-
1
-
-
22244458625
-
Applications of DNA microarrays in biology
-
Stoughton R.B. Applications of DNA microarrays in biology. Annu. Rev. Biochem. 2005, 74:53-82.
-
(2005)
Annu. Rev. Biochem.
, vol.74
, pp. 53-82
-
-
Stoughton, R.B.1
-
2
-
-
0035375137
-
Computational analysis of microarray data
-
Quackenbush J. Computational analysis of microarray data. Nat. Rev. Genet. 2001, 2:418-427.
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 418-427
-
-
Quackenbush, J.1
-
3
-
-
59649119053
-
Overview of mRNA expression profiling using DNA microarrays
-
Katagiri F., Glazebrook J. Overview of mRNA expression profiling using DNA microarrays. Curr. Protoc. Mol. Biol. 2009, 85:22.4.1-22.4.13.
-
(2009)
Curr. Protoc. Mol. Biol.
, vol.85
-
-
Katagiri, F.1
Glazebrook, J.2
-
4
-
-
12244284624
-
DNA microarray experiments: biological and technological aspects
-
Nguyen D.V., Arpat A.B., Wang N., Carroll R.J. DNA microarray experiments: biological and technological aspects. Biometrics 2002, 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
-
5
-
-
33646761944
-
Microarray analysis of gene expression: considerations in data mining and statistical treatment
-
Verducci J.S., Melfi V.F., Lin S., Wang Z., Roy S., Sen C.K. Microarray analysis of gene expression: considerations in data mining and statistical treatment. Physiol. Genomics 2006, 25:355-363.
-
(2006)
Physiol. Genomics
, vol.25
, pp. 355-363
-
-
Verducci, J.S.1
Melfi, V.F.2
Lin, S.3
Wang, Z.4
Roy, S.5
Sen, C.K.6
-
6
-
-
78650179097
-
-
Microarray data analysis, Date last accessed: March 29
-
Microarray data analysis, [http://www.nslij-genetics.org/microarray/], Date last accessed: March 29, 2010.
-
(2010)
-
-
-
7
-
-
10944267202
-
Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology
-
Ewart K.V., Belanger J.C., Williams J., Karakach T., Penny S., Tsoi S.C.M., Richards R.C., Douglas S.E. Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology. Dev. Comp. Immunol. 2005, 29:333-347.
-
(2005)
Dev. Comp. Immunol.
, vol.29
, pp. 333-347
-
-
Ewart, K.V.1
Belanger, J.C.2
Williams, J.3
Karakach, T.4
Penny, S.5
Tsoi, S.C.M.6
Richards, R.C.7
Douglas, S.E.8
-
9
-
-
0026108692
-
Light-directed, spatially addressable parallel chemical synthesis
-
Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991, 251:767-773.
-
(1991)
Science
, vol.251
, pp. 767-773
-
-
Fodor, S.P.1
Read, J.L.2
Pirrung, M.C.3
Stryer, L.4
Lu, A.T.5
Solas, D.6
-
10
-
-
0032846163
-
Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array
-
Singh-Gasson S., Green R.D., Yue Y., Nelson C., Blattner F., Sussman M.R., Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 1999, 17:974-978.
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 974-978
-
-
Singh-Gasson, S.1
Green, R.D.2
Yue, Y.3
Nelson, C.4
Blattner, F.5
Sussman, M.R.6
Cerrina, F.7
-
11
-
-
45249107311
-
Electrochemically generated acid and its containment to 100micron reaction areas for the production of DNA microarrays
-
Maurer K., Cooper J., Caraballo M., Crye J., Suciu D., Ghindilis A., Leonetti J.A., Wang W., Rossi F.M., Stöver A.G., Larson C., Gao H., Dill K., McShea A. Electrochemically generated acid and its containment to 100micron reaction areas for the production of DNA microarrays. PLoS ONE 2006, 1:e34.
-
(2006)
PLoS ONE
, vol.1
-
-
Maurer, K.1
Cooper, J.2
Caraballo, M.3
Crye, J.4
Suciu, D.5
Ghindilis, A.6
Leonetti, J.A.7
Wang, W.8
Rossi, F.M.9
Stöver, A.G.10
Larson, C.11
Gao, H.12
Dill, K.13
McShea, A.14
-
13
-
-
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 1995, 270:467-470.
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
14
-
-
78650171879
-
-
Inkjet technology for precise, high throughput manufacture of protein microarrays Advances in Microarray Technology
-
D.J. Hall, Inkjet technology for precise, high throughput manufacture of protein microarrays Advances in Microarray Technology, [http://mms.technologynetworks.net/hall/player.html] (2005).
-
(2005)
-
-
Hall, D.J.1
-
15
-
-
0031029961
-
Rapid determination of single base mismatch mutations in DNA hybrids by direct field control
-
Sosnowski R.G., Tu E., Butler W.F., O'Connell J.P., Heller M.J. Rapid determination of single base mismatch mutations in DNA hybrids by direct field control. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:1119-1123.
-
(1997)
Proc. Natl. Acad. Sci. U. S. A.
, vol.94
, pp. 1119-1123
-
-
Sosnowski, R.G.1
Tu, E.2
Butler, W.F.3
O'Connell, J.P.4
Heller, M.J.5
-
16
-
-
0032823523
-
Genome-wide analysis of DNA copy-number changes using cDNA microarrays
-
Pollack J.R., Perou C.M., Alizadeh A.A., Eisen M.B., Pergamenschikov A., Williams C.F., Jeffrey S.S., Botstein D., Brown P.O. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 1999, 23:41-46.
-
(1999)
Nat. Genet.
, vol.23
, pp. 41-46
-
-
Pollack, J.R.1
Perou, C.M.2
Alizadeh, A.A.3
Eisen, M.B.4
Pergamenschikov, A.5
Williams, C.F.6
Jeffrey, S.S.7
Botstein, D.8
Brown, P.O.9
-
17
-
-
84896320699
-
Single-nucleotide polymorphism genotyping using microarrays
-
Chapter 2, Unit 2.9
-
Patil N., Nouri N., McAllister L., Matsukaki H., Ryder T. Single-nucleotide polymorphism genotyping using microarrays. Curr. Protoc. Hum. Genet. 2001, Chapter 2, Unit 2.9.
-
(2001)
Curr. Protoc. Hum. Genet.
-
-
Patil, N.1
Nouri, N.2
McAllister, L.3
Matsukaki, H.4
Ryder, T.5
-
18
-
-
0034924450
-
Predicting splice variant from DNA chip expression data
-
Hu G.K., Madore S.J., Moldover B., Jatkoe T., Balaban D., Thomas J., Wang Y. Predicting splice variant from DNA chip expression data. Genome Res. 2001, 11:1237-1245.
-
(2001)
Genome Res.
