-
1
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu, T., Miyano, S., and Kuhara, S. 1999. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac. Symp. on Biocomputing, 17-28.
-
(1999)
Pac. Symp. on Biocomputing
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
3
-
-
0015732744
-
On the parametrizatioh of autoregressive models by partial autocorrelations
-
Barndorff-Nielsen, O., and Schou, G. 1973. On the parametrizatioh of autoregressive models by partial autocorrelations. J. Multivariate Anal. 3, 408-419.
-
(1973)
J. Multivariate Anal.
, vol.3
, pp. 408-419
-
-
Barndorff-Nielsen, O.1
Schou, G.2
-
4
-
-
0042125048
-
Revising regulatory networks: From expression data to linear causal models
-
Bay, S.D., Shrager, J., Pohorille, A., and Langley, P. 2002. Revising regulatory networks: From expression data to linear causal models. J. Biomedical Informatics, 35, 289-297.
-
(2002)
J. Biomedical Informatics
, vol.35
, pp. 289-297
-
-
Bay, S.D.1
Shrager, J.2
Pohorille, A.3
Langley, P.4
-
6
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., and Davis, R.W. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 2, 65-73.
-
(1998)
Molecular Cell
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
Campbell, M.J.2
Winzeler, E.A.3
Steinmetz, L.4
Conway, A.5
Wodicka, L.6
Wolfsberg, T.G.7
Gabrielian, A.E.8
Landsman, D.9
Lockhart, D.J.10
Davis, R.W.11
-
8
-
-
34249832377
-
A Bayesian method for the induction of probabilistic networks from data
-
Cooper, G.F., and Herskovits, E.H. 1992. A Bayesian method for the induction of probabilistic networks from data. Machine Learning 9, 309-347.
-
(1992)
Machine Learning
, vol.9
, pp. 309-347
-
-
Cooper, G.F.1
Herskovits, E.H.2
-
9
-
-
0034564139
-
A probabilistic learning approach to whole-genome operon prediction
-
Craven, M., Page, D., Shavlik, J., Bockhorst, J., and Glasner, J. 2000. A probabilistic learning approach to whole-genome operon prediction. Proc. 8th Int. Conf. on Intelligent Systems for Molecular Biology, 116-127.
-
(2000)
Proc. 8th Int. Conf. on Intelligent Systems for Molecular Biology
, pp. 116-127
-
-
Craven, M.1
Page, D.2
Shavlik, J.3
Bockhorst, J.4
Glasner, J.5
-
10
-
-
0034354940
-
Graphical interaction models for multivariate time series
-
Dahlhaus, R. 2000. Graphical interaction models for multivariate time series. Metrika 51, 157-172.
-
(2000)
Metrika
, vol.51
, pp. 157-172
-
-
Dahlhaus, R.1
-
11
-
-
0043130707
-
Inferring gene regulatory networks from time-ordered gene expression data of bacillus subtilis using differential equations
-
de Hoon, M.J.L., Imoto, S., Kobayashi, K., Ogasawara, N., and Miyano, S. 2003. Inferring gene regulatory networks from time-ordered gene expression data of bacillus subtilis using differential equations. Proc. Pac. Symp. on Biocomputing, 17-28.
-
(2003)
Proc. Pac. Symp. on Biocomputing
, pp. 17-28
-
-
De Hoon, M.J.L.1
Imoto, S.2
Kobayashi, K.3
Ogasawara, N.4
Miyano, S.5
-
12
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
D'Haeseleer, P., Liang, S., and Somogyi, R. 2000. Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics 16, 707-726.
-
(2000)
Bioinformatics
, vol.16
, pp. 707-726
-
-
D'Haeseleer, P.1
Liang, S.2
Somogyi, R.3
-
13
-
-
0032612220
-
Linear modeling of mRNA expression levels during CNS development and injury
-
D'Haeseleer, P., Wen, X., Fuhrman, S., and Somogyi, R. 1999. Linear modeling of mRNA expression levels during CNS development and injury. Pac. Symp. on Biocomputing, 41-52.
-
(1999)
Pac. Symp. on Biocomputing
, pp. 41-52
-
-
D'Haeseleer, P.1
Wen, X.2
Fuhrman, S.3
Somogyi, R.4
-
14
-
-
85101445097
-
-
John Wiley, New York
-
Draper, N.R., and Smith, H. 1981. Applied Regression Analysis, 2nd ed., John Wiley, New York.
