-
1
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary dna microarray
-
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
2
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 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
Horton, H.10
Brown, E.L.11
-
3
-
-
84984932472
-
Exploring the new world of the genome with dna microarrays
-
Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21:33-37
-
(1999)
Nat Genet
, vol.21
, pp. 33-37
-
-
Brown, P.O.1
Botstein, D.2
-
4
-
-
44849117559
-
Making a new technology work: The standardization and regulation of microarrays
-
Rogers S, Cambrosio A (2007) Making a new technology work: the standardization and regulation of microarrays. Yale J Biol Med 80:165-178
-
(2007)
Yale J Biol Med
, vol.80
, pp. 165-178
-
-
Rogers, S.1
Cambrosio, A.2
-
5
-
-
1542290446
-
Expression pro filing-best practices for data generation and interpretation in clinical trials
-
The Tumor Analysis Best Practices Working Group
-
The Tumor Analysis Best practices Working Group (2004) Expression pro filing-best practices for data generation and interpretation in clinical trials. Nat Rev 5:229-237
-
(2004)
Nat Rev
, vol.5
, pp. 229-237
-
-
-
6
-
-
85083615193
-
-
http://www.fda.gov/downloads/Drugs/Guidance ComplianceRegulator yInformation/Guidances/UCM079855.pdf
-
-
-
-
7
-
-
33748491517
-
The microarray quality control (maqc) project shows inter-and intraplatform reproducibility of gene expression measurements
-
Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ et al (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151-1161
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1151-1161
-
-
Shi, L.1
Reid, L.H.2
Jones, W.D.3
Shippy, R.4
Warrington, J.A.5
Baker, S.C.6
Collins, P.J.7
De Longueville, F.8
Kawasaki, E.S.9
Lee, K.Y.10
Luo, Y.11
Sun, Y.A.12
Willey, J.C.13
Setterquist, R.A.14
Fischer, G.M.15
Tong, W.16
Dragan, Y.P.17
Dix, D.J.18
-
8
-
-
33644871376
-
Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: Practical considerations and perspectives
-
Clarke JD, Zhu T (2006) Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. Plant J 45:630-650
-
(2006)
Plant J
, vol.45
, pp. 630-650
-
-
Clarke, J.D.1
Zhu, T.2
-
9
-
-
33748494248
-
A framework for the use of genomics data at the epa
-
Dix DJ, Gallagher K, Benson WH, Groskinsky BL, McClintock T, Dear field KL, Farland WH (2006) A framework for the use of genomics data at the EPA. Nat Biotechnol 24: 1108-1111
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1108-1111
-
-
Dix, D.J.1
Gallagher, K.2
Benson, W.H.3
Groskinsky, B.L.4
McClintock, T.5
Dearfield, K.L.6
Farland, W.H.7
-
10
-
-
84892860272
-
Experimental design
-
In: Scherer A (ed) Wiley, West Sussex, ISBN:978-0-470-74138-74142
-
Grass P (2009) Experimental design, pp 19-31. In: Scherer A (ed) Batch effects and noise in microarray experiments. Wiley, West Sussex, ISBN:978-0-470-74138-2
-
(2009)
Batch Effects and Noise in Microarray Experiments.
, pp. 19-31
-
-
Grass, P.1
-
11
-
-
33344473340
-
Bias in research studies
-
Sica GT (2006) Bias in research studies. Radiology 238:780-789
-
(2006)
Radiology
, vol.238
, pp. 780-789
-
-
Sica, G.T.1
-
12
-
-
27444437395
-
Bioinformatic analysis of circadian gene oscillation in mouse aorta
-
Rudic RD, McNamara P, Reilly D, Grosser T, Curtis AM, Price TS, Panda S, Hogenesch JB, FitzGerald GA (2005) Bioinformatic analysis of circadian gene oscillation in mouse aorta. Circulation 112:2716-2724
-
(2005)
Circulation
, vol.112
, pp. 2716-2724
-
-
Rudic, R.D.1
McNamara, P.2
Reilly, D.3
Grosser, T.4
Curtis, A.M.5
Price, T.S.6
Panda, S.7
Hogenesch, J.B.8
FitzGerald, G.A.9
-
13
-
-
0036399459
-
Identifying and quantifying sources of variation in microarray data using high-density cdna membrane arrays
-
Coombes KR, Highsmith WE, Krogmann TA, Baggerly KA, Stivers DN, Abruzzo LV (2002) Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. J Comp Biol 9: 655-669
-
(2002)
J Comp Biol
, vol.9
, pp. 655-669
-
-
Coombes, K.R.1
Highsmith, W.E.2
Krogmann, T.A.3
Baggerly, K.A.4
Stivers, D.N.5
Abruzzo, L.V.6
-
15
-
-
25444496949
-
Sources of variation in affymetrix microarray experiments
-