, vol.11
, pp. 1237-1245
-
-
Hu, G.K.1
Madore, S.J.2
Moldover, B.3
Jatkoe, T.4
Balaban, D.5
Thomas, J.6
Wang, Y.7
-
19
-
-
13944262052
-
A custom microarray platform for analysis of microRNA gene expression
-
Thomson J.M., Parker J., Perou C.M., Hammond S.M. A custom microarray platform for analysis of microRNA gene expression. Nat. Meth. 2004, 1:47-53.
-
(2004)
Nat. Meth.
, vol.1
, pp. 47-53
-
-
Thomson, J.M.1
Parker, J.2
Perou, C.M.3
Hammond, S.M.4
-
20
-
-
0036900895
-
Fundamentals of experimental design for cDNA microarrays
-
Suppl
-
Churchill G.A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 2002, 32:490-495. Suppl.
-
(2002)
Nat. Genet.
, vol.32
, pp. 490-495
-
-
Churchill, G.A.1
-
21
-
-
0037335024
-
Experimental design of DNA microarray experiments
-
Simon R.M., Dobbin K. Experimental design of DNA microarray experiments. BioTechniques Suppl 2003, 16-21.
-
(2003)
BioTechniques Suppl
, pp. 16-21
-
-
Simon, R.M.1
Dobbin, K.2
-
22
-
-
0034598746
-
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
-
Alizadeh A.A., Eisen M.B., Davis R.E., Ma C., Lossos I.S., Rosenwald A., Boldrick J.C., Sabet H., Tran T., Yu X., Powell J.I., Yang L., Marti G.E., Moore T., Hudson J., Lu L., Lewis D.B., Tibshirani R., Sherlock G., Chan W.C., Greiner T.C., Weisenburger D.D., Armitage J.O., Warnke R., Levy R., Wilson W., Grever M.R., Byrd J.C., Botstein D., Brown P.O., Staudt L.M. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
-
(2000)
Nature
, vol.403
, pp. 503-511
-
-
Alizadeh, A.A.1
Eisen, M.B.2
Davis, R.E.3
Ma, C.4
Lossos, I.S.5
Rosenwald, A.6
Boldrick, J.C.7
Sabet, H.8
Tran, T.9
Yu, X.10
Powell, J.I.11
Yang, L.12
Marti, G.E.13
Moore, T.14
Hudson, J.15
Lu, L.16
Lewis, D.B.17
Tibshirani, R.18
Sherlock, G.19
Chan, W.C.20
Greiner, T.C.21
Weisenburger, D.D.22
Armitage, J.O.23
Warnke, R.24
Levy, R.25
Wilson, W.26
Grever, M.R.27
Byrd, J.C.28
Botstein, D.29
Brown, P.O.30
Staudt, L.M.31
more..
-
23
-
-
0033569406
-
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
-
Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., Bloomfield C.D., Lander E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
-
(1999)
Science
, vol.286
, pp. 531-537
-
-
Golub, T.R.1
Slonim, D.K.2
Tamayo, P.3
Huard, C.4
Gaasenbeek, M.5
Mesirov, J.P.6
Coller, H.7
Loh, M.L.8
Downing, J.R.9
Caligiuri, M.A.10
Bloomfield, C.D.11
Lander, E.S.12
-
24
-
-
8844277626
-
Analyzing time series gene expression data
-
Bar-Joseph Z. Analyzing time series gene expression data. Bioinformatics 2004, 20:2493-2503.
-
(2004)
Bioinformatics
, vol.20
, pp. 2493-2503
-
-
Bar-Joseph, Z.1
-
25
-
-
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., Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 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
-
26
-
-
0036796488
-
Comparative analysis of multiple genome-scale data sets
-
Werner-Washburne M., Wylie B., Boyack K., Fuge E., Galbraith J., Weber J., Davidson G. Comparative analysis of multiple genome-scale data sets. Genome Res. 2002, 12:1564-1573.
-
(2002)
Genome Res.
, vol.12
, pp. 1564-1573
-
-
Werner-Washburne, M.1
Wylie, B.2
Boyack, K.3
Fuge, E.4
Galbraith, J.5
Weber, J.6
Davidson, G.7
-
27
-
-
0032901303
-
Microarrays and toxicology: the advent of toxicogenomics
-
Nuwaysir E.F., Bittner M., Trent J., Barrett J.C., Afshari C.A. Microarrays and toxicology: the advent of toxicogenomics. Mol. Carcinog. 1999, 24:153-159.
-
(1999)
Mol. Carcinog.
, vol.24
, pp. 153-159
-
-
Nuwaysir, E.F.1
Bittner, M.2
Trent, J.3
Barrett, J.C.4
Afshari, C.A.5
-
28
-
-
0031730097
-
Drug target validation and identification of secondary drug target effects using DNA microarrays
-
Marton M.J., DeRisi J.L., Bennett H.A., Iyer V.R., Meyer M.R., Roberts C.J., Stoughton R., Burchard J., Slade D., Dai H., Bassett D.E., Hartwell L.H., Brown P.O., Friend S.H. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 1998, 4:1293-1301.
-
(1998)
Nat. Med.
, vol.4
, pp. 1293-1301
-
-
Marton, M.J.1
DeRisi, J.L.2
Bennett, H.A.3
Iyer, V.R.4
Meyer, M.R.5
Roberts, C.J.6
Stoughton, R.7
Burchard, J.8
Slade, D.9
Dai, H.10
Bassett, D.E.11
Hartwell, L.H.12
Brown, P.O.13
Friend, S.H.14
-
29
-
-
9444223924
-
Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress
-
Shapira M., Segal E., Botstein D. Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol. Biol. Cell 2004, 15:5659-5669.
-
(2004)
Mol. Biol. Cell
, vol.15
, pp. 5659-5669
-
-
Shapira, M.1
Segal, E.2
Botstein, D.3
-
30
-
-
0036855402
-
Comparison of microarray designs for class comparison and class discovery
-
Dobbin K., Simon R. Comparison of microarray designs for class comparison and class discovery. Bioinformatics 2002, 18:1438-1445.
-
(2002)
Bioinformatics
, vol.18
, pp. 1438-1445
-
-
Dobbin, K.1
Simon, R.2
-
31
-
-
4243071596
-
The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
-
Bozdech Z., Llinas M., Pulliam B.L., Wong E.D., Zhu J.C., Derisi J.L. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 2003, 1:85-100.
-
(2003)
PLoS Biol.
, vol.1
, pp. 85-100
-
-
Bozdech, Z.1
Llinas, M.2
Pulliam, B.L.3
Wong, E.D.4
Zhu, J.C.5
Derisi, J.L.6
-
32
-
-
33644854445
-
Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains
-
Llinás M., Bozdech Z., Wong E.D., Adai A.T., DeRisi J.L. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res. 2006, 34:1166-1173.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1166-1173
-
-
Llinás, M.1
Bozdech, Z.2
Wong, E.D.3
Adai, A.T.4
DeRisi, J.L.5
-
33
-
-
0037183901
-
Gene expression during the life cycle of Drosophila melanogaster
-
Arbeitman M.N., Furlong E.E.M., Imam F., Johnson E., Null B.H., Baker B.S., Krasnow M.A., Scott M.P., Davis R.W., White K.P. Gene expression during the life cycle of Drosophila melanogaster. Science 2002, 297:2270-2275.
