-
1
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
T. Akutsu, S. Miyano and S. Kuhara. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pacific Symposium on Biocomputing, 4, 17-28, 1999.
-
(1999)
Pacific Symposium on Biocomputing
, vol.4
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
2
-
-
0033737840
-
Inferring qualitative relations in genetic networks and metabolic pathways
-
T. Akutsu, S. Miyano and S. Kuhara. Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics, 16, 727-734, 2000
-
(2000)
Bioinformatics
, vol.16
, pp. 727-734
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
3
-
-
0035171884
-
BIND-The biomolecular interaction network database
-
G.D. Bader, I. Donaldson, C. Wolting, B.F.F. Ouellette, T. Pawson and C.W.V. Hogue. BIND-The biomolecular interaction network database. Nucleic Acids Research, 29, 242-245, 2001.
-
(2001)
Nucleic Acids Research
, vol.29
, pp. 242-245
-
-
Bader, G.D.1
Donaldson, I.2
Wolting, C.3
Ouellette, B.F.F.4
Pawson, T.5
Hogue, C.W.V.6
-
4
-
-
0642313001
-
A string pattern regression algorithm and its application to pattern discovery in long introns
-
H. Bannai, S. Inenaga, A. Shinohara, M. Takeda and S. Miyano. A string pattern regression algorithm and its application to pattern discovery in long introns. Genome Informatics, 13, 3-11, 2002.
-
(2002)
Genome Informatics
, vol.13
, pp. 3-11
-
-
Bannai, H.1
Inenaga, S.2
Shinohara, A.3
Takeda, M.4
Miyano, S.5
-
5
-
-
85026993300
-
-
BIND http://www.blueprint.org/
-
BIND
-
-
-
6
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
H.J. Bussemaker,H. Li and E.D. Siggia. Regulatory element detection using correlation with expression. Nature Genetics, 27, 167-171, 2001.
-
(2001)
Nature Genetics
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
8
-
-
0002211373
-
Approximate predictive likelihood
-
A.C. Davison. Approximate predictive likelihood. Biometrika, 73, 323-332, 1986.
-
(1986)
Biometrika
, vol.73
, pp. 323-332
-
-
Davison, A.C.1
-
10
-
-
84949748343
-
Inferring gene regulatory networks from time-ordered gene expression data using differential equations
-
Proc. 5th International Conference on Discovery Science, Springer-Verlag
-
M.J.L. de Hoon, S. Imoto and S. Miyano. Inferring gene regulatory networks from time-ordered gene expression data using differential equations. Proc. 5th International Conference on Discovery Science, Lecture Note in Artificial Intelligence, 2534, Springer-Verlag, 267-274, 2002.
-
(2002)
Lecture Note in Artificial Intelligence
, vol.2534
, pp. 267-274
-
-
De Hoon, M.J.L.1
Imoto, S.2
Miyano, S.3
-
11
-
-
0043130707
-
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations
-
M.J.L. de Hoon, S. Imoto, K. Kobayashi, N. Ogasawara and S. Miyano. Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pacific Symposium on Biocomputing, 8, 17-28, 2003.
-
(2003)
Pacific Symposium on Biocomputing
, vol.8
, pp. 17-28
-
-
De Hoon, M.J.L.1
Imoto, S.2
Kobayashi, K.3
Ogasawara, N.4
Miyano, S.5
-
12
-
-
25444532788
-
Flexible smoothing with B-splines and penalties (with discussion)
-
P.H.C. Eilers and B. Marx. Flexible smoothing with B-splines and penalties (with discussion). Statistical Science, 11, 89-121, 1996.
-
(1996)
Statistical Science
, vol.11
, pp. 89-121
-
-
Eilers, P.H.C.1
Marx, B.2
-
14
-
-
0033707946
-
Using Bayesian network to analyze expression data
-
N. Friedman, M. Linial, I. Nachman and D. Pe'er. Using Bayesian network to analyze expression data. J. Comp. Biol., 7, 601-620, 2000.
-
(2000)
J. Comp. Biol.
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
16
-
-
85026984291
-
-
GRID http://biodata.mshri.on.ca/grid/servlet/Index
-
GRID
-
-
-
17
-
-
0035221560
-
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks
-
A.J. Hartemink, D.K. Gifford, T.S. Jaakkola and R.A. Young. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pacific Symposium on Biocomputing, 6, 422-433, 2001.
