메뉴 건너뛰기




Volumn 5, Issue 9, 2010, Pages 1-10

Petri nets with fuzzy logic (PNFL): Reverse engineering and parametrization

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AREA UNDER THE CURVE; ARTICLE; COMPUTER MODEL; FUZZY LOGIC; GENE EXPRESSION; GENE MUTATION; GENETIC DATABASE; GENETIC ENGINEERING; GENETIC REGULATION; KNOCKOUT GENE; MATHEMATICAL ANALYSIS; RELIABILITY; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; C57BL MOUSE; FEMALE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; HUMAN; MALE; METHODOLOGY; MOUSE;

EID: 77958508515     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012807     Document Type: Article
Times cited : (35)

References (31)
  • 1
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9(1): 67-103.
    • (2002) J Comput Biol , vol.9 , Issue.1 , pp. 67-103
    • de Jong, H.1
  • 2
    • 0036843965 scopus 로고    scopus 로고
    • Gene networks: How to put the function in genomics
    • Brazhnik P, de la Fuente A, Mendes P (2002) Gene networks: how to put the function in genomics. Trends Biotechnol 20(11): 467-72.
    • (2002) Trends Biotechnol , vol.20 , Issue.11 , pp. 467-72
    • Brazhnik, P.1    de la Fuente, A.2    Mendes, P.3
  • 4
    • 38449088751 scopus 로고    scopus 로고
    • Inferring cellular networks-a review
    • Markowetz F, Spang R (2007) Inferring cellular networks-a review. BMC Bioinformatics 8 Suppl 6: S5.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 6
    • Markowetz, F.1    Spang, R.2
  • 6
    • 61349180117 scopus 로고    scopus 로고
    • Gene regulatory network inference: Data integration in dynamic models-a review
    • Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R (2008) Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96(1): 86-103.
    • (2008) Biosystems , vol.96 , Issue.1 , pp. 86-103
    • Hecker, M.1    Lambeck, S.2    Toepfer, S.3    van Someren, E.4    Guthke, R.5
  • 7
    • 70549083891 scopus 로고    scopus 로고
    • Inference of gene regulatory networks using timeseries data: A survey
    • Sima C, Hua J, Jung S (2009) Inference of gene regulatory networks using timeseries data: a survey. Curr Genomics 10(6): 416-29.
    • (2009) Curr Genomics , vol.10 , Issue.6 , pp. 416-29
    • Sima, C.1    Hua, J.2    Jung, S.3
  • 8
    • 0036683181 scopus 로고    scopus 로고
    • Linking the genes: Inferring quantitative gene networks from microarray data
    • de la Fuente A, Brazhnik P, Mendes P (2002) Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet 18(8): 395-8.
    • (2002) Trends Genet , vol.18 , Issue.8 , pp. 395-398
    • de la Fuente, A.1    Brazhnik, P.2    Mendes, P.3
  • 9
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301(5629): 102-5.
    • (2003) Science , vol.301 , Issue.5629 , pp. 102-105
    • Gardner, T.S.1    di Bernardo, D.2    Lorenz, D.3    Collins, J.J.4
  • 10
    • 14844307159 scopus 로고    scopus 로고
    • Inferring quantitative models of regulatory networks from expression data
    • Nachman I, Regev A, Friedman N (2004) Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 Suppl 1: i248-56.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Nachman, I.1    Regev, A.2    Friedman, N.3
  • 11
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context
    • Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, et al. (2006) ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context. BMC Bioinformatics 7(Suppl 1): S7.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 1
    • Margolin, A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky, G.5
  • 13
    • 34547844096 scopus 로고    scopus 로고
    • Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: Synthetic versus real data
    • Soranzo N, Bianconi G, Altafini C (2007) Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data. Bioinformatics 23(13): 1640-7.
    • (2007) Bioinformatics , vol.23 , Issue.13 , pp. 1640-1647
    • Soranzo, N.1    Bianconi, G.2    Altafini, C.3
  • 15
    • 66449116353 scopus 로고    scopus 로고
    • Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
    • Michoel T, De Smet R, Joshi A, Van de Peer Y, Marchal K (2009) Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst Biol 3: 49.
    • (2009) BMC Syst Biol , vol.3 , pp. 49
    • Michoel, T.1    de Smet, R.2    Joshi, A.3    van de Peer, Y.4    Marchal, K.5
  • 16
    • 67650927399 scopus 로고    scopus 로고
