-
1
-
-
0036207347
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
12
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. Journal of Computational Biology 7(3): 601-620.
-
(2000)
Journal of Computational Biology
, vol.7
, Issue.3
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
13
-
-
34547844096
-
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
-
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
-
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
-
17
-
-
77950910419
-
Revealing strengths and weaknesses of methods for gene network inference
-
Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A 107(14): 6286-91.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.14
, pp. 6286-91
-
-
Marbach, D.1
Prill, R.J.2
Schaffter, T.3
Mattiussi, C.4
Floreano, D.5
-
18
-
-
77958482102
-
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
-
19
-
-
77949644952
-
Towards a rigorous assessment of systems biology models: The DREAM3 challenges
-
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, et al. (2010) Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One 5(2): e9202.
-
(2010)
PLoS One
, vol.5
, Issue.2
-
-
Prill, R.J.1
Marbach, D.2
Saez-Rodriguez, J.3
Sorger, P.K.4
Alexopoulos, L.G.5
-
20
-
-
59649110273
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|