-
(1981)
Applied Regression Analysis, 2nd Ed.
-
-
Draper, N.R.1
Smith, H.2
-
15
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman, N., Linial, M., Nachman, I., and Pe'er, D. 2000. Using Bayesian networks to analyze expression data. J. Comp. Biol. 7, 601-620.
-
(2000)
J. Comp. Biol.
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
16
-
-
0003870537
-
-
Academic Press, New York
-
Glymour, C., Scheines, R., Spirtes, P., and Kelly, K. 1987. Discovering Causal Structure: Artificial Intelligence, Philosophy of Science, and Statistical Modeling, Academic Press, New York.
-
(1987)
Discovering Causal Structure: Artificial Intelligence, Philosophy of Science, and Statistical Modeling
-
-
Glymour, C.1
Scheines, R.2
Spirtes, P.3
Kelly, K.4
-
17
-
-
0000351727
-
Investigating causal relations by econometric models and cross-spectral methods
-
Granger, C.W.J. 1969. Investigating causal relations by econometric models and cross-spectral methods. Econometrica 37, 424-438.
-
(1969)
Econometrica
, vol.37
, pp. 424-438
-
-
Granger, C.W.J.1
-
19
-
-
0002370418
-
A tutorial on learning Bayesian networks
-
M. Jordan, ed., MIT Press, Cambridge, MA
-
Heckerman, D. 1999. A tutorial on learning Bayesian networks. In M. Jordan, ed., Learning in Graphical Models, MIT Press, Cambridge, MA.
-
(1999)
Learning in Graphical Models
-
-
Heckerman, D.1
-
20
-
-
0035037364
-
DNA microarray analysis of cyanobacterial gene expression during acclimation to high light
-
Hihara, Y., Kamei, A., Kanehisa, M., Kaplan, A., and Ikeuchi, M. 2001. DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell 13, 793-806.
-
(2001)
Plant Cell
, vol.13
, pp. 793-806
-
-
Hihara, Y.1
Kamei, A.2
Kanehisa, M.3
Kaplan, A.4
Ikeuchi, M.5
-
22
-
-
0035875010
-
Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria
-
Kalir, S., McClure, J., Pabbaraju, K., Southward, C., Ronen, M., Leibler, S., Surette, M.G., and Alon, U. 2001. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292, 2080-2083.
-
(2001)
Science
, vol.292
, pp. 2080-2083
-
-
Kalir, S.1
McClure, J.2
Pabbaraju, K.3
Southward, C.4
Ronen, M.5
Leibler, S.6
Surette, M.G.7
Alon, U.8
-
23
-
-
84962446666
-
A Bayesian modeling framework for genetic regulation
-
Khan, R., Zeng, Y., Garcia-Frias, J., and Gao, G. 2002. A Bayesian modeling framework for genetic regulation. Proc. IEEE Computer Society Bioinformatics Conference.
-
(2002)
Proc. IEEE Computer Society Bioinformatics Conference
-
-
Khan, R.1
Zeng, Y.2
Garcia-Frias, J.3
Gao, G.4
-
24
-
-
0034710992
-
DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli
-
Khodursky, A., Peter, B.J., Cozzarelli, N.R., Botstein, D., Brown, P.O., and Yanofsky, C. 2000. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc. Natl. Acad. Sci. 97(22), 12170-12175.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, Issue.22
, pp. 12170-12175
-
-
Khodursky, A.1
Peter, B.J.2
Cozzarelli, N.R.3
Botstein, D.4
Brown, P.O.5
Yanofsky, C.6
-
25
-
-
8444230205
-
-
Technical report, Columbia University
-
Kundaje, A., Antar, O., Jebara, T., and Leslie, C. 2002. Learning Regulatory Networks from Sparsely Sampled Time Series Expression Data. Technical report, Columbia University.
-
(2002)
Learning Regulatory Networks from Sparsely Sampled Time Series Expression Data
-
-
Kundaje, A.1
Antar, O.2
Jebara, T.3
Leslie, C.4
-
26
-
-
0031616241
-
REVEAL, a general reverse engineering algorithm for inference of genetic network architectures
-
Liang, S., Fuhrman, S., and Somogyi, R. 1998. REVEAL, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. on Biocomputing, 18-29.
