-
1
-
-
0034518604
-
Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis
-
Andrews,J., Bouffard,G.G., Cheadle,C., Lu,J., Becker,K.G. and Oliver,B. (2000) Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res., 10, 2030-2043.
-
(2000)
Genome Res.
, vol.10
, pp. 2030-2043
-
-
Andrews, J.1
Bouffard, G.G.2
Cheadle, C.3
Lu, J.4
Becker, K.G.5
Oliver, B.6
-
2
-
-
0035687492
-
Identifying differentially expressed genes in CDNA microarray experiments
-
Baggerly,K.A., Coombes,K.R., Hess,K.R., Stivers,D.N., Abruzzo,L.V. and Zhang,W. (2001) Identifying differentially expressed genes in CDNA microarray experiments. J. Comput. Biol., 8, 639-659.
-
(2001)
J. Comput. Biol.
, vol.8
, pp. 639-659
-
-
Baggerly, K.A.1
Coombes, K.R.2
Hess, K.R.3
Stivers, D.N.4
Abruzzo, L.V.5
Zhang, W.6
-
3
-
-
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
-
4
-
-
0034518156
-
Processing and quality control of DNA array hybridization data
-
Beissbarth,T., Fellenberg,K., Brors,B., Arribas-Prat,R., Boer,J., Hauser,N.C., Scheideler,M., Hoheisel,J.D., Schutz,G., Poustka,A. and Vingron,M. (2000) Processing and quality control of DNA array hybridization data. Bioinformatics, 16, 1014-1022.
-
(2000)
Bioinformatics
, vol.16
, pp. 1014-1022
-
-
Beissbarth, T.1
Fellenberg, K.2
Brors, B.3
Arribas-Prat, R.4
Boer, J.5
Hauser, N.C.6
Scheideler, M.7
Hoheisel, J.D.8
Schutz, G.9
Poustka, A.10
Vingron, M.11
-
5
-
-
19044380776
-
Loss of a FYN-regulated differentiation and growth arrest pathway in advanced stage neuroblastoma
-
Berwanger,B., Hartmann,O., Bergmann,E., Bernard,S., Nielsen,D., Krause,M., Kartal,A., Flynn,D., Wiedemeyer,R., Schwab,M., Schafer,H., Christiansen,H. and Eilers,M. (2002) Loss of a FYN-regulated differentiation and growth arrest pathway in advanced stage neuroblastoma. Cancer Cell, 2, 377-386.
-
(2002)
Cancer Cell
, vol.2
, pp. 377-386
-
-
Berwanger, B.1
Hartmann, O.2
Bergmann, E.3
Bernard, S.4
Nielsen, D.5
Krause, M.6
Kartal, A.7
Flynn, D.8
Wiedemeyer, R.9
Schwab, M.10
Schafer, H.11
Christiansen, H.12
Eilers, M.13
-
6
-
-
0035184764
-
Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array
-
Boer,J.M., Huber,W.K., Sültmann,H., Wilmer,F., von Heydebreck,A., Haas,S., Korn,B., Gunawan,B., Vente,A., Fuzesi,L,, Vingron,M. and Poustka,A. (2001) Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array. Genome Res., 11, 1861-1870.
-
(2001)
Genome Res.
, vol.11
, pp. 1861-1870
-
-
Boer, J.M.1
Huber, W.K.2
Sültmann, H.3
Wilmer, F.4
von Heydebreck, A.5
Haas, S.6
Korn, B.7
Gunawan, B.8
Vente, A.9
Fuzesi, L.10
Vingron, M.11
Poustka, A.12
-
7
-
-
0038238080
-
Statistical methods for ranking differentially expressed genes
-
Broberg,P. (2003) Statistical methods for ranking differentially expressed genes. Genome Biol., 4, R41.
-
(2003)
Genome Biol.
, vol.4
-
-
Broberg, P.1
-
8
-
-
0003747844
-
-
CSIRO Mathematical and Information Sciences Sydney, Australia
-
Buckley,M.J. (2000) Spot User's Guide. CSIRO Mathematical and Information Sciences, Sydney, Australia.
-
(2000)
Spot User's Guide
-
-
Buckley, M.J.1
-
9
-
-
1842564359
-
-
Blackwell Publishing, Malden, MA
-
Causton,H.C., Quackenbush,J. and Brazma,A. (2003) Microarray Gene Expression Data Analysis: A Beginner's Guide. Blackwell Publishing, Malden, MA.
