-
1
-
-
0034948896
-
A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes
-
Baldi, P. and Long, A. D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
-
(2001)
Bioinformatics
, vol.17
, pp. 509-519
-
-
Baldi, P.1
Long, A.D.2
-
2
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph, Z., Gerber, G. K., Lee, T. I., Rinaldi, N. J., Yoo, J. Y., Robert, F., Gordon, D. B., Fraenkel, E., Jaakkola, T. S., Young, R. A. and Gifford, D. K. (2003). Computational discovery of gene modules and regulatory networks. Nature Biotechnology 21, 1337-1342.
-
(2003)
Nature Biotechnology
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
Rinaldi, N.J.4
Yoo, J.Y.5
Robert, F.6
Gordon, D.B.7
Fraenkel, E.8
Jaakkola, T.S.9
Young, R.A.10
Gifford, D.K.11
-
3
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289-300.
-
(1995)
J. Roy. Statist. Soc. Ser. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
4
-
-
31344436263
-
ChIPOTle: A use friendly tool for the analysis of ChIP-chip data
-
Buck, M. J., Nobel, A. B. and Lieb, J. D. (2005). ChIPOTle: a use friendly tool for the analysis of ChIP-chip data. Genome Biology 6:R97.
-
(2005)
Genome Biology
, vol.6
-
-
Buck, M.J.1
Nobel, A.B.2
Lieb, J.D.3
-
5
-
-
0037453009
-
Integrating regulatory motif discovery and genome-wide expression analysis
-
Conlon, E. M., Liu, X. S., Lieb, J. D. and Liu, J. S. (2003). Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl. Acad. Sci. USA 100, 3339-3344.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3339-3344
-
-
Conlon, E.M.1
Liu, X.S.2
Lieb, J.D.3
Liu, J.S.4
-
6
-
-
85044699856
-
Improved statistical tests for differential gene expression by shrinking variance components estimates
-
To appear in
-
Cui, X., Hwang, J. T. G., Qiu, J., Blades, N. J. and Churchill, C. R. (2004). Improved statistical tests for differential gene expression by shrinking variance components estimates. To appear in Biostatistics.
-
(2004)
Biostatistics
-
-
Cui, X.1
Hwang, J.T.G.2
Qiu, J.3
Blades, N.J.4
Churchill, C.R.5
-
7
-
-
15844417905
-
A simple procedure for estimating the false discovery rate
-
Dalmasso, C., Broet, P. and Moreau, T. (2005). A simple procedure for estimating the false discovery rate. Bioinformatics 21, 660-668.
-
(2005)
Bioinformatics
, vol.21
, pp. 660-668
-
-
Dalmasso, C.1
Broet, P.2
Moreau, T.3
-
8
-
-
18444401138
-
A Bayesian mixture model for differential gene expression
-
Do, K.-A., Muller, P. and Tang, F. (2005). A Bayesian mixture model for differential gene expression. Appl. Statist. 54, 627-644.
-
(2005)
Appl. Statist
, vol.54
, pp. 627-644
-
-
Do, K.-A.1
Muller, P.2
Tang, F.3
-
9
-
-
2142732441
-
Large-scale simultaneous hypothesis testing: The choice of a null hypothesis
-
Efron, B. (2004). Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. J. Amer. Statist. Assoc. 99, 96-104.
-
(2004)
J. Amer. Statist. Assoc
, vol.99
, pp. 96-104
-
-
Efron, B.1
-
10
-
-
1542784653
-
Empirical Bayes analysis of a microarray experiment
-
Efron, B., Tibshirani, R., Storey, J. D. and Tusher, V. G. (2001). Empirical Bayes analysis of a microarray experiment. J. Amer. Statist. Assoc. 96, 1151-1160.
-
(2001)
J. Amer. Statist. Assoc
, vol.96
, pp. 1151-1160
-
-
Efron, B.1
Tibshirani, R.2
Storey, J.D.3
Tusher, V.G.4
-
11
-
-
0742306126
-
Enhanced software for model-based clustering, discriminant analysis, and density estimation: MCLUST
-
Fraley, C. and Raftery, A. E. (2003). Enhanced software for model-based clustering, discriminant analysis, and density estimation: MCLUST. J. Classification 20, 263-286.