-
(2002)
Science
, vol.297
, pp. 2270-2275
-
-
Arbeitman, M.N.1
Furlong, E.E.M.2
Imam, F.3
Johnson, E.4
Null, B.H.5
Baker, B.S.6
Krasnow, M.A.7
Scott, M.P.8
Davis, R.W.9
White, K.P.10
-
34
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch A.P., Spellman P.T., Kao C.M., Carmel-Harel O., Eisen M.B., Storz G., Botstein D., Brown P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 2000, 11:4241-4257.
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
35
-
-
9444282110
-
Genomic analysis of stationary phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes
-
Martinez M.J., Roy S., Archuletta A.B., Wentzell P.D., Anna-Arriola S.S., Rodriguez A.L., Aragon A.D., Quinones G., Allen C., Werner-Washburne M. Genomic analysis of stationary phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Mol. Biol. Cell 2004, 15:5295-5305.
-
(2004)
Mol. Biol. Cell
, vol.15
, pp. 5295-5305
-
-
Martinez, M.J.1
Roy, S.2
Archuletta, A.B.3
Wentzell, P.D.4
Anna-Arriola, S.S.5
Rodriguez, A.L.6
Aragon, A.D.7
Quinones, G.8
Allen, C.9
Werner-Washburne, M.10
-
36
-
-
0036319960
-
Design issues for cDNA microarray experiments
-
Yang Y.H., Speed T. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 2002, 3:579-588.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 579-588
-
-
Yang, Y.H.1
Speed, T.2
-
37
-
-
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 2004, 5:89-111.
-
(2004)
Biostatistics
, vol.5
, pp. 89-111
-
-
Glonek, G.F.V.1
Solomon, P.J.2
-
38
-
-
0000884487
-
Experimental design for gene expression microarrays
-
Kerr M.K., Churchill G.A. Experimental design for gene expression microarrays. Biostatistics 2001, 2:183-201.
-
(2001)
Biostatistics
, vol.2
, pp. 183-201
-
-
Kerr, M.K.1
Churchill, G.A.2
-
39
-
-
9244226546
-
Design and analysis of experiments with high throughput biological assay data
-
Rocke D.M. Design and analysis of experiments with high throughput biological assay data. Semin. Cell Dev. Biol. 2004, 15:703-713.
-
(2004)
Semin. Cell Dev. Biol.
, vol.15
, pp. 703-713
-
-
Rocke, D.M.1
-
40
-
-
0346733313
-
Design considerations for efficient and effective microarray studies
-
Kerr M.K. Design considerations for efficient and effective microarray studies. Biometrics 2003, 59:822-828.
-
(2003)
Biometrics
, vol.59
, pp. 822-828
-
-
Kerr, M.K.1
-
41
-
-
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., Gibson G. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet. 2001, 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
-
42
-
-
0347621463
-
Statistical implications of pooling RNA samples for microarray experiments
-
Peng X., Wood C., Blalock E., Chen K., Landfield P., Stromberg A. Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinform. 2003, 4:26.
-
(2003)
BMC Bioinform.
, vol.4
, pp. 26
-
-
Peng, X.1
Wood, C.2
Blalock, E.3
Chen, K.4
Landfield, P.5
Stromberg, A.6
-
43
-
-
0034927555
-
Analysis of variance for gene expression microarray data
-
Kerr M.K., Martin M., Churchill G.A. Analysis of variance for gene expression microarray data. J. Comput. Biol. 2000, 7:819-837.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 819-837
-
-
Kerr, M.K.1
Martin, M.2
Churchill, G.A.3
-
44
-
-
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. 2001, 77:123-128.
-
(2001)
Genet. Res.
, vol.77
, pp. 123-128
-
-
Kerr, M.K.1
Churchill, G.A.2
-
45
-
-
66749149901
-
Statistical analysis of microarray data with replicated spots: a case study with Synechococcus WH8102
-
Thomas E.V., Phillippy K.H., Brahamsha B., Haaland D.M., Timlin J.A., Elbourne L.D.H., Palenik B., Paulsen I.T. Statistical analysis of microarray data with replicated spots: a case study with Synechococcus WH8102. Comp. Funct. Genomics 2009, 2009:950171.
-
(2009)
Comp. Funct. Genomics
, vol.2009
, pp. 950171
-
-
Thomas, E.V.1
Phillippy, K.H.2
Brahamsha, B.3
Haaland, D.M.4
Timlin, J.A.5
Elbourne, L.D.H.6
Palenik, B.7
Paulsen, I.T.8
-
46
-
-
0141798522
-
Quantitative assessment of the importance of dye switching and biological replication in cDNA microarray studies
-
Liang M., Briggs A.G., Rute E., Greene A.S., Cowley J. Quantitative assessment of the importance of dye switching and biological replication in cDNA microarray studies. Physiol. Genomics 2003, 14:199-207.
-
(2003)
Physiol. Genomics
, vol.14
, pp. 199-207
-
-
Liang, M.1
Briggs, A.G.2
Rute, E.3
Greene, A.S.4
Cowley, J.5
-
47
-
-
0037620681
-
Statistical design of reverse dye microarrays
-
Dobbin K., Shih J.H., Simon R. Statistical design of reverse dye microarrays. Bioinformatics 2003, 19:803-810.
-
(2003)
Bioinformatics
, vol.19
, pp. 803-810
-
-
Dobbin, K.1
Shih, J.H.2
Simon, R.3
-
48
-
-
0024428018
-
Detection of DNA targets with biotinylated and fluoresceinated RNA probes. Effects of the extent of derivitization on detection sensitivity
-
Folsom V., Hunkeler M.J., Haces A., Harding J.D. Detection of DNA targets with biotinylated and fluoresceinated RNA probes. Effects of the extent of derivitization on detection sensitivity. Anal. Biochem. 1989, 182:309-314.
-
(1989)
Anal. Biochem.
, vol.182
, pp. 309-314
-
-
Folsom, V.1
Hunkeler, M.J.2
Haces, A.3
Harding, J.D.4
-
49
-
-
0030820621
-
Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes
-
Randolph J.B., Waggoner A.S. Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes. Nucleic Acids Res. 1997, 25:2923-2929.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 2923-2929
-
-
Randolph, J.B.1
Waggoner, A.S.2
-
50
-
-
3042561451
-
Evaluation of five different cDNA labeling methods for microarrays using spike controls
-
Badiee A., Eiken H.G., Steen V.M., Løvlie R. Evaluation of five different cDNA labeling methods for microarrays using spike controls. BMC Biotechnol. 2003, 3:23.
-
(2003)
BMC Biotechnol.