-
(2001)
Pacific Symposium on Biocomputing
, vol.6
, pp. 422-433
-
-
Hartemink, A.J.1
Gifford, D.K.2
Jaakkola, T.S.3
Young, R.A.4
-
18
-
-
0036366689
-
Combining location and expression data for principled discovery of genetic regulatory networkmodels
-
A.J. Hartemink, D.K. Gifford, T.S. Jaakkola and R.A. Young. Combining location and expression data for principled discovery of genetic regulatory networkmodels. Pacific Symposium on Biocomputing, 7, 437-449, 2002.
-
(2002)
Pacific Symposium on Biocomputing
, vol.7
, pp. 437-449
-
-
Hartemink, A.J.1
Gifford, D.K.2
Jaakkola, T.S.3
Young, R.A.4
-
21
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
ISMB 2002
-
T. Ideker, O. Ozier, B. Schwikowski and A.F. Siegel. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18 (ISMB 2002), S233-S240, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. S233-S240
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
22
-
-
0036372453
-
Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression
-
S. Imoto, T. Goto and S. Miyano. Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pacific Symposium on Biocomputing, 7, 175-186, 2002.
-
(2002)
Pacific Symposium on Biocomputing
, vol.7
, pp. 175-186
-
-
Imoto, S.1
Goto, T.2
Miyano, S.3
-
23
-
-
84960351939
-
Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network
-
in press
-
S. Imoto, S. Kim, T. Goto, S. Aburatani, K. Tashiro, S. Kuhara and S. Miyano. Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. Journal of Bioinformatics and Computational Biology, in press.
-
Journal of Bioinformatics and Computational Biology
-
-
Imoto, S.1
Kim, S.2
Goto, T.3
Aburatani, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
25
-
-
84960366283
-
Selection of smoothing parameters in B-spline nonparametric regressionmodels using information criteria
-
in press
-
S. Imoto and S. Konishi. Selection of smoothing parameters in B-spline nonparametric regressionmodels using information criteria. Ann. Inst. Statist. Math., in press.
-
Ann. Inst. Statist. Math.
-
-
Imoto, S.1
Konishi, S.2
-
26
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori and Y. Sakaki.A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA, 97, 4569-4574, 2001.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
28
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
T.-K. Jenssen, A. L greid. J. Komorowski and E. Hovig. A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics, 28, 21-28.
-
Nature Genetics
, vol.28
, pp. 21-28
-
-
Jenssen, T.-K.1
Greid, A.L.2
Komorowski, J.3
Hovig, E.4
-
29
-
-
85026989023
-
-
KEGG http://www.genome.ad.jp/kegg/kegg2.html
-
KEGG
-
-
-
30
-
-
84958595689
-
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data
-
Proc. 1st International Workshop on Computational Methods in Systems Biology, Springer-Verlag
-
S. Kim, S. Imoto and S. Miyano. Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Proc. 1st International Workshop on Computational Methods in Systems Biology, Lecture Note in Computer Science, 2602, Springer-Verlag, 104-113, 2003.
-
(2003)
Lecture Note in Computer Science
, vol.2602
, pp. 104-113
-
-
Kim, S.1
Imoto, S.2
Miyano, S.3
-
32
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G. Jennings, H.L. Murray, D.B. Gordon, B.Ren, J.J. Wyrick, J-B. Tagne, T.L. Volkert, E. Fraenkel, D.K. Gifford and R.A. Young. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804, 2002
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.-B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
33
-
-
0035221090
-
Development of a system for the inference of large scale genetic networks
-
Y. Maki, D. Tominaga, M. Okamoto, S. Watanabe and Y. Eguchi. Development of a system for the inference of large scale genetic networks. Pacific Symposium on Biocomputing, 6, 446-458, 2001.
-
(2001)
Pacific Symposium on Biocomputing
, vol.6
, pp. 446-458
-
-
Maki, Y.1
Tominaga, D.2
Okamoto, M.3
Watanabe, S.4
Eguchi, Y.5
-
34
-
-
0035031110
-
Linking microarray data to the literature
-
D.R. Masys. Linking microarray data to the literature. Nature Genetics, 28, 9-10, 2001.
