-
1
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
Alexa, A., Rahnenfuhrer, J., Lengauer, T.: Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22 1600–1607 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenfuhrer, J.2
Lengauer, T.3
-
2
-
-
0742305866
-
Network biology: Understanding the cell’s functional organization
-
Barabasi, A.-L., Oltvai, Z.N.: Network biology: Understanding the cell’s functional organization. Nature Rev. Genet. 5 101–113 (2004).
-
(2004)
Nature Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabasi, A.-L.1
Oltvai, Z.N.2
-
3
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y., Hochberg, Y.: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Royal Stat. Soc. B 57 289–300 (1995).
-
(1995)
J. Royal Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad, B.M., Irizarry, R.A., Astrand, M., Speed, T.P.: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19 185–193 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
7
-
-
0028340280
-
Purification of CpG islands using a methylated DNA binding column
-
Cross, S.H., Charlton, J.A., Nan, X., Bird, A.P.: Purification of CpG islands using a methylated DNA binding column. Nature Genet. 6 236–244 (1994).
-
(1994)
Nature Genet
, vol.6
, pp. 236-244
-
-
Cross, S.H.1
Charlton, J.A.2
Nan, X.3
Bird, A.P.4
-
9
-
-
0030669030
-
Exploring the metabolic and genetic control of gene expression on a genomic scale
-
DeRisi, J.L., Iyer, V.R., Brown, P.O.: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278 680–686 (1997).
-
(1997)
Science
, vol.278
, pp. 680-686
-
-
Derisi, J.L.1
Iyer, V.R.2
Brown, P.O.3
-
10
-
-
19544383638
-
Sample size determination in microarray experiments for class comparison and prognostic classification
-
Dobbin, K., Simon, R.: Sample size determination in microarray experiments for class comparison and prognostic classification. Biostatistics 6 27–38 (2005).
-
(2005)
Biostatistics
, vol.6
, pp. 27-38
-
-
Dobbin, K.1
Simon, R.2
-
11
-
-
0036376993
-
Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments
-
Dudoit, S., Yang, Y.H., Callow, M.J., Speed, T.P.: Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments. Stat. Sin. 12 111–139 (2002).
-
(2002)
Stat. Sin.
, vol.12
, pp. 111-139
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
12
-
-
1542784653
-
Empirical Bayes analysis of a microarray experiment
-
References Efron, B., Tibshirani, R., Storey, J.D., Tusher, V.: Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc. 96 1151– 1160 (2001).
-
(2001)
J. Am. Stat. Assoc.
, vol.96
, pp. 1151-1160
-
-
References Efron, B.1
Tibshirani, R.2
Storey, J.D.3
Tusher, V.4
-
13
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D.: Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A. 95 14863–14868 (1998).
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
14
-
-
34250376888
-
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
-
Emanuelsson, O., Nagalakshmi, U., Zheng, D., Rozowsky, J.S., Urban, A.E., Du, J., Lian, Z., Stolc, V., Weissman, S., Snyder, M., Gerstein, M.B.: Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res. 17 886–897 (2006).
-
(2006)
Genome Res
, vol.17
, pp. 886-897
-
-
Emanuelsson, O.1
Nagalakshmi, U.2
Zheng, D.3
Rozowsky, J.S.4
Urban, A.E.5
Du, J.6
Lian, Z.7
Stolc, V.8
Weissman, S.9
Snyder, M.10
Gerstein, M.B.11
-
15
-
-
34250305146
-
Project consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
The ENCODE Project consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 799–816 (2007).
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
16
-
-
4444277447
-
Factorial and time course designs for cDNA microarray experiments
-
Glonek, G.F.V., Solomon, P.J.: Factorial and time course designs for cDNA microarray experiments. Biostatistics 5 89–111 (2004).
-
(2004)
Biostatistics
, vol.5
, pp. 89-111
-
-
Glonek, G.F.V.1
Solomon, P.J.2
-
17
-
-
21144457070
-
CpG island microarray probe sequences derived from a physical library are representative of CpG islands annotated on the human genome
-
Heisler, L.E., Torti, D., Boutros, P.C., Watson, J., Chan, C., Winegarden, N., Takahashi, M., Yau, P., Huang, T.H.-M., Farnham, P.J., Jurisica, I., Woodgett, J.R., Bremner, R., Penn, L.Z., Der, S.D.: CpG island microarray probe sequences derived from a physical library are representative of CpG islands annotated on the human genome. Nucleic Acids Res. 33 2952–2961 (2005).