-
(2003)
Microarray Gene Expression Data Analysis: A Beginner's Guide
-
-
Causton, H.C.1
Quackenbush, J.2
Brazma, A.3
-
10
-
-
0035992248
-
Empirical Bayes methods and false discovery rates for microarrays
-
Efron,B. and Tibshirani,R. (2002) Empirical Bayes methods and false discovery rates for microarrays. Genet. Epidemiol., 23, 70-86.
-
(2002)
Genet. Epidemiol.
, vol.23
, pp. 70-86
-
-
Efron, B.1
Tibshirani, R.2
-
11
-
-
1542784653
-
Empirical Bayes analysis of a microarray experiment
-
Efron,B., Tibshirani,R., Storey,J.D. and Tusher,V. (2001) Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc., 96, 1151-1160.
-
(2001)
J. Am. Stat. Assoc.
, vol.96
, pp. 1151-1160
-
-
Efron, B.1
Tibshirani, R.2
Storey, J.D.3
Tusher, V.4
-
12
-
-
0842321044
-
Normalization and analysis of CDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine
-
Fan,J., Tam,P., Woude,G.V. and Ren,Y. (2004) Normalization and analysis of CDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine. Proc. Natl Acad. Sci. USA, 101, 1135-1140.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 1135-1140
-
-
Fan, J.1
Tam, P.2
Woude, G.V.3
Ren, Y.4
-
13
-
-
0036228716
-
DNA microarrays: Boundless technology or bound by technology? Guidelines for Studies Using Microarray Technology
-
Firestein,G.S. and Pisetsky,D.S. (2002) DNA microarrays: boundless technology or bound by technology? Guidelines for studies using microarray technology. Arthritis Rheum., 46, 859-861.
-
(2002)
Arthritis Rheum.
, vol.46
, pp. 859-861
-
-
Firestein, G.S.1
Pisetsky, D.S.2
-
14
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman,R.C., Carey,V.J., Bates,D.M., Bolstad,B., Dettling,M., Dudoit,S., Ellis,B., Gautier,L., Ge,Y., Gentry,J., Hornik,K., Hothorn,T., Huber,W., Iacus,S., Irizarry,R., Leisch,F., Li,C., Maechler,M., Rossini,A.J., Sawitzki,G., Smith,C. Smyth,G., Tierney,L., Yang,J.Y. and Zhang,J. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
-
(2004)
Genome Biol.
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
Hornik, K.11
Hothorn, T.12
Huber, W.13
Iacus, S.14
Irizarry, R.15
Leisch, F.16
Li, C.17
Maechler, M.18
Rossini, A.J.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.Y.24
Zhang, J.25
more..
-
15
-
-
0037173373
-
Identification of Schistosoma mansoni gender-associated gene transcripts by cDNA microarray profiling
-
Hoffmann,K.F., Johnston,D.A. and Dunne,D.W. (2002) Identification of Schistosoma mansoni gender-associated gene transcripts by cDNA microarray profiling. Genome Biol., 3, Research0041.
-
(2002)
Genome Biol.
, vol.3
-
-
Hoffmann, K.F.1
Johnston, D.A.2
Dunne, D.W.3
-
16
-
-
0037100632
-
Analysis of repeatability in spotted cDNA microarrays
-
Jenssen,T.K., Langaas,M., Kuo,W.P., Smith-Sorensen,B., Myklebost,O. and Hovig,E. (2002) Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res., 30, 3235-3244.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3235-3244
-
-
Jenssen, T.K.1
Langaas, M.2
Kuo, W.P.3
Smith-Sorensen, B.4
Myklebost, O.5
Hovig, E.6
-
17
-
-
0035733752
-
The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster
-
Jin,W., Riley,R.M. Wolfinger,R.D. White,K.P. Passador-Gurgel,G. and Gibson,G. (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet., 29, 389-395.
-
(2001)
Nat. Genet.
, vol.29
, pp. 389-395
-
-
Jin, W.1
Riley, R.M.2
Wolfinger, R.D.3
White, K.P.4
Passador-Gurgel, G.5
Gibson, G.6
-
18
-
-
0037504378
-
Genome-wide array analysis of normal and malformed human hearts
-
Kaynak,B., von Heydebreck,A., Mebus,S., Seelow,D., Hennig,S., Vogel,J., Sperling,H.P., Pregla,R., Alexi-Meskishvili,V., Hetzer,R., Lange,P.E., Vingron,M., Lehrach,H. and Sperling,S. (2003) Genome-wide array analysis of normal and malformed human hearts. Circulation, 107, 2467-2474.
