-
1
-
-
33746353952
-
Applying dynamic Bayesian networks to perturbed gene expression data
-
Dojer N, Gambin A, Mizera A, Wilczynski B, Tiuryn J, Applying dynamic Bayesian networks to perturbed gene expression data, BMC Bioinformatics 7:249, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 249
-
-
Dojer, N.1
Gambin, A.2
Mizera, A.3
Wilczynski, B.4
Tiuryn, J.5
-
2
-
-
3042738945
-
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data
-
Kim S, Imoto S, Miyano S, Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data, Biosystems 75:57-65, 2004.
-
(2004)
Biosystems
, vol.75
, pp. 57-65
-
-
Kim, S.1
Imoto, S.2
Miyano, S.3
-
3
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
Friedman N, Inferring cellular networks using probabilistic graphical models, Science 303:799-805, 2004.
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
4
-
-
0036372453
-
Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression
-
Imoto S, Goto T, Miyano S, Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression, Pac Symp Biocomput 7:175-186, 2002.
-
(2002)
Pac Symp Biocomput
, vol.7
, pp. 175-186
-
-
Imoto, S.1
Goto, T.2
Miyano, S.3
-
5
-
-
3242891560
-
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
-
Tamada Y, Kim S, Bannai H, Imoto S, Tashiro K, Kuhara S, Miyano S, Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection, Bioinformatics 19:227-236, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 227-236
-
-
Tamada, Y.1
Kim, S.2
Bannai, H.3
Imoto, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
6
-
-
1642403354
-
Identification of genetic networks
-
Xiong M, Li J, Fang X, Identification of genetic networks, Genetics 166:1037-1052, 2004.
-
(2004)
Genetics
, vol.166
, pp. 1037-1052
-
-
Xiong, M.1
Li, J.2
Fang, X.3
-
7
-
-
0033677274
-
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function
-
Akutsu T, Miyano S, Kuhara S, Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function, J Comput Biol 7:331-343, 2000.
-
(2000)
J Comput Biol
, vol.7
, pp. 331-343
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
8
-
-
16344368806
-
Intervention in context-sensitive probabilistic Boolean networks
-
Pal R, Datta A, Bittner ML, Dougherty ER, Intervention in context-sensitive probabilistic Boolean networks, Bioinformatics 21:1211-1218, 2005.
-
(2005)
Bioinformatics
, vol.21
, pp. 1211-1218
-
-
Pal, R.1
Datta, A.2
Bittner, M.L.3
Dougherty, E.R.4
-
9
-
-
0036772705
-
Gene perturbation and intervention in probabilistic Boolean networks
-
Shmulevich I, Dougherty ER, Mang W, Gene perturbation and intervention in probabilistic Boolean networks, Bioinformatics 18 1319-13317, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. 1319-13317
-
-
Shmulevich, I.1
Dougherty, E.R.2
Mang, W.3
-
10
-
-
15944364151
-
An empirical Bayes approach to inferring large-scale gene association networks
-
Schäfer J, Strimmer K, An empirical Bayes approach to inferring large-scale gene association networks, Bioinformatics 21 754-764, 2005.
-
(2005)
Bioinformatics
, vol.21
, pp. 754-764
-
-
Schäfer, J.1
Strimmer, K.2
-
11
-
-
0034729586
-
A fuzzy logic approach to analyzing gene expression data
-
Woolf PJ, Wang Y, A fuzzy logic approach to analyzing gene expression data, Physiol Genomics 3:9-15, 2000.
-
(2000)
Physiol Genomics
, vol.3
, pp. 9-15
-
-
Woolf, P.J.1
Wang, Y.2
-
12
-
-
0028844979
-
A mathematical framework for describing and analyzing gene regulatory networks
-
Mestl T, Plahte E, Omholt SW, A mathematical framework for describing and analyzing gene regulatory networks, J Theor Biol 176 291-300, 1995.
-
(1995)
J Theor Biol
, vol.176
, pp. 291-300
-
-
Mestl, T.1
Plahte, E.2
Omholt, S.W.3
-
13
-
-
85032779470
-
Finding module-based gene networks in time-course gene expression data with state space models
-
Yamaguchi R, Yoshida R, Imoto S, Higuchi T, Miyano S, Finding module-based gene networks in time-course gene expression data with state space models, JEEE Signal Process Mag 24:37-46, 2007.
-
(2007)
JEEE Signal Process Mag
, vol.24
, pp. 37-46
-
-
Yamaguchi, R.1
Yoshida, R.2
Imoto, S.3
Higuchi, T.4
Miyano, S.5
-
14
-
-
34248147537
-
State space modeling of yeast gene expression dynamics
-
Haavisto O, Hyotyniemi H, Roos C, State space modeling of yeast gene expression dynamics, J Bioinform Comput Biol 5:31-46, 2007.
-
(2007)
J Bioinform Comput Biol
, vol.5
, pp. 31-46
-
-
Haavisto, O.1
Hyotyniemi, H.2
Roos, C.3
-
15
-
-
33751008680
-
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
-
Sanguinetti G, Lawrence ND, Rattray M, Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities, Bioinformatics 22:27775 2781, 2006.