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2952-2961
-
-
Heisler, L.E.1
Torti, D.2
Boutros, P.C.3
Watson, J.4
Chan, C.5
Winegarden, N.6
Takahashi, M.7
Yau, P.8
Huang, T.H.-M.9
Farnham, P.J.10
Jurisica, I.11
Woodgett, J.R.12
Bremner, R.13
Penn, L.Z.14
Der, S.D.15
-
19
-
-
84945709501
-
Outline for a logical theory of adaptive systems
-
Holland, J.H.: Outline for a logical theory of adaptive systems. JACM 3 297–314 (1962).
-
(1962)
JACM
, vol.3
, pp. 297-314
-
-
Holland, J.H.1
-
20
-
-
33747856481
-
Transcript mapping with high-density oligonucleotide tiling arrays
-
Huber, W., Toedling, J., Steinmetz, L.M.: Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22 1963–1970 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 1963-1970
-
-
Huber, W.1
Toedling, J.2
Steinmetz, L.M.3
-
21
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., Speed, T.P.: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4 249–264 (2003).
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
Speed, T.P.7
-
22
-
-
12144287461
-
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
-
Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., Gingeras, T.R.: Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14 331–342 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 331-342
-
-
Kampa, D.1
Cheng, J.2
Kapranov, P.3
Yamanaka, M.4
Brubaker, S.5
Cawley, S.6
Drenkow, J.7
Piccolboni, A.8
Bekiranov, S.9
Helt, G.10
Tammana, H.11
Gingeras, T.R.12
-
24
-
-
15444364657
-
On the utility of pooling biological samples in microarray experiments
-
Kendziorski, C., Irizarry, R.A., Chen, K.-S., Haag, J.D., Gould, M.N.: On the utility of pooling biological samples in microarray experiments. Proc. Natl. Acad. Sci. U.S.A. 102 4252–4257 (2005).
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 4252-4257
-
-
Kendziorski, C.1
Irizarry, R.A.2
Chen, K.-S.3
Haag, J.D.4
Gould, M.N.5
-
25
-
-
0000884487
-
Experimental design for gene expression microarrays
-
Kerr, M.K., Churchill, G.A.: Experimental design for gene expression microarrays. Biostatistics 2 183–201 (2001).
-
(2001)
Biostatistics
, vol.2
, pp. 183-201
-
-
Kerr, M.K.1
Churchill, G.A.2
-
26
-
-
0035032570
-
Statistical design and the analysis of gene expression microarray data
-
Kerr, M.K., Churchill, G.A.: Statistical design and the analysis of gene expression microarray data. Genet. Res. 77 123–128 (2001).
-
(2001)
Genet. Res.
, vol.77
, pp. 123-128
-
-
Kerr, M.K.1
Churchill, G.A.2
-
27
-
-
35548985891
-
Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns
-
Lezon, T.R., Banavar, J.R., Cieplak, M., Maritan, A., Fedoroff, N.V.: Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc. Natl. Acad. Sci. U.S.A. 103 19033–19038 (2006).
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 19033-19038
-
-
Lezon, T.R.1
Banavar, J.R.2
Cieplak, M.3
Maritan, A.4
Fedoroff, N.V.5
-
28
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., Brown, E.L.: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14 1675– 1680 (1996).
-
(1996)
Nature Biotechnol
, vol.14
, pp. 1675-1680
-
-
Lockhart, D.J.1
Dong, H.2
Byrne, M.C.3
Follettie, M.T.4
Gallo, M.V.5
Chee, M.S.6
Mittmann, M.7
Wang, C.8
Kobayashi, M.9
Horton, H.10
Brown, E.L.11
-
29
-
-
0036012343
-
Replicated microarray data
-
Lönnstedt, I., Speed, T.P.: Replicated microarray data. Stat. Sin. 12 31–46 (2002).
-
(2002)
Stat. Sin.
, vol.12
, pp. 31-46
-
-
Lönnstedt, I.1
Speed, T.P.2
-
30
-
-
33748491517
-
The microarray quality control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
-
MAQC Consortium: The microarray quality control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nature Biotechnol. 24 1151–1161 (2006).
-
(2006)
Nature Biotechnol
, vol.24
, pp. 1151-1161
-
-
-
31
-
-
0000238336
-
A simplex method for function minimization
-
Nelder, J.A., Mead, R.: A simplex method for function minimization. Comp. J 7 308–313 (1965).
