메뉴 건너뛰기




Volumn 10, Issue 1, 2011, Pages

Fitting Boolean networks from steady state perturbation data

Author keywords

Bayesian modeling; boolean network; gene perturbation

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; BOOLEAN TETWORK; CANCER CELL; GENE PERTURBATION; GENE REGULATORY NETWORK; GENETIC ANALYSIS; METHODOLOGY; STATISTICAL ANALYSIS; STEADY STATE; TUMOR GENE;

EID: 80455132486     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1727     Document Type: Article
Times cited : (7)

References (40)
  • 3
    • 0002892773 scopus 로고    scopus 로고
    • (E. Aarts, J.K. Lenstra eds) Princeton, NJ: Princeton University Press, chapter Simulated Annealing
    • Aarts, E., J. Korst, and P. van Laarhoven (1997): Local Search in Combinatorial Optimization (E. Aarts, J.K. Lenstra eds), Princeton, NJ: Princeton University Press, chapter Simulated Annealing, 91-120.
    • (1997) Local Search in Combinatorial Optimization , pp. 91-120
    • Aarts, E.1    Korst, J.2    Van Laarhoven, P.3
  • 4
    • 0038620466 scopus 로고    scopus 로고
    • A simulated annealing algorithm for maximum likelihood pedigree reconstruction
    • DOI 10.1016/S0040-5809(02)00048-5
    • Almudevar, A. (2003): "A simulated annealing algorithm for maximum likelihood pedigree reconstruction" Theoretical Population Biology, 63, 63-75. (Pubitemid 38042770)
    • (2003) Theoretical Population Biology , vol.63 , Issue.2 , pp. 63-75
    • Almudevar, A.1
  • 5
    • 33846596160 scopus 로고    scopus 로고
    • A graphical approach to relatedness inference
    • DOI 10.1016/j.tpb.2006.10.005, PII S0040580906001328
    • Almudevar, A. (2007): "A graphical approach to relatedness inference" Theoretical Population Biology, 71, 213-229. (Pubitemid 46186471)
    • (2007) Theoretical Population Biology , vol.71 , Issue.2 , pp. 213-229
    • Almudevar, A.1
  • 9
    • 0000419877 scopus 로고    scopus 로고
    • Error-Free and Best-Fit Extensions of Partially Defined Boolean Functions
    • Boros, E., T. Ibaraki, and K. Makino (1998): "Error-free and best-fit extensions of partially defined boolean functions" Inform Comput, 140, 254-283. (Pubitemid 128453343)
    • (1998) Information and Computation , vol.140 , Issue.2 , pp. 254-283
    • Boros, E.1    Ibaraki, T.2    Makino, K.3
  • 10
    • 32344446687 scopus 로고
    • Understanding the Metropolis-Hastings Algorithm
    • Chib, S. and E. Greenberg (1995): "Understanding the metropolis-hastings algorithm" The American Statistician, 49, 327-335. (Pubitemid 126008969)
    • (1995) American Statistician , vol.49 , Issue.4 , pp. 327-335
    • Chib, S.1    Greenberg, E.2
  • 11
    • 33646182727 scopus 로고    scopus 로고
    • Organizing cell renewal in the intestine: Stem cells, signals and combinatorial control
    • Crosnier, C., D. Stamataki, and J. Lewis (2006): "Organizing cell renewal in the intestine: stem cells, signals and combinatorial control" Nature Reviews Genetics, 7, 349-359.
    • (2006) Nature Reviews Genetics , vol.7 , pp. 349-359
    • Crosnier, C.1    Stamataki, D.2    Lewis, J.3
  • 14
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan, D. and R. A. Weinberg (2000): "The hallmarks of cancer" Cell, 100, 57-70. (Pubitemid 30046295)
    • (2000) Cell , vol.100 , Issue.1 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 15
    • 77956890234 scopus 로고
    • Monte carlo sampling methods using Markov chains and their applications
    • Hastings, W. K. (1970): "Monte Carlo sampling methods using Markov chains and their applications" Biometrika, 57, 97-109, URL .
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 16