-
(2003)
J. Classification
, vol.20
, pp. 263-286
-
-
Fraley, C.1
Raftery, A.E.2
-
12
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao, F., Foat, B. C. and Bussemaker, H. J. (2004). Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5:31.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
13
-
-
0034564606
-
Finding regulatory elements using joint likelihoods for sequence and expression profile data
-
Holmes, I. and Bruno, W. J. (2000). Finding regulatory elements using joint likelihoods for sequence and expression profile data. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 202-210.
-
(2000)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.8
, pp. 202-210
-
-
Holmes, I.1
Bruno, W.J.2
-
14
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka, R. and Gentleman, R. (1996). R: A language for data analysis and graphics. J. Comput. Graph. Statist. 5, 299-314.
-
(1996)
J. Comput. Graph. Statist
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
15
-
-
24644462724
-
TileMap: Create chromosomal map of tiling array hybridizations
-
Ji, H. and Wong, W. H. (2005). TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21, 3629-3636.
-
(2005)
Bioinformatics
, vol.21
, pp. 3629-3636
-
-
Ji, H.1
Wong, W.H.2
-
16
-
-
0346888587
-
On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
-
Kendziorski, C. M., Newton, M. A., Lan, H. and Gould, M. N. (2003). On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statist. Medicine 22, 3899-3914.
-
(2003)
Statist. Medicine
, vol.22
, pp. 3899-3914
-
-
Kendziorski, C.M.1
Newton, M.A.2
Lan, H.3
Gould, M.N.4
-
17
-
-
0036966431
-
A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays
-
Lee, M.-L. T., Bulyk, M. L., Whitmore, G. A. and Church, G. M. (2002). A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics 58, 981-988.
-
(2002)
Biometrics
, vol.58
, pp. 981-988
-
-
Lee, M.-L.T.1
Bulyk, M.L.2
Whitmore, G.A.3
Church, G.M.4
-
18
-
-
33645059429
-
Bayesian modelling of differential gene expression
-
Lewin, A., Richardson, S., Marshall, C., Glazier, A. and Aitman, T. (2006). Bayesian modelling of differential gene expression. Biometrics 62, 1-9.
-
(2006)
Biometrics
, vol.62
, pp. 1-9
-
-
Lewin, A.1
Richardson, S.2
Marshall, C.3
Glazier, A.4
Aitman, T.5
-
19
-
-
0442325057
-
Markovian structures in biological sequence alignments
-
Liu, J. S., Neuwald, A. F. and Lawrence, C. E. (1999). Markovian structures in biological sequence alignments. J. Amer. Statist. Assoc. 94, 1-15.
-
(1999)
J. Amer. Statist. Assoc
, vol.94
, pp. 1-15
-
-
Liu, J.S.1
Neuwald, A.F.2
Lawrence, C.E.3
-
20
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments
-
Liu, X. S., Brutlag, D. L. and Liu, J. S. (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835-839.
-
(2002)
Nat. Biotechnol
, vol.20
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
21
-
-
33745606461
-
A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays
-
McLachlan, G.J., Bean, R.W., Jones, L.B.-T. (2006). A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays. Bioinformatics 22, 1608-1615.
-
(2006)
Bioinformatics
, vol.22
, pp. 1608-1615
-
-
McLachlan, G.J.1
Bean, R.W.2
Jones, L.B.-T.3
-
22
-
-
0034923013
-
-
Newton, M. A, Kendziorski, C. M., Richmond, C. C., Blattner, F.R. and Tsui, K. W. (2001). On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Computational Biology 8, 37-52.
-
Newton, M. A, Kendziorski, C. M., Richmond, C. C., Blattner, F.R. and Tsui, K. W. (2001). On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Computational Biology 8, 37-52.
-
-
-
-
23
-
-
4444235995
-
Detecting differential gene expression with a semiparametric hierarchical mixture method
-
Newton, M. A., Noueiry, A., Sarkar, D. and Ahlquist, P. (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5, 155-176.
