.5
  • 78
  • 79
    • 0032600734 scopus 로고    scopus 로고
    • Nonlinear metabolic control analysis
    • 10.1006/mben.1998.0108
    • Hatzimanikatis V Nonlinear metabolic control analysis Metab Eng 1999, 1(1):75-87 10.1006/mben.1998.0108 10935756
    • (1999) Metab Eng , vol.1 , Issue.1 , pp. 75-87
    • Hatzimanikatis, V.1
  • 80
    • 0034791625 scopus 로고    scopus 로고
    • Modeling genetic regulatory dynamics in neural development
    • 10.1089/106652701752236223 11571076
    • Wahde M Hertz J Modeling genetic regulatory dynamics in neural development J Comput Biol 2001, 8(4):429-442 10.1089/106652701752236223 11571076
    • (2001) J Comput Biol , vol.8 , Issue.4 , pp. 429-442
    • Wahde, M.1    Hertz, J.2
  • 81
    • 0036843965 scopus 로고    scopus 로고
    • Gene networks: How to put the function in genomics
    • 10.1016/S0167-7799(02)02053-X 12413821
    • Brazhnik P de la Fuente A Mendes P Gene networks: How to put the function in genomics Trends Biotechnol 2002, 20(11):467-472 10.1016/ S0167-7799(02)02053-X 12413821
    • (2002) Trends Biotechnol , vol.20 , Issue.11 , pp. 467-472
    • Brazhnik, P.1    de la Fuente, A.2    Mendes, P.3
  • 82
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • 10.1089/10665270252833208 11911796
    • de Jong H Modeling and simulation of genetic regulatory systems: A literature review J Comput Biol 2002, 9(1):67-103 10.1089/ 10665270252833208 11911796
    • (2002) J Comput Biol , vol.9 , Issue.1 , pp. 67-103
    • de Jong, H.1
  • 83
    • 0033725197 scopus 로고    scopus 로고
    • Mathematical modeling of gene networks
    • 10.1016/S0896-6273(00)81194-0 10896154
    • Smolen P Baxter DA Byrne JH Mathematical modeling of gene networks Neuron 2000, 26(3):567-580 10.1016/S0896-6273(00)81194-0 10896154
    • (2000) Neuron , vol.26 , Issue.3 , pp. 567-580
    • Smolen, P.1    Baxter, D.A.2    Byrne, J.H.3
  • 85
    • 0034644270 scopus 로고    scopus 로고
    • The segment polarity network is a robust developmental module
    • 10.1038/35018085 10910359
    • von Dassow G Meir E Munro EM Odell GM The segment polarity network is a robust developmental module Nature 2000, 406(6792):188-192 10.1038/ 35018085 10910359
    • (2000) Nature , vol.406 , Issue.6792 , pp. 188-192
    • von Dassow, G.1    Meir, E.2    Munro, E.M.3    Odell, G.M.4
  • 86
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
    • (Oxford, England) 10.1093/bioinformatics/btg015 12611808
    • Hucka M Finney A Sauro HM Bolouri H Doyle JC Kitano H Arkin AP Bornstein BJ Bray D Cornish-Bowden A The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models Bioinformatics (Oxford, England) 2003, 19(4):524-531 10.1093/ bioinformatics/btg015 12611808
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6    Arkin, A.P.7    Bornstein, B.J.8    Bray, D.9    Cornish-Bowden, A.10
  • 87
    • 0032499741 scopus 로고    scopus 로고
    • Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
    • 22622 9618484 10.1073/pnas.95.12.6750
    • Goss PJ Peccoud J Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets Proc Natl Acad Sci USA 1998, 95(12):6750-6755 22622 9618484 10.1073/pnas.95.12.6750
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.12 , pp. 6750-6755
    • Goss, P.J.1    Peccoud, J.2
  • 88
    • 33645299531 scopus 로고    scopus 로고
    • A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals
    • 10.1142/S021972000600176X 16568547
    • Matsuno H Inouye ST Okitsu Y Fujii Y Miyano S A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals J Bioinform Comput Biol 2006, 4(1):139-153 10.1142/ S021972000600176X 16568547
    • (2006) J Bioinform Comput Biol , vol.4 , Issue.1 , pp. 139-153
    • Matsuno, H.1    Inouye, S.T.2    Okitsu, Y.3    Fujii, Y.4    Miyano, S.5