    • 0034715919 scopus 로고    scopus 로고
    • Shape-Dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks
    • Huang, S. and D. E. Ingber (2000): "Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks" Exp Cell Res, 261, 91-103.
    • (2000) Exp Cell Res , vol.261 , pp. 91-103
    • Huang, S.1    Ingber, D.E.2
  • 17
    • 0000660076 scopus 로고    scopus 로고
    • Discovery of regulatory interactions through perturbation: Inference and experimental design
    • Ideker, T. E., V. Thorsson, and R. M. Karp (2000): "Discovery of regulatory interactions through perturbation: Inference and experimental design" Pacific Symposium on Biocomputing, 5, 302-313.
    • (2000) Pacific Symposium on Biocomputing , vol.5 , pp. 302-313
    • Ideker, T.E.1    Thorsson, V.2    Karp, R.M.3
  • 19
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman, S. (1969): "Metabolic stability and epigenesis in randomly constructed genetic nets" J Theor Biol., 22, 437-467.
    • (1969) J Theor Biol. , vol.22 , pp. 437-467
    • Kauffman, S.1
  • 20
    • 0034287393 scopus 로고    scopus 로고
    • General nonlinear framework for the analysis of gene interaction via multivariate expression arrays
    • DOI 10.1117/1.1289142
    • Kim, S., E. R. Dougherty, M. L. Bittner, Y. Chen, K. Sivakumar, P. Meltzer, and J. M. Trent (2000): "General nonlinear framework for the analysis of gene interaction via multivariate expression arrays" Journal of Biomedical Optics, 5, 411-424. (Pubitemid 32067274)
    • (2000) Journal of Biomedical Optics , vol.5 , Issue.4 , pp. 411-424
    • Kim, S.1    Dougherty, E.R.2    Bittner, M.L.3    Chen, Y.4    Sivakumar, K.5    Meltzer, P.6    Trent, J.M.7
  • 22
    • 0038047901 scopus 로고    scopus 로고
    • On learning gene regulatory networks under the boolean network model
    • Lahdesmaki, H., I. Shmulevich, and O. Yli-Harja (2003): "On learning gene regulatory networks under the boolean network model" Machine Learning, 52, 147-167.
    • (2003) Machine Learning , vol.52 , pp. 147-167
    • Lahdesmaki, H.1    Shmulevich, I.2    Yli-Harja, O.3
  • 23
    • 0035924702 scopus 로고    scopus 로고
    • Id proteins at the cross-road of development and cancer
    • DOI 10.1038/sj/onc/1205093
    • Lasorella, A., T. Uo, and A. Iavarone (2001): "Id proteins at the cross-road of development and cancer" Oncogene, 20, 8326-8333. (Pubitemid 34121903)
    • (2001) Oncogene , vol.20 , Issue.REV. ISS. 8 , pp. 8326-8333
    • Lasorella, A.1    Uo, T.2    Iavarone, A.3
  • 27
    • 27744569877 scopus 로고    scopus 로고
    • Generating Boolean networks with a prescribed attractor structure
    • DOI 10.1093/bioinformatics/bti664
    • Pal, R., I. Ivanov, A. Datta, and E. R. Dougherty (2005): "Generating boolean networks with a prescribed attractor structure" Bioinformatics, 21, 4021-4025. (Pubitemid 41631844)
    • (2005) Bioinformatics , vol.21 , Issue.21 , pp. 4021-4025
    • Pal, R.1    Ivanov, I.2    Datta, A.3    Bittner, M.L.4    Dougherty, E.R.5
  • 28
    • 17644427718 scopus 로고    scopus 로고
    • Causal protein-signaling networks derived from multiparameter single-cell data
    • DOI 10.1126/science.1105809
    • Sachs, K., O. Perez, D. Pe'er, D. A. Lauffenburger, and G. P. Nolan (2005): "Causal protein-signaling networks derived from multiparameter single-cell data" Science, 308, 523-529. (Pubitemid 40570578)
    • (2005) Science , vol.308 , Issue.5721 , pp. 523-529
    • Sachs, K.1    Perez, O.2    Pe'er, D.3    Lauffenburger, D.A.4    Nolan, G.P.5
  • 29
    • 0030871667 scopus 로고    scopus 로고
    • High-intensity Raf signal causes cell cycle arrest mediated by p21(Cip1)