-
(2004)
Biostatistics
, vol.5
, pp. 155-176
-
-
Newton, M.A.1
Noueiry, A.2
Sarkar, D.3
Ahlquist, P.4
-
24
-
-
0028977927
-
Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: Dominant negative mutations in lrp
-
Oshima, T., Ito, K., Kabayama, H. and Nakamura, Y. (1995). Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp. Mol Gen Genet. 247, 521-528.
-
(1995)
Mol Gen Genet
, vol.247
, pp. 521-528
-
-
Oshima, T.1
Ito, K.2
Kabayama, H.3
Nakamura, Y.4
-
25
-
-
0035999977
-
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
-
Pan, W. (2002). A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 12, 546-554.
-
(2002)
Bioinformatics
, vol.12
, pp. 546-554
-
-
Pan, W.1
-
26
-
-
0041592555
-
On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression
-
Pan, W. (2003). On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression. Bioinformatics 19, 1333-1340.
-
(2003)
Bioinformatics
, vol.19
, pp. 1333-1340
-
-
Pan, W.1
-
27
-
-
2142854576
-
A mixture model approach to detecting differentially expressed genes with microarray data
-
Pan, W., Lin, J. and Le, C. (2003). A mixture model approach to detecting differentially expressed genes with microarray data. Functional and Integrative Genomics 3, 117-124.
-
(2003)
Functional and Integrative Genomics
, vol.3
, pp. 117-124
-
-
Pan, W.1
Lin, J.2
Le, C.3
-
28
-
-
4444294164
-
Improving false discovery rate estimation
-
Pounds, S. and Cheng, C. (2004). Improving false discovery rate estimation. Bioinformatics, 20, 1737-1745.
-
(2004)
Bioinformatics
, vol.20
, pp. 1737-1745
-
-
Pounds, S.1
Cheng, C.2
-
29
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren, B., Robert, F., Wyrick, J. J., Aparicio, O., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T. L., Wilson, C. J., Bell, S. P. and Young, R. A. (2000). Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309.
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
30
-
-
0038048164
-
Statistical issues in cDNA microarray data analysis
-
Edited by M. J. Brownstein and A. B. Khodursky, Methods in Molecular Biology 224, Humana Press, Totowa, NJ
-
Smyth, G. K., Yang, Y. H. and Speed, T. (2003). Statistical issues in cDNA microarray data analysis. In Functional Genomics: Methods and Protocols (Edited by M. J. Brownstein and A. B. Khodursky), 111-136, Methods in Molecular Biology Volume 224, Humana Press, Totowa, NJ.
-
(2003)
Functional Genomics: Methods and Protocols
, pp. 111-136
-
-
Smyth, G.K.1
Yang, Y.H.2
Speed, T.3
-
31
-
-
0042424602
-
Statistical significance for genome-wide experiments
-
Storey, J. D. and Tibshirani, R. (2003). Statistical significance for genome-wide experiments. Proc. Natl Acad. Sci. USA 100, 9440-9445.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
32
-
-
33744501241
-
Bayesian error analysis model for reconstructing transcriptional regulatory networks
-
Sun, N., Carroll, R.J. and Zhao, H. (2006). Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc. Natl. Acad. Sci. USA 103, 7988-7993.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 7988-7993
-
-
Sun, N.1
Carroll, R.J.2
Zhao, H.3
-
33
-
-
0037109068
-
Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis
-
Tani, T., Khodursky, A., Blumenthal, R., Brown, P., and Matthews, R. (2002). Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99, 13471-13476.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 13471-13476
-
-
Tani, T.1
Khodursky, A.2
Blumenthal, R.3
Brown, P.4
Matthews, R.5
-
34
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V.G., Tibshirani, R. and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Nat. Acad. Sci. USA 98, 5116-5121.
