-
1
-
-
33747890494
-
A mixture model with random-effects components for clustering correlated gene-expression profiles
-
10.1093/bioinformatics/btl165, 16675467
-
Ng SK, McLachlan GJ, Wang K, Jones LB-T, Ng S-W. A mixture model with random-effects components for clustering correlated gene-expression profiles. Bioinformatics 2006, 22:1745-1752. 10.1093/bioinformatics/btl165, 16675467.
-
(2006)
Bioinformatics
, vol.22
, pp. 1745-1752
-
-
Ng, S.K.1
McLachlan, G.J.2
Wang, K.3
Jones, L.B.-T.4
Ng, S.-W.5
-
2
-
-
0037941585
-
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
-
10.1038/ng1165, 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, 34:166-176. 10.1038/ng1165, 12740579.
-
(2003)
Nat Genet
, vol.34
, 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
-
3
-
-
77951942705
-
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data
-
10.1093/bioinformatics/btq094, 2853688, 20223837
-
Shiraishi Y, et al. Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. Bioinformatics 2010, 26:1073-1081. 10.1093/bioinformatics/btq094, 2853688, 20223837.
-
(2010)
Bioinformatics
, vol.26
, pp. 1073-1081
-
-
Shiraishi, Y.1
-
4
-
-
0141993704
-
A gene co-expression network for global discovery of conserved genetics modules
-
10.1126/science.1087447, 12934013
-
Stuart JM, Segal E, Koller D, Kim SK. A gene co-expression network for global discovery of conserved genetics modules. Science 2003, 302:249-55. 10.1126/science.1087447, 12934013.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
5
-
-
85032779470
-
Finding module-based networks with state-space models - mining high-dimensional and short time-course gene expression data
-
Yamaguchi R, Yoshida R, Imoto S, Higuchi T, Miyano S. Finding module-based networks with state-space models - mining high-dimensional and short time-course gene expression data. IEEE Signal Process Mag 2007, 24:37-46.
-
(2007)
IEEE Signal Process Mag
, vol.24
, pp. 37-46
-
-
Yamaguchi, R.1
Yoshida, R.2
Imoto, S.3
Higuchi, T.4
Miyano, S.5
-
6
-
-
0000351727
-
Investigating causal relationships by econometric models and cross-spectral methods
-
Granger CWJ. Investigating causal relationships by econometric models and cross-spectral methods. Econometrica 1969, 37:424-438.
-
(1969)
Econometrica
, vol.37
, pp. 424-438
-
-
Granger, C.W.J.1
-
9
-
-
34547852213
-
Time-varying modeling of gene expression regulatory networks using wavelet dynamic vector autoregressive method
-
Fujita A, Sato JR, Garay-Malpartida HM, Morettin PA, Sogayar MC, Ferreira CE. Time-varying modeling of gene expression regulatory networks using wavelet dynamic vector autoregressive method. Bioinformatics 2007a, 23:16253-1630.
-
(2007)
Bioinformatics
, vol.23
, pp. 16253-21630
-
-
Fujita, A.1
Sato, J.R.2
Garay-Malpartida, H.M.3
Morettin, P.A.4
Sogayar, M.C.5
Ferreira, C.E.6
-
10
-
-
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 2007b, 1:39.
-
(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
-
11
-
-
54949116637
-
Modeling nonlinear gene regulatory networks from time-series gene expression data
-
Fujita A, Sato JR, Garay-Malpartida HM, Sogayar MC, Ferreira CE, Miyano S. Modeling nonlinear gene regulatory networks from time-series gene expression data. J Bioinf Comput Biol 2008, 6:961-79.
-
(2008)
J Bioinf Comput Biol
, vol.6
, pp. 961-979
-
-
Fujita, A.1
Sato, J.R.2
Garay-Malpartida, H.M.3
Sogayar, M.C.4
Ferreira, C.E.5
Miyano, S.6
-
12
-
-
75649122871
-
The impact of measurement error in the identification of regulatory networks
-
Fujita A, Patriota AG, Sato JR, Miyano S. The impact of measurement error in the identification of regulatory networks. BMC Bioinf 2009, 10:412.