, vol.3
, pp. 23
-
-
Badiee, A.1
Eiken, H.G.2
Steen, V.M.3
Løvlie, R.4
-
51
-
-
0036752147
-
Comparison of fluorescent tag DNA labeling methods used for expression analysis by DNA microarrays
-
630
-
Richter A., Schwager C., Hentze S., Ansorge W., Hentze M.W., Muckenthaler M. Comparison of fluorescent tag DNA labeling methods used for expression analysis by DNA microarrays. Biotechniques 2002, 33:620-628. 630.
-
(2002)
Biotechniques
, vol.33
, pp. 620-628
-
-
Richter, A.1
Schwager, C.2
Hentze, S.3
Ansorge, W.4
Hentze, M.W.5
Muckenthaler, M.6
-
52
-
-
0023664582
-
Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides
-
Haralambidis J., Chai M., Tregear G.W. Preparation of base-modified nucleosides suitable for non-radioactive label attachment and their incorporation into synthetic oligodeoxyribonucleotides. Nucleic Acids Res. 1987, 15:4857-4876.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 4857-4876
-
-
Haralambidis, J.1
Chai, M.2
Tregear, G.W.3
-
53
-
-
0027339723
-
Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms
-
Wallner G., Amann Rudolf, Beisker Wolfgang Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 1993, 14:136-143.
-
(1993)
Cytometry
, vol.14
, pp. 136-143
-
-
Wallner, G.1
Amann, R.2
Beisker, W.3
-
54
-
-
0037015215
-
Comparison of different labeling methods for two-channel high-density microarray experiments
-
Manduchi E., Scearce L.M., Brestelli J.E., Grant G.R., Kaestner K.H., Stoeckert C.J. Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol. Genomics 2002, 10:169-179.
-
(2002)
Physiol. Genomics
, vol.10
, pp. 169-179
-
-
Manduchi, E.1
Scearce, L.M.2
Brestelli, J.E.3
Grant, G.R.4
Kaestner, K.H.5
Stoeckert, C.J.6
-
55
-
-
0036976368
-
Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays
-
Yu J., Othman M.I., Farjo R., Zareparsi S., MacNee S.P., Yoshida S., Swaroop A. Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays. Mol. Vis. 2002, 8:130-137.
-
(2002)
Mol. Vis.
, vol.8
, pp. 130-137
-
-
Yu, J.1
Othman, M.I.2
Farjo, R.3
Zareparsi, S.4
MacNee, S.P.5
Yoshida, S.6
Swaroop, A.7
-
56
-
-
0032547321
-
Dendritic nucleic acid probes for DNA biosensors
-
Wang J., Jiang M., Nilsen T.W., Getts R.C. Dendritic nucleic acid probes for DNA biosensors. J. Am. Chem. Soc. 1998, 120:8281-8282.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 8281-8282
-
-
Wang, J.1
Jiang, M.2
Nilsen, T.W.3
Getts, R.C.4
-
57
-
-
0034625797
-
A novel, sensitive detection system for high-density microarrays using dendrimer technology
-
Stears R.L., Getts R.C., Gullans S.R. A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol. Genomics 2000, 3:93-99.
-
(2000)
Physiol. Genomics
, vol.3
, pp. 93-99
-
-
Stears, R.L.1
Getts, R.C.2
Gullans, S.R.3
-
59
-
-
0034164631
-
Signal amplification through nucleotide extension and excision on a dendritic DNA platform
-
Capaldi S., Getts R.C., Jayasena S.D. Signal amplification through nucleotide extension and excision on a dendritic DNA platform. Nucleic Acids Res. 2000, 28:e21.
-
(2000)
Nucleic Acids Res.
, vol.28
-
-
Capaldi, S.1
Getts, R.C.2
Jayasena, S.D.3
-
60
-
-
0041336612
-
Effects of atmospheric ozone on microarray data quality
-
Fare T.L., Coffey E.M., Dai H., He Y.D., Kessler D.A., Kilian K.A., Koch J.E., LeProust E., Marton M.J., Meyer M.R., Stoughton R.B., Tokiwa G.Y., Wang Y. Effects of atmospheric ozone on microarray data quality. Anal. Chem. 2003, 75:4672-4675.
-
(2003)
Anal. Chem.
, vol.75
, pp. 4672-4675
-
-
Fare, T.L.1
Coffey, E.M.2
Dai, H.3
He, Y.D.4
Kessler, D.A.5
Kilian, K.A.6
Koch, J.E.7
LeProust, E.8
Marton, M.J.9
Meyer, M.R.10
Stoughton, R.B.11
Tokiwa, G.Y.12
Wang, Y.13
-
61
-
-
78650176243
-
-
Ozone Prevention, Date last accessed: April 1,
-
Ozone Prevention, [http://cmgm.stanford.edu/pbrown/protocols/Ozone_Prevention.pdf], Date last accessed: April 1, 2010.
-
(2010)
-
-
-
62
-
-
78650173161
-
-
Genisphere-3DNA Array Detection DyeSaver™2, Date last accessed: April 1
-
Genisphere-3DNA Array Detection DyeSaver™2, [http://www.genisphere.com/array_detection_dyesaver.html] , Date last accessed: April 1, 2010.
-
(2010)
-
-
-
63
-
-
58149330210
-
Development of a novel ozone- and photo-stable HyPer5 red fluorescent dye for array CGH and microarray gene expression analysis with consistent performance irrespective of environmental conditions
-
Dar M., Giesler T., Richardson R., Cai C., Cooper M., Lavasani S., Kille P., Voet T., Vermeesch J. Development of a novel ozone- and photo-stable HyPer5 red fluorescent dye for array CGH and microarray gene expression analysis with consistent performance irrespective of environmental conditions. BMC Biotechnol. 2008, 8:86.
-
(2008)
BMC Biotechnol.
, vol.8
, pp. 86
-
-
Dar, M.1
Giesler, T.2
Richardson, R.3
Cai, C.4
Cooper, M.5
Lavasani, S.6
Kille, P.7
Voet, T.8
Vermeesch, J.9
-
64
-
-
0026612858
-
Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ
-
Maskos U., Southern E.M. Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ. Nucleic Acids Res. 1992, 20:1679-1684.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 1679-1684
-
-
Maskos, U.1
Southern, E.M.2
-
65
-
-
0024441819
-
An oligonucleotide hybridization approach to DNA sequencing
-
Khrapko K.R., Lysov YuP A.A., Khorlyn V.V., Shick V.L., Florentiev, Mirzabekov A.D. An oligonucleotide hybridization approach to DNA sequencing. FEBS Lett. 1989, 256:118-122.
-
(1989)
FEBS Lett.
, vol.256
, pp. 118-122
-
-
Khrapko, K.R.1
Lysov YuP, A.A.2
Khorlyn, V.V.3
Shick, V.L.4
Florentiev Mirzabekov, A.D.5
-
66
-
-
0032608229
-
Making and reading microarrays
-
Cheung V.G., Morley M., Aguilar F., Massimi A., Kucherlapati R., Childs G. Making and reading microarrays. Nat. Genet. 1999, 21:15-19.
-
(1999)
Nat. Genet.