-
(1965)
Comp. J
, vol.7
, pp. 308-313
-
-
Nelder, J.A.1
Mead, R.2
-
32
-
-
33745012299
-
Modularity and community structure in networks
-
Newman, M.E.J.: Modularity and community structure in networks. Proc. Natl. Acad. Sci. U.S.A. 103 8577–8582 (2006).
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 8577-8582
-
-
Newman, M.E.J.1
-
34
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner, L.R.: A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77 257–286 (1989).
-
(1989)
Proc. IEEE
, vol.77
, pp. 257-286
-
-
Rabiner, L.R.1
-
35
-
-
22144467302
-
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
-
Royce, T.E., Rozowsky, J.S., Bertone, P., Samanta, M., Stolc, V., Weissman, S., Snyder, M., Gerstein, M.: Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. TRENDS Genetics 21 466–475 (2005).
-
(2005)
TRENDS Genetics
, vol.21
, pp. 466-475
-
-
Royce, T.E.1
Rozowsky, J.S.2
Bertone, P.3
Samanta, M.4
Stolc, V.5
Weissman, S.6
Snyder, M.7
Gerstein, M.8
-
36
-
-
34249730556
-
Assessing the need for sequence-based normalization in tiling microarray experiments
-
Royce, T.E., Rozowsky, J.S., Gerstein, M.B.: Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 23 988–997 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 988-997
-
-
Royce, T.E.1
Rozowsky, J.S.2
Gerstein, M.B.3
-
37
-
-
0342349799
-
Recasting nonlinear differential equations as S-systems: A canonical nonlinear form
-
Savageau, M.A., Voit, E.O.: Recasting nonlinear differential equations as S-systems: a canonical nonlinear form. Math. Biosci. 87 83–115 (1987).
-
(1987)
Math. Biosci.
, vol.87
, pp. 83-115
-
-
Savageau, M.A.1
Voit, E.O.2
-
38
-
-
0031626858
-
Rules for the evolution of gene circuitry
-
Savageau, M.A.: Rules for the evolution of gene circuitry. Pacific Symp. on Biocomp. 3 54–65 (1998).
-
(1998)
Pacific Symp. on Biocomp.
, vol.3
, pp. 54-65
-
-
Savageau, M.A.1
-
39
-
-
27844521293
-
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
-
Schäfer, J., Strimmer, K.: A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statist. Appl. Genet. Mol. Biol. 4 32 (2005).
-
(2005)
Statist. Appl. Genet. Mol. Biol.
, vol.4
, Issue.32
-
-
Schäfer, J.1
Strimmer, K.2
-
40
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena, M., Shalon, D., Davis, R.W., Brown, P.O.: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 467–470 (1995).
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
41
-
-
32644448942
-
Microarray-based DNA methylation profiling: Technology and applications
-
Schumacher, A., Kapranov, P., Kaminsky, Z., Flanagan, J., As-sadzadeh, A., Yau, P., Virtanen, C., Winegarden, N., Cheng, J., Gingeras, T., Petronis, A.: Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res. 34 528– 542 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 528-542
-
-
Schumacher, A.1
Kapranov, P.2
Kaminsky, Z.3
Flanagan, J.4
As-Sadzadeh, A.5
Yau, P.6
Virtanen, C.7
Winegarden, N.8
Cheng, J.9
Gingeras, T.10
Petronis, A.11
-
42
-
-
0000120766
-
Estimating the dimension of a model
-
Schwartz, G.: Estimating the dimension of a model. Ann. Statist. 6 461–464 (1978).
-
(1978)
Ann. Statist.
, vol.6
, pp. 461-464
-
-
Schwartz, G.1
-
43
-
-
0037335024
-
Experimental design of DNA microarray experiments
-
Simon, R.M., Dobbin, K.: Experimental design of DNA microarray experiments. BioTechniques 34, Supplement S16–S21 (2003).
-
(2003)
Biotechniques
, vol.34
-
-
Simon, R.M.1
Dobbin, K.2
-
44
-
-
0242302282
-
METHODS: Selecting candidate genes from DNA array screens: Application to neuroscience
-
Normalization of cDNA microarray data. In: Carter, D. (ed.)
-
Smyth, G.K., Speed, T.P.: Normalization of cDNA microarray data. In: Carter, D. (ed.) METHODS: Selecting candidate genes from DNA array screens: application to neuroscience. Methods 31 (4) 265–273 (2003).