-
(2009)
BMC Bioinf
, vol.10
, pp. 412
-
-
Fujita, A.1
Patriota, A.G.2
Sato, J.R.3
Miyano, S.4
-
13
-
-
44949262939
-
Uncovering interactions in the frequency domain
-
10.1371/journal.pcbi.1000087, 2398781, 18516243
-
Guo S, Wu J, Ding M, Feng J. Uncovering interactions in the frequency domain. PLoS Comput Biol 2008, 4:e1000087. 10.1371/journal.pcbi.1000087, 2398781, 18516243.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Guo, S.1
Wu, J.2
Ding, M.3
Feng, J.4
-
14
-
-
67649947772
-
Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data
-
Kojima K, Fujita A, Shimamura T, Imoto S, Miyano S. Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data. Genome Informatics 2008, 20:37-51.
-
(2008)
Genome Informatics
, vol.20
, pp. 37-51
-
-
Kojima, K.1
Fujita, A.2
Shimamura, T.3
Imoto, S.4
Miyano, S.5
-
15
-
-
66349115724
-
Grouped graphical Granger modeling for gene expression regulatory networks discovery
-
10.1093/bioinformatics/btp199, 2687953, 19477976
-
Lozano AC, Abe N, Liu Y, Rosset S. Grouped graphical Granger modeling for gene expression regulatory networks discovery. Bioinformatics 2009, 25:i110-i118. 10.1093/bioinformatics/btp199, 2687953, 19477976.
-
(2009)
Bioinformatics
, vol.25
-
-
Lozano, A.C.1
Abe, N.2
Liu, Y.3
Rosset, S.4
-
16
-
-
33847348163
-
Causality and pathway search in microarray time series experiments
-
10.1093/bioinformatics/btl598, 17158516
-
Mukhopadhyay ND, Chatterjee S. Causality and pathway search in microarray time series experiments. Bioinformatics 2007, 23:442-449. 10.1093/bioinformatics/btl598, 17158516.
-
(2007)
Bioinformatics
, vol.23
, pp. 442-449
-
-
Mukhopadhyay, N.D.1
Chatterjee, S.2
-
17
-
-
65849504774
-
A note on inferring acyclic network structures using Granger causality tests
-
Nagarajan R. A note on inferring acyclic network structures using Granger causality tests. Int J Biostatistics 2009, 5:10.
-
(2009)
Int J Biostatistics
, vol.5
, pp. 10
-
-
Nagarajan, R.1
-
18
-
-
77956514067
-
Discovering graphical Granger causality using the truncating lasso penalty
-
10.1093/bioinformatics/btq377, 2935442, 20823316
-
Shojaie A, Michailidis G. Discovering graphical Granger causality using the truncating lasso penalty. Bioinformatics 2010, 26:i517-i523. 10.1093/bioinformatics/btq377, 2935442, 20823316.
-
(2010)
Bioinformatics
, vol.26
-
-
Shojaie, A.1
Michailidis, G.2
-
19
-
-
0035377249
-
Partial directed coherence: A new concept in neural structure determination
-
Baccala LA, Sameshima K. Partial directed coherence: A new concept in neural structure determination. Biol Cybernetics 2001, 84:463-474.
-
(2001)
Biol Cybernetics
, vol.84
, pp. 463-474
-
-
Baccala, L.A.1
Sameshima, K.2
-
20
-
-
77955588771
-
Identification of Granger causality between gene sets
-
Fujita A, Sato JR, Kojima K, Gomes LR, Nagasaki M, Sogayar MC, Miyano S. Identification of Granger causality between gene sets. J Bioinf Comput Biol 2010a, 8:679-701.