-
(2003)
Circulation
, vol.107
, pp. 2467-2474
-
-
Kaynak, B.1
von Heydebreck, A.2
Mebus, S.3
Seelow, D.4
Hennig, S.5
Vogel, J.6
Sperling, H.P.7
Pregla, R.8
Alexi-Meskishvili, V.9
Hetzer, R.10
Lange, P.E.11
Vingron, M.12
Lehrach, H.13
Sperling, S.14
-
19
-
-
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. Stat. Med., 22, 3899-3914.
-
(2003)
Stat. Med.
, vol.22
, pp. 3899-3914
-
-
Kendziorski, C.M.1
Newton, M.A.2
Lan, H.3
Gould, M.N.4
-
20
-
-
2342533801
-
Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design
-
König,R., Baidessari,D., Pollet,N., Niehrs,C. and Eils,R. (2004) Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res., 32, e29.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
König, R.1
Baidessari, D.2
Pollet, N.3
Niehrs, C.4
Eils, R.5
-
21
-
-
0036012343
-
Replicated microarray data
-
Lönnstedt,I. and Speed,T. (2002) Replicated microarray data. Stat. Sinica, 12, 31-46.
-
(2002)
Stat. Sinica
, vol.12
, pp. 31-46
-
-
Lönnstedt, I.1
Speed, T.2
-
22
-
-
9144229663
-
Whole-genome microarrays of fission yeast: Characteristics, accuracy, reproducibility, and processing of array data
-
Lyne,R., Burns,G., Mata,J., Penkett,C.J., Rustici,G., Chen,D., Langford,C., Vetrie,D. and Bahler,J. (2003) Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics, 4, 27.
-
(2003)
BMC Genomics
, vol.4
, pp. 27
-
-
Lyne, R.1
Burns, G.2
Mata, J.3
Penkett, C.J.4
Rustici, G.5
Chen, D.6
Langford, C.7
Vetrie, D.8
Bahler, J.9
-
23
-
-
0034923013
-
On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data
-
Newton,M.A., Kendziorski,C.M., Richmond,C.S., 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. Comput. Biol., 8, 37-52.
-
(2001)
J. Comput. Biol.
, vol.8
, pp. 37-52
-
-
Newton, M.A.1
Kendziorski, C.M.2
Richmond, C.S.3
Blattner, F.R.4
Tsui, K.W.5
-
24
-
-
4444235995
-
Detecting differential gene expression with a semiparametric hierarchical mixture method
-
Newton,M.A., Noueiry,A., Sarkar,D. and Ahiquist,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
Ahiquist, P.4
-
25
-
-
12244284624
-
DNA microarray experiments: Biological and technological aspects
-
Nguyen,D.V., Arpat,A.B., Wang,N. and Carroll,R.J. (2002) DNA microarray experiments: biological and technological aspects. Biometrics, 58, 701-717.
-
(2002)
Biometrics
, vol.58
, pp. 701-717
-
-
Nguyen, D.V.1
Arpat, A.B.2
Wang, N.3
Carroll, R.J.4
-
26
-
-
0141871186
-
-
(eds) Springer-Verlag, NY
-
Parmigiani,G., Garret,E.S., Irizarry,R.A. and Zeger,S.L. (eds) (2003) The Analysis of Gene Expression Data. Statistics for Biology and Health. Springer-Verlag, NY.
-
(2003)
The Analysis of Gene Expression Data Statistics for Biology and Health
-
-
Parmigiani, G.1
Garret, E.S.2
Irizarry, R.A.3
Zeger, S.L.4
-
28
-
-
0004264401
-
-
Wiley series in probability and mathematical statistics. Applied Probability and Statistics Wiley, NY
-
Searle,S.R., Casella,G. and McCulloch,C.E. (1992) Variance Components. Wiley series in probability and mathematical statistics. Applied probability and statistics. Wiley, NY.
-
(1992)
Variance Components
-
-
Searle, S.R.1
Casella, G.2
McCulloch, C.E.3
-
29
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Article 3
-
Smyth,G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article 3.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
30
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth,G.K. and Speed,T. (2003) Normalization of cDNA microarray data. Methods, 31, 265-273.
