-
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
-
-
3242880202
-
-
BIND
-
BIND http://www.blueprint.org/
-
-
-
-
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
-
-
34249832377
-
"A Bayesian method for the induction of probabilistic networks from data"
-
G. Cooper and E. Herskovits, "A Bayesian method for the induction of probabilistic networks from data," Machine Learning 9, 309-347 (1992).
-
(1992)
Machine Learning
, vol.9
, pp. 309-347
-
-
Cooper, G.1
Herskovits, E.2
-
9
-
-
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
-
11
-
-
84949748343
-
"Inferring gene regulatory networks from time-ordered gene expression data using differential equations"
-
Lecture Note in Artificial Intelligence, 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)
Proc. 5th International Conference on Discovery Science
, vol.2534
, pp. 267-274
-
-
de Hoon, M.J.L.1
Imoto, S.2
Miyano, S.3
-
12
-
-
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
-
13
-
-
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
-
15
-
-
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
-
-
3242882981
-
"Chain functions and scoring functions in genetic networks"
-
(ISMB2003)
-
I. Gat-Viks and R. Shamir, "Chain functions and scoring functions in genetic networks," Bioinformatics 19(ISMB2003), i108-i117 (2003).
-
(2003)
Bioinformatics
, vol.19
-
-
Gat-Viks, I.1
Shamir, R.2
-
18
-
-
3242889990
-
-
GRID
-
GRID http://biodata.mshri.on.ca/grid/servlet/Index
-
-
-
-
19
-
-
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
-
20
-
-
0036366689
-
"Combining location and expression data for principled discovery of genetic regulatory network models"
-
A. J. Hartemink, D. K. Gifford, T. S. Jaakkola and R. A. Young, "Combining location and expression data for principled discovery of genetic regulatory network models," 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
-
23
-
-
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
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
24
-
-
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
-
25
-
-
3042698613
-
"Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network"
-
(Preliminary version has appeared in Proc. 1st IEEE Computer Society Bioinformatics Conference, 219-227)
-
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 1(2), 231-252. (Preliminary version has appeared in Proc. 1st IEEE Computer Society Bioinformatics Conference, 219-227, 2002.)
-
(2002)
Journal of Bioinformatics and Computational Biology
, vol.1
, Issue.2
, pp. 231-252
-
-
Imoto, S.1
Kim, S.2
Goto, T.3
Aburatani, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
26
-
-
3242876379
-
"Selection of smoothing parameters in B-spline nonparametric regression models using information criteria"
-
S. Imoto and S. Konishi, "Selection of smoothing parameters in B-spline nonparametric regression models using information criteria," Ann. Inst. Statist. Math. 5, 671-687.
-
Ann. Inst. Statist. Math.
, vol.5
, pp. 671-687
-
-
Imoto, S.1
Konishi, S.2
-
27
-
-
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
-
29
-
-
0035042776
-
"A literature network of human genes for high-throughput analysis of gene expression"
-
T.-K. Jenssen, A. Lægreid. 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
Lægreid, A.2
Komorowski, J.3
Hovig, E.4
-
30
-
-
0036081062
-
"The KEGG databases at GenomeNet"
-
M. Kanehisa, S. Goto, S. Kawashima and A. Nakaya, "The KEGG databases at GenomeNet," Nucleic Acids Res. 30, 42-46 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 42-46
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Nakaya, A.4
-
31
-
-
3242888779
-
-
KEGG
-
KEGG http://www.genome.ad.jp/kegg/kegg2.html
-
-
-
-
32
-
-
84958595689
-
"Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data"
-
Lecture Note in Computer Science 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)
Proc. 1st International Workshop on Computational Methods in Systems Biology
, vol.2602
, pp. 104-113
-
-
Kim, S.1
Imoto, S.2
Miyano, S.3
-
33
-
-
0842309206
-
"Inferring gene networks from time series microarray data using dynamic Bayesian networks"
-
S. Kim, S. Imoto and S. Miyano, "Inferring gene networks from time series microarray data using dynamic Bayesian networks," Briefings in Bioinformatics 4(3), 228-235.