-
(2010)
J Bioinf Comput Biol
, vol.8
, pp. 679-701
-
-
Fujita, A.1
Sato, J.R.2
Kojima, K.3
Gomes, L.R.4
Nagasaki, M.5
Sogayar, M.C.6
Miyano, S.7
-
21
-
-
77956502764
-
A fast and robust statistical test based on Likelihood ratio with Bartlett correction to identify Granger causality between gene sets
-
Fujita A, Kojima K, Patriota AG, Sato JR, Severino P, Miyano S. A fast and robust statistical test based on Likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinformatics 2010b, 26:2349-2351.
-
(2010)
Bioinformatics
, vol.26
, pp. 2349-2351
-
-
Fujita, A.1
Kojima, K.2
Patriota, A.G.3
Sato, J.R.4
Severino, P.5
Miyano, S.6
-
22
-
-
77954959510
-
Analyzing the connectivity between regions of interest: An approach based on cluster Granger causality for fMRI data analysis
-
10.1016/j.neuroimage.2010.05.022, 20472076
-
Sato JR, Fujita A, Cardoso EF, Thomaz CE, Brammer MJ, Amaro E. Analyzing the connectivity between regions of interest: An approach based on cluster Granger causality for fMRI data analysis. NeuroImage 2010, 52:1444-1455. 10.1016/j.neuroimage.2010.05.022, 20472076.
-
(2010)
NeuroImage
, vol.52
, pp. 1444-1455
-
-
Sato, J.R.1
Fujita, A.2
Cardoso, E.F.3
Thomaz, C.E.4
Brammer, M.J.5
Amaro, E.6
-
23
-
-
0031927480
-
Functional clustering: identifying strongly interactive brain regions in neuroimaging data
-
10.1006/nimg.1997.0313, 9558645
-
Tononi G, McIntosh AR, Russel DP, Edelman GM. Functional clustering: identifying strongly interactive brain regions in neuroimaging data. NeuroImage 1998, 7:133-149. 10.1006/nimg.1997.0313, 9558645.
-
(1998)
NeuroImage
, vol.7
, pp. 133-149
-
-
Tononi, G.1
McIntosh, A.R.2
Russel, D.P.3
Edelman, G.M.4
-
24
-
-
84873702847
-
Graph clustering using distance-k cliques
-
Berlin, Heidelberg, Germany: Springer-Verlag GmbH, Smith Y
-
Edachery J, Sen A, Brandenburg F. Graph clustering using distance-k cliques. Proceedings of the Seventh International Symposium on Graph Drawing. Lecture Notes in Computer Science. vol. 1731 1999-1999. Berlin, Heidelberg, Germany: Springer-Verlag GmbH, Smith Y.
-
Proceedings of the Seventh International Symposium on Graph Drawing. Lecture Notes in Computer Science. vol. 1731
, pp. 1999-1999
-
-
Edachery, J.1
Sen, A.2
Brandenburg, F.3
-
26
-
-
44349106021
-
Divisive correlation clustering algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles
-
10.1093/bioinformatics/btn133, 18407922
-
Bhattacharya A, De RK. Divisive correlation clustering algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. Bioinformatics 2008, 24:1359-1366. 10.1093/bioinformatics/btn133, 18407922.
-
(2008)
Bioinformatics
, vol.24
, pp. 1359-1366
-
-
Bhattacharya, A.1
De, R.K.2
-
27
-
-
33751327438
-
Comparative gene expression analysis by differential clustering approach: applications to the Candida albicans transcription program
-
10.1371/journal.pgen.0010039, 1239936, 16470937
-
Ihmels J, Bergmann S, Berman J, Barkai N. Comparative gene expression analysis by differential clustering approach: applications to the Candida albicans transcription program. PLoS Genet 2005, 1:e39. 10.1371/journal.pgen.0010039, 1239936, 16470937.
-
(2005)
PLoS Genet
, vol.1
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
28
-
-
0023453329
-
Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
-
Rousseeuw PJ. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 1987, 20:53-65.