-
(2003)
Methods
, vol.31
, Issue.4
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.P.2
-
45
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Smyth, G.K.: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3 No. 1 Article 3 (2004).
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
, Issue.1
-
-
Smyth, G.K.1
-
46
-
-
33644872577
-
Limma: Linear models for microarray data
-
Gentleman, R., Carey, V., Huber, W., Irizarry, R., Dudoit, S. (eds.), Springer, New York
-
Smyth, G.K.: limma: linear models for microarray data. In: Gentleman, R., Carey, V., Huber, W., Irizarry, R., Dudoit, S. (eds.) Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pp 397–420, Springer, New York (2005).
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
47
-
-
4644250416
-
-
Kluwer Academic Publishers, Boston, August
-
Wang, S.-C.: Genetic algorithm, in Interdisciplinary Computing in Java Programming Language, pp. 101–116. Kluwer Academic Publishers, Boston, August 2003.
-
(2003)
Genetic Algorithm, in Interdisciplinary Computing in Java Programming Language
, pp. 101-116
-
-
Wang, S.-C.1
-
48
-
-
4644238174
-
Reconstructing genetic networks from time ordered gene expression data using Bayesian method with global search algorithm
-
Wang, S.-C.: Reconstructing genetic networks from time ordered gene expression data using Bayesian method with global search algorithm. J. Bioinf. Comput. Biol. 2 441–458 (2004).
-
(2004)
J. Bioinf. Comput. Biol.
, vol.2
, pp. 441-458
-
-
Wang, S.-C.1
-
49
-
-
23044514626
-
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
-
Weber, M., Davies, J.J., Wittig, D., Oakeley, E.J., Haase, M., Lam, W.L., Schubeler, D.: Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genet. 37 853–862 (2005).
-
(2005)
Nature Genet
, vol.37
, pp. 853-862
-
-
Weber, M.1
Davies, J.J.2
Wittig, D.3
Oakeley, E.J.4
Haase, M.5
Lam, W.L.6
Schubeler, D.7
-
50
-
-
0035687554
-
Assessing gene significance from cDNA microarray expression data via mixed models
-
Wolfinger, R.D., Gibson, G., Wolfinger, E.D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C., Paules, R.S.: Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol. 8 625–637 (2001).
-
(2001)
J. Comput. Biol.
, vol.8
, pp. 625-637
-
-
Wolfinger, R.D.1
Gibson, G.2
Wolfinger, E.D.3
Bennett, L.4
Hamadeh, H.5
Bushel, P.6
Afshari, C.7
Paules, R.S.8
-
51
-
-
0036360488
-
Differential methylation hybridization using CpG island arrays
-
Yan, P.S., Wei, S.H., Huang, T.H.: Differential methylation hybridization using CpG island arrays. Methods Mol. Biol. 200 87– 100 (2002).
-
(2002)
Methods Mol. Biol.
, vol.200
, pp. 87-100
-
-
Yan, P.S.1
Wei, S.H.2
Huang, T.H.3
-
52
-
-
0034869983
-
Normalization for cDNA microarray data
-
Bittner, M.L., Chen, Y., Dorsel, A.N., Dougherty, E.R. (eds.)
-
Yang, Y.H., Dudoit, S., Luu, P., Speed, T.P.: Normalization for cDNA microarray data. In: Bittner, M.L., Chen, Y., Dorsel, A.N., Dougherty, E.R. (eds.) Microarrays: Optical Technologies and Informatics, Proceedings of SPIE, 4266 141–152 (2001).
-
(2001)
Microarrays: Optical Technologies and Informatics, Proceedings of SPIE
, vol.4266
, pp. 141-152
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Speed, T.P.4
-
53
-
-
1342294092
-
Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
-
Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., Speed, T.P.: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30 e15 (2002).
-
(2002)
Nucleic Acids Res
, vol.e15
, pp. 30
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Lin, D.M.4
Peng, V.5
Ngai, J.6
Speed, T.P.7
-
54
-
-
34250366235
-
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
-
Zhang, Z.D., Paccanaro, A., Fu, Y., Weissman, S., Weng, Z., Chang, J., Snyder, M., Gerstein, M.B.: Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 17 787–797 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 787-797
-
-
Zhang, Z.D.1
Paccanaro, A.2
Fu, Y.3
Weissman, S.4
Weng, Z.5
Chang, J.6
Snyder, M.7
Gerstein, M.B.8
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