    • Granger causality vs. dynamic Bayesian network inference: A comparative study
    • Zou C, Denby KJ, Feng J (2009) Granger causality vs. dynamic Bayesian network inference: a comparative study. BMC Bioinformatics 10: 122.
    • (2009) BMC Bioinformatics , vol.10 , pp. 122
    • Zou, C.1    Denby, K.J.2    Feng, J.3
  • 18
    • 77958482102 scopus 로고    scopus 로고
    • Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics
    • P-136
    • Windhager L, Zimmer R (2008) Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. German Conference on Bioinformatics, Lecture Notes in Informatics P-136: 106-115.
    • (2008) Lecture Notes In Informatics , pp. 106-115
    • Windhager, L.1    Zimmer, R.2
  • 20
    • 59649110273 scopus 로고    scopus 로고
    • Generating realistic in silico gene networks for performance assessment of reverse engineering methods
    • Marbach D, Schaffter T, Mattiussi C, Floreano D (2009) Generating realistic in silico gene networks for performance assessment of reverse engineering methods. J Comput Biol 16(2): 229-39.
    • (2009) J Comput Biol , vol.16 , Issue.2 , pp. 229-39
    • Marbach, D.1    Schaffter, T.2    Mattiussi, C.3    Floreano, D.4
  • 21
    • 33845417184 scopus 로고    scopus 로고
    • Application of Petri net based analysis techniques to signal transduction pathways
    • Sackmann A, Heiner M, Koch I (2006) Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics 7: 482.
    • (2006) BMC Bioinformatics , vol.7 , pp. 482
    • Sackmann, A.1    Heiner, M.2    Koch, I.3
  • 22
    • 3042699469 scopus 로고    scopus 로고
    • Model validation of biological pathways using Petri nets-demonstrated for apoptosis
    • Heiner M, Koch I, Will J (2004) Model validation of biological pathways using Petri nets-demonstrated for apoptosis. Biosystems 75(1-3): 15-28.
    • (2004) Biosystems , vol.75 , Issue.1-3 , pp. 15-28
    • Heiner, M.1    Koch, I.2    Will, J.3
  • 23
    • 33947508946 scopus 로고    scopus 로고
    • Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets
    • Chen L, Qi-Wei G, Nakata M, Matsuno H, Miyano S (2007) Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. Journal of Biosciences 32(1): 113-127.
    • (2007) Journal of Biosciences , vol.32 , Issue.1 , pp. 113-127
    • Chen, L.1    Qi-Wei, G.2    Nakata, M.3    Matsuno, H.4    Miyano, S.5
  • 25
    • 0024645936 scopus 로고
    • Petri nets: Properties, analysis and applications
    • Murata T (1989) Petri nets: Properties, analysis and applications. Proceedings of the IEEE 77(4): 541-580.
    • (1989) Proceedings of the IEEE , vol.77 , Issue.4 , pp. 541-580
    • Murata, T.1
  • 26
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • Chaouiya C (2007) Petri net modelling of biological networks. Brief Bioinformatics 8(4): 210-219.
    • (2007) Brief Bioinformatics , vol.8 , Issue.4 , pp. 210-219
    • Chaouiya, C.1
  • 27
    • 0345170900 scopus 로고    scopus 로고
    • Biopathways representation and simulation on hybrid functional Petri net
    • Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, et al. (2003) Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol 3(3): 389-404.
    • (2003) Silico Biol , vol.3 , Issue.3 , pp. 389-404
    • Matsuno, H.1    Tanaka, Y.2    Aoshima, H.3    Doi, A.4    Matsui, M.5
  • 29
    • 0029270928 scopus 로고
    • Fuzzy logic systems for engineering: A tutorial
    • Mendel LM (1995) Fuzzy logic systems for engineering: a tutorial. Proceedings of the IEEE 83(3): 345-377.
    • (1995) Proceedings of the IEEE , vol.83 , Issue.3 , pp. 345-377
    • Mendel, L.M.1
  • 30
    • 17044396348 scopus 로고    scopus 로고
    • Logic functions of the genomic cis-regulatory code
    • Istrail S, Davidson EH (2005) Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci U S A 102(14): 4954-9.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.14 , pp. 4954-4959
    • Istrail, S.1    Davidson, E.H.2
  • 31
    • 63849258962 scopus 로고    scopus 로고
    • Combining multiple results of a reverse-engineering algorithm: Application to the DREAM five-gene network challenge
    • Marbach D, Mattiussi C, Floreano D (2009) Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge. Ann N Y Acad Sci 1158: 102-13.
    • (2009) Ann N Y Acad Sci , vol.1158 , pp. 102-13
    • Marbach, D.1    Mattiussi, C.2    Floreano, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.