-
(1987)
J Comput Appl Math
, vol.20
, pp. 53-65
-
-
Rousseeuw, P.J.1
-
29
-
-
0001626339
-
A classification EM algorithm for clustering and two stochastic versions
-
Celeux G, Govaert G. A classification EM algorithm for clustering and two stochastic versions. Comput Stat Data Anal 1992, 14:315-332.
-
(1992)
Comput Stat Data Anal
, vol.14
, pp. 315-332
-
-
Celeux, G.1
Govaert, G.2
-
30
-
-
0035985177
-
Identification of genes periodically expressed in the human cell cycle and their expression in tumors
-
10.1091/mbc.02-02-0030., 117619, 12058064
-
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 2002, 13:1977-2000. 10.1091/mbc.02-02-0030., 117619, 12058064.
-
(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
-
31
-
-
40749103000
-
A signal network involving coactivated NF-κB and STAT3 and altered p53 modulates BAX/BCL-XL expression and promotes cell survival of head and neck squamous cell carcinomas
-
10.1002/ijc.23324, 18172861
-
Lee TL, Yeh J, Friedman J, Yan B, Yang X, Yeh NT, Waes CV, Chen Z. A signal network involving coactivated NF-κB and STAT3 and altered p53 modulates BAX/BCL-XL expression and promotes cell survival of head and neck squamous cell carcinomas. Int J Cancer 2008, 122:1987-1998. 10.1002/ijc.23324, 18172861.
-
(2008)
Int J Cancer
, vol.122
, pp. 1987-1998
-
-
Lee, T.L.1
Yeh, J.2
Friedman, J.3
Yan, B.4
Yang, X.5
Yeh, N.T.6
Waes, C.V.7
Chen, Z.8
-
32
-
-
44949236232
-
FGF-1-induced matrix metalloproteinase-9 expression in breast cancer cells is mediated by increased activities of NF-κB and activating protein-1
-
10.1002/mc.20398, 18041768
-
Lungu G, Covaleda L, Mendes O, Martini-Stoica H, Stoica G. FGF-1-induced matrix metalloproteinase-9 expression in breast cancer cells is mediated by increased activities of NF-κB and activating protein-1. Mol Carcinog 2008, 47:424-435. 10.1002/mc.20398, 18041768.
-
(2008)
Mol Carcinog
, vol.47
, pp. 424-435
-
-
Lungu, G.1
Covaleda, L.2
Mendes, O.3
Martini-Stoica, H.4
Stoica, G.5
-
33
-
-
78650984035
-
The Receptor Tyrosine Kinase FGFR4 Negatively Regulates NF-kappaB Signaling
-
10.1371/journal.pone.0014412, 3008709, 21203561
-
Drafahl KA, McAndrew CW, Meyer AN, Haas M, Donoghue DJ. The Receptor Tyrosine Kinase FGFR4 Negatively Regulates NF-kappaB Signaling. PLoS ONE 2010, 5:e14412. 10.1371/journal.pone.0014412, 3008709, 21203561.
-
(2010)
PLoS ONE
, vol.5
-
-
Drafahl, K.A.1
McAndrew, C.W.2
Meyer, A.N.3
Haas, M.4
Donoghue, D.J.5
-
34
-
-
77950436631
-
A temporal precedence based clustering method for gene expression microarray data
-
Krishna R, Li CT, Buchanan-Wollaston V. A temporal precedence based clustering method for gene expression microarray data. BMC Bioinf 2010, 11:68.
-
(2010)
BMC Bioinf
, vol.11
, pp. 68
-
-
Krishna, R.1
Li, C.T.2
Buchanan-Wollaston, V.3
-
35
-
-
70149096300
-
A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
-
Witten DM, Tibshirani R, Hastie T. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 2010, 10:515-534.
-
(2010)
Biostatistics
, vol.10
, pp. 515-534
-
-
Witten, D.M.1
Tibshirani, R.2
Hastie, T.3
|