-
(2001)
Proc. Nat. Acad. Sci. USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
35
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., Bork, P. (2002). Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
36
-
-
0028211316
-
Regulation of the Escherichia coli lrp gene
-
Wang, Q., Wu, J., Friedberg, D., Plakto, J. and Calvo, J. M. (1994). Regulation of the Escherichia coli lrp gene. J. Bacteriol. 176, 1831-1839.
-
(1994)
J. Bacteriol
, vol.176
, pp. 1831-1839
-
-
Wang, Q.1
Wu, J.2
Friedberg, D.3
Plakto, J.4
Calvo, J.M.5
-
37
-
-
13844319583
-
Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation
-
Wang, W., Cherry, J. M., Nochomovitz, Y., Jolly, E., Botstein, D. and Li, H. (2005). Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc. Nat. Acad. Sci. USA 102, 1998-2003.
-
(2005)
Proc. Nat. Acad. Sci. USA
, vol.102
, pp. 1998-2003
-
-
Wang, W.1
Cherry, J.M.2
Nochomovitz, Y.3
Jolly, E.4
Botstein, D.5
Li, H.6
-
38
-
-
0348143180
-
A random variance model for detection of differential gene expression in small microarray experiments
-
Wright, G. W. and Simon, R. M. (2003). A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19, 2448-2455.
-
(2003)
Bioinformatics
, vol.19
, pp. 2448-2455
-
-
Wright, G.W.1
Simon, R.M.2
-
39
-
-
31044452892
-
Gene function prediction by a combined analysis of gene expression data and protein-protein interaction data
-
Xiao, G. and Pan, W. (2005). Gene function prediction by a combined analysis of gene expression data and protein-protein interaction data. J. Bioinformatics and Computational Biology 3, 1371-1389.
-
(2005)
J. Bioinformatics and Computational Biology
, vol.3
, pp. 1371-1389
-
-
Xiao, G.1
Pan, W.2
-
40
-
-
4444350754
-
A case study on choosing normalization methods and test statistics for microarray data
-
Xie, Y., Jeong, K. S., Pan, W., Khodursky, A. and Carlin, B. P. (2004). A case study on choosing normalization methods and test statistics for microarray data. Comparative and Functional Genomics 5, 432-444.
-
(2004)
Comparative and Functional Genomics
, vol.5
, pp. 432-444
-
-
Xie, Y.1
Jeong, K.S.2
Pan, W.3
Khodursky, A.4
Carlin, B.P.5
-
41
-
-
34247590196
-
Incorporating prior information via shrinkage: A combined analysis of genome-wide location data and gene expression data
-
Xie, Y., Pan, W., Jeong, K. S. and Khodursky, A. (2007). Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data. Statist. Medicine 26, 2258-2275.
-
(2007)
Statist. Medicine
, vol.26
, pp. 2258-2275
-
-
Xie, Y.1
Pan, W.2
Jeong, K.S.3
Khodursky, A.4
-
42
-
-
0037101842
-
A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model
-
Xu, X. L., Olson, J. M. and Zhao, L. P. (2002). A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model. Human Molecular Genetics 11, 1977-1985.
-
(2002)
Human Molecular Genetics
, vol.11
, pp. 1977-1985
-
-
Xu, X.L.1
Olson, J.M.2
Zhao, L.P.3
-
43
-
-
1342294092
-
Normalization for cDNA Microarray Data
-
Yang, Y. H., Dudoit, S., Luu, P., and Speed, T. (2002). Normalization for cDNA Microarray Data. Nucleic Acids Research 30, e15.
-
(2002)
Nucleic Acids Research
, vol.30
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Speed, T.4
-
44
-
-
21844466280
-
DNA-protein binding and gene expression patterns
-
Science and Statistics: A Festschrift for Terry Speed Edited by D. R. Goldstein
-
Zhao, H., Wu, B. and Sun, N. (2003). DNA-protein binding and gene expression patterns. In Science and Statistics: A Festschrift for Terry Speed (Edited by D. R. Goldstein), 259-274. IMS Lecture Notes-Monograph Series 40.
-
(2003)
IMS Lecture Notes-Monograph Series
, vol.40
, pp. 259-274
-
-
Zhao, H.1
Wu, B.2
Sun, N.3
|