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.2
-
31
-
-
0038048164
-
Statistical issues in cDNA microarray data analysis
-
Smyth,G.K., Yang,Y.H. and Speed,T. (2003) Statistical issues in cDNA microarray data analysis. Methods Mol. Biol., 224, 111-136.
-
(2003)
Methods Mol. Biol.
, vol.224
, pp. 111-136
-
-
Smyth, G.K.1
Yang, Y.H.2
Speed, T.3
-
34
-
-
0041737820
-
DNA Microarrays: Vital statistics
-
Tilstone,C. (2003) DNA microarrays: vital statistics. Nature, 424, 610-612.
-
(2003)
Nature
, vol.424
, pp. 610-612
-
-
Tilstone, C.1
-
35
-
-
18744422885
-
Microarray optimizations: Increasing spot accuracy and automated identification of true microarray signals
-
Tran,P.H., Peiffer,D.A., Shin,Y. Meek,L.M. Brody,J.P. and Cho,K.W. (2002) Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res., 30, e54.
-
(2002)
Nucleic Acids Res.
, vol.30
-
-
Tran, P.H.1
Peiffer, D.A.2
Shin, Y.3
Meek, L.M.4
Brody, J.P.5
Cho, K.W.6
-
36
-
-
0035875553
-
Issues in CDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects
-
Tseng,G.C., Oh,M.K. Rohlin,L., Liao,J.C. and Wong,W.H. (2001) Issues in CDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res., 29, 2549-2557.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2549-2557
-
-
Tseng, G.C.1
Oh, M.K.2
Rohlin, L.3
Liao, J.C.4
Wong, W.H.5
-
37
-
-
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. Natl Acad. Sci. USA, 98, 5116-5121.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
38
-
-
0035433128
-
Quantitative quality control in microarray image processing and data acquisition
-
Wang,X. Ghosh,S. and Guo,S.W. (2001) Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res., 29, E75-5.
-
(2001)
Nucleic Acids Res.
, vol.29
-
-
Wang, X.1
Ghosh, S.2
Guo, S.W.3
-
39
-
-
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. and Paules,R.S. (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol., 8, 625-637.
-
(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
-
40
-
-
3042661571
-
Design and analysis of comparative microarray experiments
-
Speed,T.P. (ed.), Chapman and Hall/CRC Press, FL
-
Yang,Y.H. and Speed,T.P. (2003) Design and analysis of comparative microarray experiments. In Speed,T.P. (ed.), Statistical Analysis of gene Expression Microarray Data, Chapman and Hall/CRC Press, FL. pp. 35-91.
-
(2003)
Statistical Analysis of Gene Expression Microarray Data
, pp. 35-91
-
-
Yang, Y.H.1
Speed, T.P.2
-
41
-
-
0034869983
-
Normalization for cDNA microarray data
-
Bittner,M.L., Chen,Y., Dorsel,A.N. and Dougherty,E.R. (eds)
-
Yang,Y.H., Dudoit,S., Luu,P. and Speed,T.P. (2001) Normalization for cDNA microarray data. In Bittner,M.L., Chen,Y., Dorsel,A.N. and Dougherty,E.R. (eds), Microarrays: Optical Technologies and Informatics, Volume 4266 of Proceedings of SPIE, pp. 141-152.
-
(2001)
Microarrays: Optical Technologies and Informatics Volume 4266 of Proceedings of SPIE
, pp. 141-152
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Speed, T.P.4
-
42
-
-
0037167899
-
Within the fold: Assessing differential expression measures and reproducibility in microarray assays
-
Yang,I.V., Chen,E., Hasseman,J.P. Liang,W., Frank,B.C. Wang,S., Sharov,V., Saeed,A.I., White,J., Li,J., Lee,N.H., Yeatman,T.J. and Quackenbush,J. (2002) Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol., 3, Research 0062.
-
(2002)
Genome Biol.
, vol.3
-
-
Yang, I.V.1
Chen, E.2
Hasseman, J.P.3
Liang, W.4
Frank, B.C.5
Wang, S.6
Sharov, V.7
Saeed, A.I.8
White, J.9
Li, J.10
Lee, N.H.11
Yeatman, T.J.12
Quackenbush, J.13
|