-
(2001)
Nature Genetics
, vol.28
, pp. 9-10
-
-
Masys, D.R.1
-
35
-
-
0004158155
-
-
Technical report, Computer Science Division, University of California, Berkeley, CA
-
K. Murphy and S. Mian. Modelling gene expression data using dynamic Bayesian networks. Technical report, Computer Science Division, University of California, Berkeley, CA. 1999.
-
(1999)
Modelling Gene Expression Data Using Dynamic Bayesian Networks
-
-
Murphy, K.1
Mian, S.2
-
37
-
-
0344844807
-
Modelling regulatory pathways in E. coli from time series expression profiles
-
ISMB2002
-
I.M. Ong, J.D. Glasner and D. Page. Modelling regulatory pathways in E. coli from time series expression profiles. Bioinformatics, 18 (ISMB2002), S241-S248, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. S241-S248
-
-
Ong, I.M.1
Glasner, J.D.2
Page, D.3
-
38
-
-
18144442687
-
Inferring subnetworks from perturbed expression profiles
-
ISMB 2001
-
D. Pe'er, A. Regev, G. Elidan and N. Friedman. Inferring subnetworks from perturbed expression profiles. Bioinformatics, 17 (ISMB 2001), S215-S224, 2001.
-
(2001)
Bioinformatics
, vol.17
, pp. S215-S224
-
-
Pe'er, D.1
Regev, A.2
Elidan, G.3
Friedman, N.4
-
39
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Y. Pilpel, P. Sudarsanam and G.M. Church. Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genetics, 29, 153-9, 2001.
-
(2001)
Nature Genetics
, vol.29
, pp. 153-159
-
-
Pilpel, Y.1
Sudarsanam, P.2
Church, G.M.3
-
40
-
-
0036898577
-
Microarray data normalization and transformation
-
J. Quackenbush. Microarray data normalization and transformation. Nature Genetics, 32, 496-501, 2002.
-
(2002)
Nature Genetics
, vol.32
, pp. 496-501
-
-
Quackenbush, J.1
-
41
-
-
85026990090
-
-
SCPD http://cgsigma.cshl.org/jian/
-
SCPD
-
-
-
42
-
-
0036376097
-
From promoter sequence to expression: A probabilistic framework
-
E. Segal, Y. Barash, I. Simon, N. Friedman and D. Koller. From promoter sequence to expression: a probabilistic framework. Proc. 6th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2002), 263-272, 2002.
-
(2002)
Proc. 6th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2002)
, pp. 263-272
-
-
Segal, E.1
Barash, Y.2
Simon, I.3
Friedman, N.4
Koller, D.5
-
43
-
-
0036184629
-
Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks
-
I. Shmulevich, E.R. Dougherty, S. Kim andW. Zhang. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics, 18, 261-274, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
44
-
-
0000042837
-
Evaluating functional network inference using simulations of complex biological systems
-
ISMB 2002
-
V.A. Smith, E.D. Jarvis and A.J. Hartemink. Evaluating functional network inference using simulations of complex biological systems. Bioinformatics, 18 (ISMB 2002), S216-S224, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. S216-S224
-
-
Smith, V.A.1
Jarvis, E.D.2
Hartemink, A.J.3
-
45
-
-
3242891560
-
Estimating gene networks from gene expression data by combining Bayesian networkmodel with promoter element detection
-
(ECCB 2003), in press
-
Y. Tamada, S. Kim, H. Bannai, S. Imoto K. Tashiro, S. Kuhara and S.Miyano. Estimating gene networks from gene expression data by combining Bayesian networkmodel with promoter element detection. Bioinformatics, (ECCB 2003), in press.
-
Bioinformatics
-
-
Tamada, Y.1
Kim, S.2
Bannai, H.3
Imoto, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
46
-
-
84950871099
-
Accurate approximations for posterior moments and marginal densities
-
L. Tinerey and J.B. Kadane. Accurate approximations for posterior moments and marginal densities. J. Amer. Statist. Assoc., 81, 82-86, 1986.
-
(1986)
J. Amer. Statist. Assoc.
, vol.81
, pp. 82-86
-
-
Tinerey, L.1
Kadane, J.B.2
-
47
-
-
85026994830
-
-
YPD http://www.incyte.com/sequence/proteome/databases/YPD.shtml
-
YPD
-
-
-
48
-
-
85026993388
-
-
YTF http://biochemie.web.med.uni-muenchen.de/YTFD/
-
YTF
-
-
|