  • 89
    • 0029028963 scopus 로고
    • Circuit simulation of genetic networks
    • 10.1126/science.7624793 7624793
    • McAdams HH Shapiro L Circuit simulation of genetic networks Science 1995, 269(5224):650-656 10.1126/science.7624793 7624793
    • (1995) Science , vol.269 , Issue.5224 , pp. 650-656
    • McAdams, H.H.1    Shapiro, L.2
  • 90
    • 33748532797 scopus 로고    scopus 로고
    • Reconstruction of gene regulatory networks under the Finite State Linear Model
    • 16901105
    • Ruklisa D Brazma A Viksna J Reconstruction of gene regulatory networks under the Finite State Linear Model Genome informatics 2005, 16(2):225-236 16901105
    • (2005) Genome Informatics , vol.16 , Issue.2 , pp. 225-236
    • Ruklisa, D.1    Brazma, A.2    Viksna, J.3
  • 91
    • 2942572373 scopus 로고    scopus 로고
    • Reverse engineering of gene regulatory networks: A finite state linear model
    • 10.1186/gb-2003-4-6-p5
    • Brazma A Schlitt T Reverse engineering of gene regulatory networks: A finite state linear model Genome Biology 2003, 4(6):P5 10.1186/ gb-2003-4-6-p5
    • (2003) Genome Biology , vol.4 , Issue.6
    • Brazma, A.1    Schlitt, T.2
  • 94
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanisms in gene expression
    • 19596 9023339 10.1073/pnas.94.3.814
    • McAdams HH Arkin A Stochastic mechanisms in gene expression Proc Natl Acad Sci USA 1997, 94(3):814-819 19596 9023339 10.1073/pnas.94.3.814
    • (1997) Proc Natl Acad Sci USA , vol.94 , Issue.3 , pp. 814-819
    • McAdams, H.H.1    Arkin, A.2
  • 95
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • 1410811 15166317 10.1126/science.1098641
    • Raser JM O'Shea EK Control of stochasticity in eukaryotic gene expression Science 2004, 304(5678):1811-1814 1410811 15166317 10.1126/ science.1098641
    • (2004) Science , vol.304 , Issue.5678 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 96
    • 0842285841 scopus 로고    scopus 로고
    • Summing up the noise in gene networks
    • 10.1038/nature02257 14749823
    • Paulsson J Summing up the noise in gene networks Nature 2004, 427(6973):415-418 10.1038/nature02257 14749823
    • (2004) Nature , vol.427 , Issue.6973 , pp. 415-418
    • Paulsson, J.1
  • 97
    • 0037687416 scopus 로고    scopus 로고
    • Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
    • 156306 12730377 10.1073/pnas.0933416100
    • Tegner J Yeung MK Hasty J Collins JJ Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling Proc Natl Acad Sci USA 2003, 100(10):5944-5949 156306 12730377 10.1073/pnas.0933416100
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.10 , pp. 5944-5949
    • Tegner, J.1    Yeung, M.K.2    Hasty, J.3    Collins, J.J.4
  • 98
    • 2342578714 scopus 로고    scopus 로고
    • Spatiotemporal control of gene expression with pulse-generating networks
    • 404049 15096621 10.1073/pnas.0307571101
    • Basu S Mehreja R Thiberge S Chen MT Weiss R Spatiotemporal control of gene expression with pulse-generating networks Proc Natl Acad Sci USA 2004, 101(17):6355-6360 404049 15096621 10.1073/pnas.0307571101
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.17 , pp. 6355-6360
    • Basu, S.1    Mehreja, R.2    Thiberge, S.3    Chen, M.T.4    Weiss, R.5
  • 99
    • 17144456808 scopus 로고    scopus 로고
    • Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion
    • 125456 11350942 10.1093/emboj/20.10.2528
    • Becskei A Seraphin B Serrano L Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion EMBO J 2001, 20(10):2528-2535 125456 11350942 10.1093/emboj/20.10.2528
    • (2001) EMBO J , vol.20 , Issue.10 , pp. 2528-2535
    • Becskei, A.1    Seraphin, B.2    Serrano, L.3
  • 100
    • 0034212551 scopus 로고    scopus 로고
    • Engineering stability in gene networks by autoregulation