, vol.21
, pp. 15-19
-
-
Cheung, V.G.1
Morley, M.2
Aguilar, F.3
Massimi, A.4
Kucherlapati, R.5
Childs, G.6
-
68
-
-
0033818954
-
A concise guide to cDNA microarray analysis
-
552-554, 556 passim
-
Hegde P., Qi R., Abernathy K., Gay C., Dharap S., Gaspard R., Hughes J.E., Snesrud E., Lee N., Quackenbush J. A concise guide to cDNA microarray analysis. BioTechniques 2000, 29:548-550. 552-554, 556 passim.
-
(2000)
BioTechniques
, vol.29
, pp. 548-550
-
-
Hegde, P.1
Qi, R.2
Abernathy, K.3
Gay, C.4
Dharap, S.5
Gaspard, R.6
Hughes, J.E.7
Snesrud, E.8
Lee, N.9
Quackenbush, J.10
-
69
-
-
84883838178
-
Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration
-
Romualdi C., Trevisan S., Celegato B., Costa G., Lanfranchi G. Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration. Nucleic Acids Res. 2003, 31:e149.
-
(2003)
Nucleic Acids Res.
, vol.31
-
-
Romualdi, C.1
Trevisan, S.2
Celegato, B.3
Costa, G.4
Lanfranchi, G.5
-
71
-
-
0036004157
-
Comparison of methods for image analysis on cDNA microarray data
-
Yang Y.H., Buckley M.J., Dudoit S., Speed T.P. Comparison of methods for image analysis on cDNA microarray data. J. Comput. Graph. Statist. 2002, 11:108-136.
-
(2002)
J. Comput. Graph. Statist.
, vol.11
, pp. 108-136
-
-
Yang, Y.H.1
Buckley, M.J.2
Dudoit, S.3
Speed, T.P.4
-
72
-
-
78650176108
-
-
CAMDA 2004 Conference Contest Datasets, Date last accessed: April 1
-
CAMDA 2004 Conference Contest Datasets, [http://www.camda.duke.edu/camda04/datasets/index.html] , Date last accessed: April 1, 2010.
-
(2010)
-
-
-
73
-
-
25444469433
-
Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data
-
Timlin J.A., Haaland D.M., Sinclair M.B., Aragon A.D., Martinez M.J., Werner-Washburne M. Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data. BMC Genomics 2005, 6:72.
-
(2005)
BMC Genomics
, vol.6
, pp. 72
-
-
Timlin, J.A.1
Haaland, D.M.2
Sinclair, M.B.3
Aragon, A.D.4
Martinez, M.J.5
Werner-Washburne, M.6
-
74
-
-
3042803763
-
Microarray image processing: current status and future directions
-
Istepanian R.S.H. Microarray image processing: current status and future directions. IEEE Trans. Nanobioscience 2003, 2:173-175.
-
(2003)
IEEE Trans. Nanobioscience
, vol.2
, pp. 173-175
-
-
Istepanian, R.S.H.1
-
76
-
-
0036740360
-
Ratio statistics of gene expression levels and applications to microarray data analysis
-
Chen Y., Kamat V., Dougherty E.R., Bittner M.L., Meltzer P.S., Trent J.M. Ratio statistics of gene expression levels and applications to microarray data analysis. Bioinformatics 2002, 18:1207-1215.
-
(2002)
Bioinformatics
, vol.18
, pp. 1207-1215
-
-
Chen, Y.1
Kamat, V.2
Dougherty, E.R.3
Bittner, M.L.4
Meltzer, P.S.5
Trent, J.M.6
-
77
-
-
78650169472
-
-
Dapple: Improved techniques for finding spots on DNA microarrays, University of Washington, Date last accessed: April 1, 2010.
-
J. Buhler, T. Ideker, and D. Haynor, Dapple: Improved techniques for finding spots on DNA microarrays, University of Washington [http://www.cs.wustl.edu/?jbuhler/dapple/dapple-tr.pdf] (2000) , Date last accessed: April 1, 2010.
-
(2000)
-
-
Buhler, J.1
Ideker, T.2
Haynor, D.3
-
78
-
-
0035433128
-
Quantitative quality control in microarray image processing and data acquisition
-
Wang X., Ghosh S., Guo S.W. Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res. 2001, 29:E75-5.
-
(2001)
Nucleic Acids Res.
, vol.29
-
-
Wang, X.1
Ghosh, S.2
Guo, S.W.3
-
79
-
-
0036180003
-
Fully automatic quantification of microarray image data
-
Jain A.N., Tokuyasu T.A., Snijders A.M., Segraves R., Albertson D.G., Pinkel D. Fully automatic quantification of microarray image data. Genome Res. 2002, 12:325-332.
-
(2002)
Genome Res.
, vol.12
, pp. 325-332
-
-
Jain, A.N.1
Tokuyasu, T.A.2
Snijders, A.M.3
Segraves, R.4
Albertson, D.G.5
Pinkel, D.6
-
80
-
-
78650170263
-
-
ScanAlyze user manual, Date last accessed: April 1
-
M.B. Eisen, ScanAlyze user manual, [http://rana.lbl.gov/manuals/ScanAlyzeDoc.pdf] , Date last accessed: April 1, 2010.
-
(2010)
-
-
Eisen, M.B.1
-
81
-
-
78650170089
-
-
TM4: Spotfinder, Date last accessed: April 1
-
TM4: Spotfinder, [http://www.tm4.org/spotfinder.html], Date last accessed: April 1, 2010.
-
(2010)
-
-
-
82
-
-
0037314037
-
Combinatorial image analysis of DNA microarray features
-
Glasbey C.A., Ghazal P. Combinatorial image analysis of DNA microarray features. Bioinformatics 2003, 19:194-203.
-
(2003)
Bioinformatics
, vol.19
, pp. 194-203
-
-
Glasbey, C.A.1
Ghazal, P.2
-
83
-
-
0035752668
-
Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data
-
Schadt E.E., Li C., Ellis B., Wong W.H. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell. Biochem. Suppl Suppl 2001, 37:120-125.
-
(2001)
J. Cell. Biochem. Suppl Suppl
, vol.37
, pp. 120-125
-
-
Schadt, E.E.1
Li, C.2
Ellis, B.3
Wong, W.H.4
-
84
-
-
67649784566
-
Probabilistically assisted spot segmentation - with application to DNA microarray images
-
Gjerstad Ø., Aakra Å., Snipen L., Indahl U. Probabilistically assisted spot segmentation - with application to DNA microarray images. Chemometr. Intell. Lab. Syst. 2009, 98:1-9.
-
(2009)
Chemometr. Intell. Lab. Syst.
, vol.98
, pp. 1-9
-
-
Gjerstad, Ø.1
Aakra, Å.2
Snipen, L.3
Indahl, U.4
-
85
-
-
0031246430
-
Ratio-based decisions on the quantitative analysis of cDNA microarray images
-
Chen Y., Dougherty E.R., Bittner M.L. Ratio-based decisions on the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 1997, 2:364-374.