-
(2006)
Bioinformatics
, vol.22
, pp. 27775-32781
-
-
Sanguinetti, G.1
Lawrence, N.D.2
Rattray, M.3
-
16
-
-
33847348163
-
Causality and pathway search in microarray time series experiment
-
Mukhopadhyay ND, Chatterjee S, Causality and pathway search in microarray time series experiment, Bioinformatics 23 412-449, 2007.
-
(2007)
Bioinformatics
, vol.23
, pp. 412-449
-
-
Mukhopadhyay, N.D.1
Chatterjee, S.2
-
17
-
-
34547852213
-
Time-vaxying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method
-
Fujita A, Sato JR, Garay-Malpartida HM, Morettin PA, Sogayar MC, Ferreira CE, Time-vaxying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method, Bioinformatics 23:1623-1630, 2007.
-
(2007)
Bioinformatics
, vol.23
, pp. 1623-1630
-
-
Fujita, A.1
Sato, J.R.2
Garay-Malpartida, H.M.3
Morettin, P.A.4
Sogayar, M.C.5
Ferreira, C.E.6
-
18
-
-
35748964479
-
Modeling gene expression regulatory networks with the sparse vector autoregressive model
-
Fujita A, Sato JR, Garay-Malpartida HM, Yamaguchi. R, Miyano S, Sogayar MC, Ferreira CE, Modeling gene expression regulatory networks with the sparse vector autoregressive model, BMC Syst Biol 1:39, 2007.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 39
-
-
Fujita, A.1
Sato, J.R.2
Garay-Malpartida, H.M.3
Yamaguchi, R.4
Miyano, S.5
Sogayar, M.C.6
Ferreira, C.E.7
-
19
-
-
0000351727
-
Investigating causal relations by econometric models and cross-spectral methods
-
Granger CWJ, Investigating causal relations by econometric models and cross-spectral methods, Econometrica 37:424-438, 1969.
-
(1969)
Econometrica
, vol.37
, pp. 424-438
-
-
Granger, C.W.J.1
-
21
-
-
54949090234
-
-
available at
-
The R Project for Statistical Computing, available at http://r-project.org/.
-
-
-
-
22
-
-
0035985177
-
Identification of genes periodically expressed in the human cell cycle and their expression in tumors
-
Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D, Identification of genes periodically expressed in the human cell cycle and their expression in tumors, Mol Biol Cell 13:1977-2000, 2002.
-
(2002)
Mol Biol Cell
, vol.13
, pp. 1977-2000
-
-
Whitfield, M.L.1
Sherlock, G.2
Saldanha, A.J.3
Murray, J.I.4
Ball, C.A.5
Alexander, K.E.6
Matese, J.C.7
Perou, C.M.8
Hurt, M.M.9
Brown, P.O.10
Botstein, D.11
-
23
-
-
0000861053
-
A non-parametric test of independence
-
Hoeffding W, A non-parametric test of independence. Annals Math Stat 19:546-557, 1948.
-
(1948)
Annals Math Stat
, vol.19
, pp. 546-557
-
-
Hoeffding, W.1
-
24
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y, Controlling the false discovery rate: A practical and powerful approach to multiple testing, J R Stat Soc Ser B Stat Methodol 57:289-300, 1995.
-
(1995)
J R Stat Soc Ser B Stat Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
25
-
-
0035211073
-
The p53 functional circuit
-
Jin S, Levine AJ, The p53 functional circuit, J Cell Sci 114 4139-4140, 2001.
-
(2001)
J Cell Sci
, vol.114
, pp. 4139-4140
-
-
Jin, S.1
Levine, A.J.2
-
26
-
-
0032192140
-
The complexity of p53 modulation: Emerging patterns from divergent signals
-
Giaccia AJ, Kastan MB, The complexity of p53 modulation: Emerging patterns from divergent signals, Genes Dev 12:2973-2983, 1998.
-
(1998)
Genes Dev
, vol.12
, pp. 2973-2983
-
-
Giaccia, A.J.1
Kastan, M.B.2
-
27
-
-
27744492975
-
Quercetin induces gadd45 expression through a p53-independent pathway
-
Yoshida T, Maeda A, Horinaka M, Shiraishi T, Nakata S, Wakada M, Yogosawa S, Sakai T, Quercetin induces gadd45 expression through a p53-independent pathway, Oncol Rep 14:1299-1303, 2005.
-
(2005)
Oncol Rep
, vol.14
, pp. 1299-1303
-
-
Yoshida, T.1
Maeda, A.2
Horinaka, M.3
Shiraishi, T.4
Nakata, S.5
Wakada, M.6
Yogosawa, S.7
Sakai, T.8
-
28
-
-
0035374609
-
The hunting of the Src
-
Martin GS, The hunting of the Src, Nat Rev Mol Cell Biol 2 467-475, 2001.
-
(2001)
Nat Rev Mol Cell Biol
, vol.2
, pp. 467-475
-
-
Martin, G.S.1
|