    • 10.1038/35014651 10850721
    • Becskei A Serrano L Engineering stability in gene networks by autoregulation Nature 2000, 405(6786):590-593 10.1038/35014651 10850721
    • (2000) Nature , vol.405 , Issue.6786 , pp. 590-593
    • Becskei, A.1    Serrano, L.2
  • 101
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • 10.1038/35002125 10659856
    • Elowitz MB Leibler S A synthetic oscillatory network of transcriptional regulators Nature 2000, 403(6767):335-338 10.1038/35002125 10659856
    • (2000) Nature , vol.403 , Issue.6767 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 102
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • 10.1038/35002131 10659857
    • Gardner TS Cantor CR Collins JJ Construction of a genetic toggle switch in Escherichia coli Nature 2000, 403(6767):339-342 10.1038/35002131 10659857
    • (2000) Nature , vol.403 , Issue.6767 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 103
  • 105
    • 0642336165 scopus 로고    scopus 로고
    • The engineering of gene regulatory networks
    • 10.1146/annurev.bioeng.5.040202.121553 14527313
    • Kaern M Blake WJ Collins JJ The engineering of gene regulatory networks Annu Rev Biomed Eng 2003, 5:179-206 10.1146/ annurev.bioeng.5.040202.121553 14527313
    • (2003) Annu Rev Biomed Eng , vol.5 , pp. 179-206
    • Kaern, M.1    Blake, W.J.2    Collins, J.J.3
  • 107
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • 25624 9843569
    • Spellman PT Sherlock G Zhang MQ Iyer VR Anders K Eisen MB Brown PO Botstein D Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 1998, 9(12):3273-3297 25624 9843569
    • (1998) Mol Biol Cell , vol.9 , Issue.12 , pp. 3273-3297
    • Spellman, P.T.1    Sherlock, G.2    Zhang, M.Q.3    Iyer, V.R.4    Anders, K.5    Eisen, M.B.6    Brown, P.O.7    Botstein, D.8    Futcher, B.9
  • 108
    • 12244267727 scopus 로고    scopus 로고
    • Global transcriptional responses of fission yeast to environmental stress
    • 140239 12529438 10.1091/mbc.E02-08-0499
    • Chen D Toone WM Mata J Lyne R Burns G Kivinen K Brazma A Jones N Bahler J Global transcriptional responses of fission yeast to environmental stress Mol Biol Cell 2003, 14(1):214-229 140239 12529438 10.1091/ mbc.E02-08-0499
    • (2003) Mol Biol Cell , vol.14 , pp. 214-229
    • Chen, D.1    Toone, W.M.2    Mata, J.3    Lyne, R.4    Burns, G.5    Kivinen, K.6    Brazma, A.7    Jones, N.8    Bahler, J.9
  • 111
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • 10.1126/science.1105103 15692050
    • de Lichtenberg U Jensen LJ Brunak S Bork P Dynamic complex formation during the yeast cell cycle Science 2005, 307(5710):724-727 10.1126/ science.1105103 15692050
    • (2005) Science , vol.307 , Issue.5710 , pp. 724-727
    • de Lichtenberg, U.1    Jensen, L.J.2    Brunak, S.3    Bork, P.4
  • 112
    • 0037135134 scopus 로고    scopus 로고
    • Systematic identification of pathways that couple cell growth and division in yeast
    • 10.1126/science.1070850 12089449
    • Jorgensen P Nishikawa JL Breitkreutz BJ Tyers M Systematic identification of pathways that couple cell growth and division in yeast Science 2002, 297(5580):395-400 10.1126/science.1070850 12089449
    • (2002) Science , vol.297 , Issue.5580 , pp. 395-400
    • Jorgensen, P.1    Nishikawa, J.L.2    Breitkreutz, B.J.3    Tyers, M.4
  • 113
    • 0015823097 scopus 로고
    • Boolean formalization of genetic control circuits
    • 10.1016/0022-5193(73)90247-6 4588055
    • Thomas R Boolean formalization of genetic control circuits J Theor Biol 1973, 42(3):563-585 10.1016/0022-5193(73)90247-6 4588055
    • (1973) J Theor Biol , vol.42 , Issue.3 , pp. 563-585
    • Thomas, R.1


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