-
(1998)
Pac. Symp. on Biocomputing
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
27
-
-
0037143808
-
Differential rates of gene expression monitored by green flourescent protein
-
Lu, C., Albano, C.R., Bentley, W.E., and Rao, G. 2002. Differential rates of gene expression monitored by green flourescent protein. Biotechnology and Bioengineering 79, 429-437.
-
(2002)
Biotechnology and Bioengineering
, vol.79
, pp. 429-437
-
-
Lu, C.1
Albano, C.R.2
Bentley, W.E.3
Rao, G.4
-
28
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
McAdams, H.H., and Arkin, A. 1997. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. 94, 814-819.
-
(1997)
Proc. Natl. Acad. Sci.
, vol.94
, pp. 814-819
-
-
McAdams, H.H.1
Arkin, A.2
-
29
-
-
0033083733
-
It's a noisy business: Genetic regulation at the nanomolar scale
-
McAdams, H.H., and Arkin, A. 1999. It's a noisy business: Genetic regulation at the nanomolar scale. Trends Genet. 15, 65-69.
-
(1999)
Trends Genet.
, vol.15
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
31
-
-
0034669669
-
Predicting regulons and their cis-regulatory motifs by comparative genomics
-
McGuire, A., and Church, G.M. 2000. Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucl. Acids Res. 28, 4523-4530.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 4523-4530
-
-
McGuire, A.1
Church, G.M.2
-
36
-
-
0032331836
-
Graphs, causality, and structural equation models
-
Pearl, J. 1998. Graphs, causality, and structural equation models. Sociological Methods and Research 27, 226-284.
-
(1998)
Sociological Methods and Research
, vol.27
, pp. 226-284
-
-
Pearl, J.1
-
37
-
-
0004161838
-
-
Cambridge University Press, London
-
Press, W.H., Teukolsky, S.A., Vetterling, W.T., and Flannery, B.P. 1992. Numerical Recipes in C: The Art of Scientific Computing, 2nd ed., Cambridge University Press, London.
-
(1992)
Numerical Recipes in C: The Art of Scientific Computing, 2nd Ed.
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
38
-
-
0043081023
-
-
Technical Report IHMC-TR-030101-01, Institute for Human and Machine Cognition
-
Saavedra, R., Spirtes, P., Ramsey, R., and Glymour, C. 2001. Issues in Learning Gene Regulation from Microarray Databases. Technical Report IHMC-TR-030101-01, Institute for Human and Machine Cognition.
-
(2001)
Issues in Learning Gene Regulation from Microarray Databases
-
-
Saavedra, R.1
Spirtes, P.2
Ramsey, R.3
Glymour, C.4
-
39
-
-
0032947086
-
Regulondb (version 2.0): A database on transcriptional regulation in Escherichia coli
-
Salgado, H., Santos, A., Garza-Ramos, U., van Helden, J., Diaz, E., and Collado-Vides, J. 1999. Regulondb (version 2.0): A database on transcriptional regulation in Escherichia coli. Proc. Natl. Acad. Sci. 27, 59-60.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.27
, pp. 59-60
-
-
Salgado, H.1
Santos, A.2
Garza-Ramos, U.3
Van Helden, J.4
Diaz, E.5
Collado-Vides, J.6
-
40
-
-
0032385984
-
The TETRAD project: Constraint based aids to causal model specification
-
Scheines, R., Spirtes, P., Glymour, C., Meek, C., and Richardson, T. 1998. The TETRAD project: Constraint based aids to causal model specification. Multivariate Behavioural Research 33, 65-118.
-
(1998)
Multivariate Behavioural Research
, vol.33
, pp. 65-118
-
-
Scheines, R.1
Spirtes, P.2
Glymour, C.3
Meek, C.4
Richardson, T.5
-
41
-
-
0002537922
-
Algorithm 808: ARFIT - A Matlab package for the estimation of parameters and eigenmodes of multivariate autoregressive models
-
Schneider, T., and Neumaier, A. 2001. Algorithm 808: ARFIT - A Matlab package for the estimation of parameters and eigenmodes of multivariate autoregressive models. ACM Transactions on Mathematical Software 27, 58-65.