-
(1997)
J. Biomed. Opt.
, vol.2
, pp. 364-374
-
-
Chen, Y.1
Dougherty, E.R.2
Bittner, M.L.3
-
86
-
-
0036791003
-
Significance and statistical errors in the analysis of DNA microarray data
-
Brody J.P., Williams B.A., Wold B.J., Quake S.R. Significance and statistical errors in the analysis of DNA microarray data. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:12975-12978.
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 12975-12978
-
-
Brody, J.P.1
Williams, B.A.2
Wold, B.J.3
Quake, S.R.4
-
87
-
-
36649002868
-
Bootstrap method for the estimation of measurement uncertainty in spotted dual-color DNA microarrays
-
Karakach T.K., Flight R.M., Wentzell P.D. Bootstrap method for the estimation of measurement uncertainty in spotted dual-color DNA microarrays. Anal. Bioanal. Chem. 2007, 389:2125-2141.
-
(2007)
Anal. Bioanal. Chem.
, vol.389
, pp. 2125-2141
-
-
Karakach, T.K.1
Flight, R.M.2
Wentzell, P.D.3
-
88
-
-
9144268360
-
Empirical evaluation of data transformations and ranking statistics for microarray analysis
-
Qin L., Kerr K.F. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res. 2004, 32:5471-5479.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5471-5479
-
-
Qin, L.1
Kerr, K.F.2
-
89
-
-
1642419159
-
A model-based analysis of microarray experimental error and normalisation
-
Fang Y., Brass A., Hoyle D.C., Hayes A., Bashein A., Oliver S.G., Waddington D., Rattray M. A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Res. 2003, 31:e96.
-
(2003)
Nucleic Acids Res.
, vol.31
-
-
Fang, Y.1
Brass, A.2
Hoyle, D.C.3
Hayes, A.4
Bashein, A.5
Oliver, S.G.6
Waddington, D.7
Rattray, M.8
-
90
-
-
78650176432
-
-
Backround analysis and cross hybridization, Agilent Technologies [] Publication 5988-236EN, Date last accessed: May 11, 2010.
-
P. Brzoska, Backround analysis and cross hybridization, Agilent Technologies [] (2001) Publication 5988-236EN, Date last accessed: May 11, 2010. http://www.chem.agilent.com/Library/technicaloverviews/Public/5988-2363%20Bknd%20Analys.pdf.
-
(2001)
-
-
Brzoska, P.1
-
91
-
-
38049173235
-
An overview of image-processing methods for Affymetrix GeneChips
-
Arteaga-Salas J.M., Zuzan H., Langdon W.B., Upton G.J.G., Harrison A.P. An overview of image-processing methods for Affymetrix GeneChips. Brief. Bioinform. 2008, 9:25-33.
-
(2008)
Brief. Bioinform.
, vol.9
, pp. 25-33
-
-
Arteaga-Salas, J.M.1
Zuzan, H.2
Langdon, W.B.3
Upton, G.J.G.4
Harrison, A.P.5
-
92
-
-
78650170569
-
-
Statistical algorithms description document, Affymetrix Date last accessed: April 1, 2010.
-
Statistical algorithms description document, Affymetrix [http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf] (2002), Date last accessed: April 1, 2010.
-
(2002)
-
-
-
93
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection
-
Li C., Wong W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:31-36.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
94
-
-
12344280017
-
Summaries of Affymetrix GeneChip probe level data
-
Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31:e15.
-
(2003)
Nucleic Acids Res.
, vol.31
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
Speed, T.P.6
-
95
-
-
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 2003, 4:249-264.
-
(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
-
96
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad B., Irizarry R., Astrand M., Speed T. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.1
Irizarry, R.2
Astrand, M.3
Speed, T.4
-
97
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman R., Carey V., Bates D., 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., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
-
(2004)
Genome Biol.
, vol.5
-
-
Gentleman, R.1
Carey, V.2
Bates, D.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.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.24
Zhang, J.25
more..
-
98
-
-
78650178298
-
-
Guide to probe logarithmic intensity error (PLIER) estimation, Affymetrix Date last accessed: April 1, 2010
-
Guide to probe logarithmic intensity error (PLIER) estimation, Affymetrix [http://www.affymetrix.com/support/technical/technotes/plier_technote.pdf] (2005), Date last accessed: April 1, 2010.
-
(2005)
-
-
-
99
-
-
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., Norton H., Brown E.L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 1996, 14:1675-1680.
-
(1996)
Nat. 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
Norton, H.10
Brown, E.L.11
-
100
-
-
27644433390
-
Low level analysis of high-density oligonucleotide array data: background, normalization and summarization
-
University of California, Berkeley
-
Bolstad B. Low level analysis of high-density oligonucleotide array data: background, normalization and summarization. Ph.D. Dissertation 2004, University of California, Berkeley.
-
(2004)
Ph.D. Dissertation
-
-
Bolstad, B.1
-
101
-
-
13244277565
-
Alternative mapping of probes to genes for Affymetrix chips
-
Gautier L., Moller M., Friis-Hansen L., Knudsen S. Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinform. 2004, 5:111.
-
(2004)
BMC Bioinform.
, vol.5
, pp. 111
-
-
Gautier, L.1
Moller, M.2
Friis-Hansen, L.3
Knudsen, S.4
-
102
-
-
78650173278
-
-
A model based background adjustment for oligonucleotide expression arrays, Johns Hopkins University Date last accessed: April 1, 2010.
-
Z. Wu, R. Irizarry, R. Gentleman, F.M. Murillo, and F. Spencer, A model based background adjustment for oligonucleotide expression arrays, Johns Hopkins University [http://www.bepress.com/jhubiostat/paper1/] (2004), Date last accessed: April 1, 2010.
-
(2004)
-
-
Wu, Z.1
Irizarry, R.2
Gentleman, R.3
Murillo, F.M.4
Spencer, F.5
-
103
-
-
2642574387
-
The statistical distribution of the intensity of pixels within spots of DNA microarrays: what is the appropriate single-value representative?
-
Nuñez-Garcia J., Mersinias V., Cho K., Smith C.P., Wolkenhauer O. The statistical distribution of the intensity of pixels within spots of DNA microarrays: what is the appropriate single-value representative?. Appl. Bioinform. 2003, 2:229-239.
-
(2003)
Appl. Bioinform.
, vol.2
, pp. 229-239
-
-
Nuñez-Garcia, J.1
Mersinias, V.2
Cho, K.3
Smith, C.P.4
Wolkenhauer, O.5
-
105
-
-
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., Tsui K.W. On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol. 2001, 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
-
106
-
-
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., Cho K.W.Y. Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res. 2002, 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.Y.6
-
107
-
-
0035841226
-
A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays
-
Yang M.C.K., Ruan Q.G., Yang J.J., Eckenrode S., Wu S., McIndoe R.A., She J.X. A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. Physiol. Genomics 2001, 7:45-53.