-
Briefings in Bioinformatics
, vol.4
, Issue.3
, pp. 228-235
-
-
Kim, S.1
Imoto, S.2
Miyano, S.3
-
35
-
-
3242882795
-
"Bayesian information criteria and smoothing parameter selection in radial basis function networks"
-
S. Konishi, T. Ando and S. Imoto, "Bayesian information criteria and smoothing parameter selection in radial basis function networks," Biometrika, 91, 27-43.
-
Biometrika
, vol.91
, pp. 27-43
-
-
Konishi, S.1
Ando, T.2
Imoto, S.3
-
36
-
-
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..
-
37
-
-
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
-
38
-
-
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
-
39
-
-
0004158155
-
Modelling gene expression data using dynamic Bayesian networks
-
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)
-
-
Murphy, K.1
Mian, S.2
-
40
-
-
2442718023
-
"Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks"
-
N. Nariai, S. Kim, S. Imoto and S. Miyano, "Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks," Pacific Symposium on Biocomputing, 9, 336-347.
-
Pacific Symposium on Biocomputing
, vol.9
, pp. 336-347
-
-
Nariai, N.1
Kim, S.2
Imoto, S.3
Miyano, S.4
-
41
-
-
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
-
-
Ong, I.M.1
Glasner, J.D.2
Page, D.3
-
42
-
-
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
-
-
Pe'er, D.1
Regev, A.2
Elidan, G.3
Friedman, N.4
-
43
-
-
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
-
44
-
-
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
-
45
-
-
3242876569
-
-
SCPD
-
SCPD http://cgsigma.cshl.org/jian/
-
-
-
-
46
-
-
0036376097
-
"From promoter sequence to expression: A probabilistic framework"
-
(RECOMB2002)
-
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 (RECOMB2002), 263-272 (2002).
-
(2002)
Proc. 6th Annual International Conference on Research in Computational Molecular Biology
, pp. 263-272
-
-
Segal, E.1
Barash, Y.2
Simon, I.3
Friedman, N.4
Koller, D.5
-
47
-
-
0842309161
-
"Discovering molecular pathways from protein interaction and gene expression data"
-
(ISMB2003)
-
E. Segal, H. Wang and D. Koller, "Discovering molecular pathways from protein interaction and gene expression data," Bioinformatics 19(ISMB2003), i264-i272 (2003).
-
(2003)
Bioinformatics
, vol.19
-
-
Segal, E.1
Wang, H.2
Koller, D.3
-
48
-
-
2442446708
-
"Genome-wide discovery of transcriptional modules from DNA sequence and gene expression"
-
(ISMB2003)
-
E. Segal, R. Yelensky and D. Koller, "Genome-wide discovery of transcriptional modules from DNA sequence and gene expression," Bioinformatics 19(ISMB2003), i273-i282 (2003).
-
(2003)
Bioinformatics
, vol.19
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
49
-
-
0036184629
-
"Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks"
-
I. Shmulevich, E. R. Dougherty, S. Kim and W. 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
-
50
-
-
0000042837
-
"Evaluating functional network inference using simulations of complex biological systems"
-
(ISMB2002)
-
V. A. Smith, E. D. Jarvis and A. J. Hartemink, "Evaluating functional network inference using simulations of complex biological systems," Bioinformatics 18(ISMB2002), S216-S224 (2002).
-
(2002)
Bioinformatics
, vol.18
-
-
Smith, V.A.1
Jarvis, E.D.2
Hartemink, A.J.3
-
52
-
-
3242891560
-
"Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection"
-
(ECCB2003)
-
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 network model with promoter element detection," Bioinformatics 19(ECCB2003), ii227-ii236.
-
Bioinformatics
, vol.19
-
-
Tamada, Y.1
Kim, S.2
Bannai, H.3
Imoto, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
53
-
-
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
-
54
-
-
3242880204
-
-
YPD
-
YPD http://www.incyte.com/sequence/proteome/databases/YPD.shtml
-
-
-
-
55
-
-
3242884420
-
-
YTF
-
YTF http://biochemie.web.med.uni-muenchen.de/YTFD/
-
-
-
|