-
(2001)
ACM Transactions on Mathematical Software
, vol.27
, pp. 58-65
-
-
Schneider, T.1
Neumaier, A.2
-
42
-
-
33847178905
-
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
-
Segal, E., Yelensky, R., and Koller, D. 2000. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 19(Suppl. 1), 1273-1282.
-
(2000)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
, pp. 1273-1282
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
43
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S., and Young, R.A. 2001. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697-708.
-
(2001)
Cell
, vol.106
, pp. 697-708
-
-
Simon, I.1
Barnett, J.2
Hannett, N.3
Harbison, C.T.4
Rinaldi, N.J.5
Volkert, T.L.6
Wyrick, J.J.7
Zeitlinger, J.8
Gifford, D.K.9
Jaakkola, T.S.10
Young, R.A.11
-
44
-
-
0002054202
-
Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation
-
Somogyi, R., and Sniegoski, C.A. 1996. Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation. Complexity 1, 145-163.
-
(1996)
Complexity
, vol.1
, pp. 145-163
-
-
Somogyi, R.1
Sniegoski, C.A.2
-
45
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization
-
Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., and Futcher, B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297.
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
46
-
-
0034564415
-
Linear modeling of genetic networks from experimental data
-
van Someren, E.P., Wessels, L.F.A., and Reinders, M.J.T. 2000. Linear modeling of genetic networks from experimental data. Proc. 8th Int. Conf. on Intelligent Systems for Molecular Biology, 355-366.
-
(2000)
Proc. 8th Int. Conf. on Intelligent Systems for Molecular Biology
, pp. 355-366
-
-
Van Someren, E.P.1
Wessels, L.F.A.2
Reinders, M.J.T.3
-
47
-
-
0034862588
-
Genetic network models: A comparative study
-
van Someren, E.P., Wessels, L.F.A., and Reinders, M.J.T. 2001. Genetic network models: A comparative study. Proc. of SPIE, Micro-arrays: Optical Technologies and Informatics (BIOS01), 236-247.
-
(2001)
Proc. of SPIE, Micro-Arrays: Optical Technologies and Informatics (BIOS01)
, pp. 236-247
-
-
Van Someren, E.P.1
Wessels, L.F.A.2
Reinders, M.J.T.3
-
48
-
-
0037197832
-
Determination of causal connectivities of species in reaction networks
-
Vance, W., Arkin, A., and Ross, J. 2002. Determination of causal connectivities of species in reaction networks. Proc. Natl. Acad. Sci. 99, 5816-5821.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 5816-5821
-
-
Vance, W.1
Arkin, A.2
Ross, J.3
-
49
-
-
0034791625
-
Modeling genetic regulatory dynamics in neural development
-
Wahde, M., and Hertz, J. 2001. Modeling genetic regulatory dynamics in neural development. J. Comp. Biol. 8, 429-442.
-
(2001)
J. Comp. Biol.
, vol.8
, pp. 429-442
-
-
Wahde, M.1
Hertz, J.2
-
50
-
-
0032617396
-
Modeling regulatory networks with weight matrices
-
Weaver, D.C., Workman, C.T., and Stormo, G.D. 1999. Modeling regulatory networks with weight matrices. Pac. Symp. on Biocomputing, 112-123.
-
(1999)
Pac. Symp. on Biocomputing
, pp. 112-123
-
-
Weaver, D.C.1
Workman, C.T.2
Stormo, G.D.3
-
51
-
-
0032472195
-
Quantitation of transcription and clonal selection of single living cells with β-lactamase as reporter
-
Zlokarnik, G., Negulescu, P.A., Knapp, T.E., Mere, L., Burres, N., Feng, L., Whitney, M., Roemer, K., and Tsien, R.Y. 1998. Quantitation of transcription and clonal selection of single living cells with β-lactamase as reporter. Science 279, 84-88.
-
(1998)
Science
, vol.279
, pp. 84-88
-
-
Zlokarnik, G.1
Negulescu, P.A.2
Knapp, T.E.3
Mere, L.4
Burres, N.5
Feng, L.6
Whitney, M.7
Roemer, K.8
Tsien, R.Y.9
|