-
(2001)
Physiol. Genomics
, vol.7
, pp. 45-53
-
-
Yang, M.C.K.1
Ruan, Q.G.2
Yang, J.J.3
Eckenrode, S.4
Wu, S.5
McIndoe, R.A.6
She, J.X.7
-
109
-
-
0035684378
-
A model for measurement error for gene expression arrays
-
Rocke D.M., Durbin B. A model for measurement error for gene expression arrays. J. Comput. Biol. 2001, 8:557-569.
-
(2001)
J. Comput. Biol.
, vol.8
, pp. 557-569
-
-
Rocke, D.M.1
Durbin, B.2
-
110
-
-
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. 2001, 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
-
111
-
-
0012572299
-
A variance-stabilizing transformation for gene-expression microarray data
-
Durbin B.P., Hardin J.S., Hawkins D.M., Rocke D.M. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002, 18(Suppl 1):S105-S110.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL 1
-
-
Durbin, B.P.1
Hardin, J.S.2
Hawkins, D.M.3
Rocke, D.M.4
-
112
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to quantification of differential expression
-
Huber W., Heydebreck A.V., Sültmann H., Poustka A., Vingron M. Variance stabilization applied to microarray data calibration and to quantification of differential expression. Bioinformatics 2002, 18:s96-s104.
-
(2002)
Bioinformatics
, vol.18
-
-
Huber, W.1
Heydebreck, A.V.2
Sültmann, H.3
Poustka, A.4
Vingron, M.5
-
113
-
-
0001072413
-
A two component model for measurement error in analytical chemistry
-
Rocke D.M., Lorenzato S. A two component model for measurement error in analytical chemistry. Technometrics 1995, 37:176-184.
-
(1995)
Technometrics
, vol.37
, pp. 176-184
-
-
Rocke, D.M.1
Lorenzato, S.2
-
114
-
-
34347344984
-
Methods for estimating and mitigating errors in spotted, dual-color DNA microarrays
-
Karakach T.K., Wentzell P.D. Methods for estimating and mitigating errors in spotted, dual-color DNA microarrays. OMICS 2007, 11:186-199.
-
(2007)
OMICS
, vol.11
, pp. 186-199
-
-
Karakach, T.K.1
Wentzell, P.D.2
-
115
-
-
0036898577
-
Microarray data normalization and transformation
-
Quackenbush J. Microarray data normalization and transformation. Nat. Genet. 2002, 32:496-501.
-
(2002)
Nat. Genet.
, vol.32
, pp. 496-501
-
-
Quackenbush, J.1
-
116
-
-
0037188875
-
Normalization and analysis of DNA microarray data by self-consistency and local regression
-
research0037.1-research0037.12
-
Kepler T., Crosby L., Morgan K. Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol. 2002, 3. research0037.1-research0037.12.
-
(2002)
Genome Biol.
, vol.3
-
-
Kepler, T.1
Crosby, L.2
Morgan, K.3
-
117
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth G.K., Speed T. Normalization of cDNA microarray data. Methods 2003, 31:265-273.
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.2
-
118
-
-
0036376993
-
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
-
Dudoit S., Yang Y.H., Callow M.J., Speed T.P. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sinica 2002, 12:111-139.
-
(2002)
Stat. Sinica
, vol.12
, pp. 111-139
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
120
-
-
0642309738
-
Evaluation of normalization methods for microarray data
-
Park T., Yi S., Kang S., Lee S., Lee Y., Simon R. Evaluation of normalization methods for microarray data. BMC Bioinform. 2003, 4:33.
-
(2003)
BMC Bioinform.
, vol.4
, pp. 33
-
-
Park, T.1
Yi, S.2
Kang, S.3
Lee, S.4
Lee, Y.5
Simon, R.6
-
121
-
-
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. 2002, 30:e15.
-
(2002)
Nucleic Acids Res.
, vol.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
-
122
-
-
84936916896
-
Robust locally weighted regression and smoothing scatterplots
-
Cleveland W.S. Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc. 1979, 74:829-836.
-
(1979)
J. Am. Stat. Assoc.
, vol.74
, pp. 829-836
-
-
Cleveland, W.S.1
-
123
-
-
78650171362
-
-
Human Genome Expression Index, Date last accessed: April 1
-
Human Genome Expression Index, [http://www.biotechnologycenter.org/hio/databases/index.html], Date last accessed: April 1, 2010.
-
(2010)
-
-
-
124
-
-
0029852580
-
Use of a cDNA microarray to analyse gene expression patterns in human cancer
-
DeRisi J., Penland L., Brown P.O., Bittner M.L., Meltzer P.S., Ray M., Chen Y., Su Y.A., Trent J.M. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 1996, 14:457-460.
-
(1996)
Nat. Genet.
, vol.14
, pp. 457-460
-
-
DeRisi, J.1
Penland, L.2
Brown, P.O.3
Bittner, M.L.4
Meltzer, P.S.5
Ray, M.6
Chen, Y.7
Su, Y.A.8
Trent, J.M.9
-
125
-
-
20844458965
-
Housekeeping genes in cancer: normalization of array data
-
Khimani A.H., Mhashilkar A.M., Mikulskis A., O'Malley M., Liao J., Golenko E.E., Mayer P., Chada S., Killian J.B., Lott S.T. Housekeeping genes in cancer: normalization of array data. BioTechniques 2005, 38:739-745.
-
(2005)
BioTechniques
, vol.38
, pp. 739-745
-
-
Khimani, A.H.1
Mhashilkar, A.M.2
Mikulskis, A.3
O'Malley, M.4
Liao, J.5
Golenko, E.E.6
Mayer, P.7
Chada, S.8
Killian, J.B.9
Lott, S.T.10
-
126
-
-
58149293012
-
Use of normalization methods for analysis of microarrays containing a high degree of gene effects
-
Ni T.T., Lemon W.J., Shyr Y., Zhong T.P. Use of normalization methods for analysis of microarrays containing a high degree of gene effects. BMC Bioinform. 2008, 9:505.
-
(2008)
BMC Bioinform.
, vol.9
, pp. 505
-
-
Ni, T.T.1
Lemon, W.J.2
Shyr, Y.3
Zhong, T.P.4
-
127
-
-
33646181805
-
LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates
-
Wang G., Kossenkov A.V., Ochs M.F. LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates. BMC Bioinform. 2006, 7:175.
-
(2006)
BMC Bioinform.
, vol.7
, pp. 175
-
-
Wang, G.1
Kossenkov, A.V.2
Ochs, M.F.3
-
128
-
-
33847098713
-
Multivariate curve resolution of time course microarray data
-
Wentzell P.D., Karakach T.K., Roy S., Martinez M.J., Allen C.P., Werner-Washburne M. Multivariate curve resolution of time course microarray data. BMC Bioinform. 2006, 7:343.
-
(2006)
BMC Bioinform.