    • Sewing, A., B. Wiseman, A. C. Lloyd, and H. Land (1997): "High-intensity raf signal causes cell cycle arrest mediated by p21cip1" Mol Cell Biol, 17, 5588- 5597. (Pubitemid 27357655)
    • (1997) Molecular and Cellular Biology , vol.17 , Issue.9 , pp. 5588-5597
    • Sewing, A.1    Wiseman, B.2    Lloyd, A.C.3    Land, H.4
  • 31
    • 0035999984 scopus 로고    scopus 로고
    • Binary analysis and optimization-based normalization of gene expression data
    • Shmulevich, I. andW. Zhang (2002): "Binary analysis and optimization-based normalization of gene expression data" Bioinformatics, 18, 555-565. (Pubitemid 34521045)
    • (2002) Bioinformatics , vol.18 , Issue.4 , pp. 555-565
    • Shmulevich, I.1    Zhang, W.2
  • 33
    • 0036138322 scopus 로고    scopus 로고
    • 2 easy steps
    • 2 easy steps" Bioinformatics, 17, 1183-1197. (Pubitemid 33735345)
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1183-1197
    • Wagner, A.1
  • 34
    • 0036177681 scopus 로고    scopus 로고
    • Estimating coarse gene network structure from large-scale gene perturbation data
    • DOI 10.1101/gr.193902
    • Wagner, A. (2002): "Estimating coarse gene network structure from large-scale gene perturbation data" Genome Research, 12, 309-315. (Pubitemid 34162997)
    • (2002) Genome Research , vol.12 , Issue.2 , pp. 309-315
    • Wagner, A.1
  • 35
    • 1842607542 scopus 로고    scopus 로고
    • Reconstructing pathways in large genetic networks from genetic perturbations
    • DOI 10.1089/106652704773416885
    • Wagner, A. (2004): "Reconstructing pathways in large genetic networks from genetic perturbations" Journal of Computational Biology, 11, 53-60. (Pubitemid 38429363)
    • (2004) Journal of Computational Biology , vol.11 , Issue.1 , pp. 53-60
    • Wagner, A.1
  • 37
    • 33847627873 scopus 로고    scopus 로고
    • Tumor suppressor p53 restricts Ras stimulation of RhoA and cancer cell motility
    • DOI 10.1038/nsmb1208, PII NSMB1208
    • 53 restricts ras stimulation of rhoa and cancer cell motility" Nat Struct Mol Biol, 14, 215-223. (Pubitemid 46355577)
    • (2007) Nature Structural and Molecular Biology , vol.14 , Issue.3 , pp. 215-223
    • Xia, M.1    Land, H.2
  • 38
    • 44049090789 scopus 로고    scopus 로고
    • Knocking down Wnt9a mRNA levels increases cellular proliferation
    • DOI 10.1007/s11033-007-9055-9
    • Xiang, Y., G. Lin, Q. Zhang, Y. Tan, and G. Lu (2008): "Knocking down wnt9a mrna levels increases cellular proliferation" Mol Biol Rep., 35, 73-79. (Pubitemid 351713234)
    • (2008) Molecular Biology Reports , vol.35 , Issue.2 , pp. 73-79
    • Xiang, Y.1    Lin, G.2    Zhang, Q.3    Tan, Y.4    Lu, G.5
  • 39
    • 1542463515 scopus 로고    scopus 로고
    • Binarization of microarray data on the basis of a mixture model
    • Zhou, X., X. Wang, and E. R. Dougherty (2003): "Binarization of microarray data on the basis of a mixture model" Molecular Cancer Therapeutics, 2, 679-684.
    • (2003) Molecular Cancer Therapeutics , vol.2 , pp. 679-684
    • Zhou, X.1    Wang, X.2    Dougherty, E.R.3
  • 40
    • 10244239406 scopus 로고    scopus 로고
    • A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks
    • DOI 10.1093/bioinformatics/bth318
    • Zhou, X., X. Wang, R. Pal, I. Ivanov, M. Bittner, and E. R. Dougherty (2004): "A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks" Bioinformatics, 20, 2918-2927, URL . (Pubitemid 39619183)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 2918-2927
    • Zhou, X.1    Wang, X.2    Pal, R.3    Ivanov, I.4    Bittner, M.5    Dougherty, E.R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.