, vol.7
, pp. 343
-
-
Wentzell, P.D.1
Karakach, T.K.2
Roy, S.3
Martinez, M.J.4
Allen, C.P.5
Werner-Washburne, M.6
-
129
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
Troyanskaya O., Cantor M., Sherlock G., Brown P., Hastie T., Tibshirani R., Botstein D., Altman R.B. Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17:520-525.
-
(2001)
Bioinformatics
, vol.17
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
Brown, P.4
Hastie, T.5
Tibshirani, R.6
Botstein, D.7
Altman, R.B.8
-
130
-
-
0242643743
-
A Bayesian missing value estimation method for gene expression profile data
-
Oba S., Sato M., Takemasa I., Monden M., Matsubara K., Ishii S. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 2003, 19:2088-2096.
-
(2003)
Bioinformatics
, vol.19
, pp. 2088-2096
-
-
Oba, S.1
Sato, M.2
Takemasa, I.3
Monden, M.4
Matsubara, K.5
Ishii, S.6
-
131
-
-
0041346457
-
Continuous representations of time-series gene expression data
-
Bar-Joseph Z., Gerber G.K., Gifford D.K., Jaakkola T.S., Simon I. Continuous representations of time-series gene expression data. J. Comput. Biol. 2003, 10:341-356.
-
(2003)
J. Comput. Biol.
, vol.10
, pp. 341-356
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Gifford, D.K.3
Jaakkola, T.S.4
Simon, I.5
-
132
-
-
0344033642
-
Missing-value estimation using linear and non-linear regression with Bayesian gene selection
-
Zhou X., Wang X., Dougherty E.R. Missing-value estimation using linear and non-linear regression with Bayesian gene selection. Bioinformatics 2003, 19:2302-2307.
-
(2003)
Bioinformatics
, vol.19
, pp. 2302-2307
-
-
Zhou, X.1
Wang, X.2
Dougherty, E.R.3
-
133
-
-
19644375092
-
Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data
-
Sehgal M.S.B., Gondal I., Dooley L.S. Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data. Bioinformatics 2005, 21:2417-2423.
-
(2005)
Bioinformatics
, vol.21
, pp. 2417-2423
-
-
Sehgal, M.S.B.1
Gondal, I.2
Dooley, L.S.3
-
134
-
-
13444304426
-
Missing value estimation for DNA microarray gene expression data: local least squares imputation
-
Kim H., Golub G.H., Park H. Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics 2005, 21:187-198.
-
(2005)
Bioinformatics
, vol.21
, pp. 187-198
-
-
Kim, H.1
Golub, G.H.2
Park, H.3
-
135
-
-
27944450456
-
DNA microarray data imputation and significance analysis of differential expression
-
Jörnsten R., Wang H., Welsh W.J., Ouyang M. DNA microarray data imputation and significance analysis of differential expression. Bioinformatics 2005, 21:4155-4161.
-
(2005)
Bioinformatics
, vol.21
, pp. 4155-4161
-
-
Jörnsten, R.1
Wang, H.2
Welsh, W.J.3
Ouyang, M.4
-
136
-
-
19344362305
-
Prediction of missing values in microarray and use of mixed models to evaluate the predictors
-
Article10
-
Feten G., Almøy T., Aastveit A.H. Prediction of missing values in microarray and use of mixed models to evaluate the predictors. Stat. Appl. Genet. Mol. Biol. 2005, 4. Article10.
-
(2005)
Stat. Appl. Genet. Mol. Biol.
, vol.4
-
-
Feten, G.1
Almøy, T.2
Aastveit, A.H.3
-
137
-
-
33645468884
-
Microarray missing data imputation based on a set theoretic framework and biological knowledge
-
Gan X., Liew A.W., Yan H. Microarray missing data imputation based on a set theoretic framework and biological knowledge. Nucleic Acids Res. 2006, 34:1608-1619.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1608-1619
-
-
Gan, X.1
Liew, A.W.2
Yan, H.3
-
138
-
-
33644856110
-
Improving missing value estimation in microarray data with gene ontology
-
Tuikkala J., Elo L., Nevalainen O.S., Aittokallio T. Improving missing value estimation in microarray data with gene ontology. Bioinformatics 2006, 22:566-572.
-
(2006)
Bioinformatics
, vol.22
, pp. 566-572
-
-
Tuikkala, J.1
Elo, L.2
Nevalainen, O.S.3
Aittokallio, T.4
-
139
-
-
33645037239
-
Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme
-
Wang X., Li A., Jiang Z., Feng H. Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme. BMC Bioinform. 2006, 7:32.
-
(2006)
BMC Bioinform.
, vol.7
, pp. 32
-
-
Wang, X.1
Li, A.2
Jiang, Z.3
Feng, H.4
-
140
-
-
33746974277
-
Improving missing value imputation of microarray data by using spot quality weights
-
Johansson P., Häkkinen J. Improving missing value imputation of microarray data by using spot quality weights. BMC Bioinform. 2006, 7:306.
-
(2006)
BMC Bioinform.
, vol.7
, pp. 306
-
-
Johansson, P.1
Häkkinen, J.2
-
141
-
-
39749093807
-
-
Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes, BMC Bioinformatics 9 12.
-
G.N. Brock, J.R. Shaffer, R.E. Blakesley, M.J. Lotz, and G.C. Tseng, Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes, BMC Bioinformatics 9 12.
-
-
-
Brock, G.N.1
Shaffer, J.R.2
Blakesley, R.E.3
Lotz, M.J.4
Tseng, G.C.5
-
142
-
-
77249129377
-
Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments
-
Celton M., Malpertuy A., Lelandais G., de Brevern A. Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. BMC Genomics 2010, 11:15.
-
(2010)
BMC Genomics
, vol.11
, pp. 15
-
-
Celton, M.1
Malpertuy, A.2
Lelandais, G.3
de Brevern, A.4
-
143
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
144
-
-
34547684291
-
A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance
-
Zhang S. A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance. BMC Bioinform. 2007, 8:230.
-
(2007)
BMC Bioinform.
, vol.8
, pp. 230
-
-
Zhang, S.1
-
145
-
-
78650179781
-
-
Significance Analysis of Microarrays
-
Significance Analysis of Microarrays, [http://www-stat.stanford.edu/?tibs/SAM/].
-
-
-
-
146
-
-
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. 1998, 95:14863-14868.
-
(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
-
147
-
-
59449098993
-
Transcriptome profiling of the feeding-to-fasting transition in chicken liver
-
Desert C., Duclos M., Blavy P., Lecerf F., Moreews F., Klopp C., Aubry M., Herault F., Le Roy P., Berri C., Douaire M., Diot C., Lagarrigue S. Transcriptome profiling of the feeding-to-fasting transition in chicken liver. BMC Genomics 2008, 9:611.
-
(2008)
BMC Genomics
, vol.9
, pp. 611
-
-
Desert, C.1
Duclos, M.2
Blavy, P.3
Lecerf, F.4
Moreews, F.5
Klopp, C.6
Aubry, M.7
Herault, F.8
Le Roy, P.9
Berri, C.10
Douaire, M.11
Diot, C.12
Lagarrigue, S.13
|