Zakharkin SO, Kim K, Mehta T, Chen L, Barnes S, Scheirer KE, Parrish RS, Allison DB, Page GP (2005) Sources of variation in Affymetrix microarray experiments. BMC Bioinform 6:214
-
(2005)
BMC Bioinform
, vol.6
, pp. 214
-
-
Zakharkin, S.O.1
Kim, K.2
Mehta, T.3
Chen, L.4
Barnes, S.5
Scheirer, K.E.6
Parrish, R.S.7
Allison, D.B.8
Page, G.P.9
-
16
-
-
0345257783
-
Chipping away at the chip bias: Rna degradation in microarray analysis
-
Auer H, Lyianarachchi S, Newsom D, Klisovic MI, Marcucci G, Kornacker K (2003) Chipping away at the chip bias: RNA degradation in microarray analysis. Nat Genet 35:292-293
-
(2003)
Nat Genet
, vol.35
, pp. 292-293
-
-
Auer, H.1
Lyianarachchi, S.2
Newsom, D.3
Klisovic, M.I.4
Marcucci, G.5
Kornacker, K.6
-
17
-
-
7044286287
-
Evaluation of quality-control criteria for microarray gene expression analysis
-
Dumur CI, Nasim S, Best AM, Archer KJ, Ladd AC, Mas VR, Wilkinson DS, Garrett CT, Ferreira-Gonzalez A (2006) Evaluation of quality-control criteria for microarray gene expression analysis. Clin Chem 50:1994-2002
-
(2006)
Clin Chem
, vol.50
, pp. 1994-2002
-
-
Dumur, C.I.1
Nasim, S.2
Best, A.M.3
Archer, K.J.4
Ladd, A.C.5
Mas, V.R.6
Wilkinson, D.S.7
Garrett, C.T.8
Ferreira-Gonzalez, A.9
-
18
-
-
33645241407
-
The rin: An rna integrity number for assigning integrity values to rna measurements
-
Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 7:3
-
(2006)
BMC Mol Biol
, vol.7
, pp. 3
-
-
Schroeder, A.1
Mueller, O.2
Stocker, S.3
Salowsky, R.4
Leiber, M.5
Gassmann, M.6
Lightfoot, S.7
Menzel, W.8
Granzow, M.9
Ragg, T.10
-
19
-
-
13444304216
-
Microarrays and molecular research: Noise discovery?
-
Ioannidis JP (2005) Microarrays and molecular research: noise discovery? Lancet 365:454-455
-
(2005)
Lancet
, vol.365
, pp. 454-455
-
-
Ioannidis, J.P.1
-
20
-
-
18944394950
-
An array of problems
-
Frantz S (2005) An array of problems. Nat Rev Drug Discov 4:362-363
-
(2005)
Nat Rev Drug Discov
, vol.4
, pp. 362-363
-
-
Frantz, S.1
-
21
-
-
33750827097
-
Arrays of hope
-
Strauss E (2006) Arrays of hope. Cell 127:657-659
-
(2006)
Cell
, vol.127
, pp. 657-659
-
-
Strauss, E.1
-
22
-
-
68449102706
-
In praise of arrays
-
Ying L, Sarwal M (2008) In praise of arrays. Pediatr Nephrol 24:1643-1659
-
(2008)
Pediatr Nephrol
, vol.24
, pp. 1643-1659
-
-
Ying, L.1
Sarwal, M.2
-
23
-
-
7444234286
-
Getting the noise out of gene arrays
-
Marshall E (2004) Getting the noise out of gene arrays. Science 306:630-631
-
(2004)
Science
, vol.306
, pp. 630-631
-
-
Marshall, E.1
-
24
-
-
13444249852
-
Prediction of cancer outcome with microarrays: A multiple random validation strategy
-
Michiels S, Koscielny S, Hill C (2005) Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365:488-492
-
(2005)
Lancet
, vol.365
, pp. 488-492
-
-
Michiels, S.1
Koscielny, S.2
Hill, C.3
-
25
-
-
33645825183
-
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
-
Ein-Dor L, Zuk O, Domany E (2006) Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 103:5923-5928
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5923-5928
-
-
Ein-Dor, L.1
Zuk, O.2
Domany, E.3
-
26
-
-
59149088407
-
Repeatability of published microarray gene expression analyses
-
Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V (2009) Repeatability of published microarray gene expression analyses. Nat Genet 41:149-155
-
(2009)
Nat Genet
, vol.41
, pp. 149-155
-
-
Ioannidis, J.P.1
Allison, D.B.2
Ball, C.A.3
Coulibaly, I.4
Cui, X.5
Culhane, A.C.6
Falchi, M.7
Furlanello, C.8
Game, L.9
Jurman, G.10
Mangion, J.11
Mehta, T.12
Nitzberg, M.13
Page, G.P.14
Petretto, E.15
Van Noort, V.16
-
27
-
-
19944429996
-
Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays
-
Dobbin KK, Beer DG, Meverson M, Yeatman TJ, Gerald WL, Jacobson JW, Conley B, Buetow KH, Heiskanen M, Simon RM, Minna JD, Girard L, Misek DE, Taylor JM, Hanash S, Naoki K, Hayes DN, Ladd-Acosta C, Enkemann SA, Viale A, Giordano TJ (2005) Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clin Cancer Res 11:565-572
-
(2005)
Clin Cancer Res
, vol.11
, pp. 565-572
-
-
Dobbin, K.K.1
Beer, D.G.2
Meverson, M.3
Yeatman, T.J.4
Gerald, W.L.5
Jacobson, J.W.6
Conley, B.7
Buetow, K.H.8
Heiskanen, M.9
Simon, R.M.10
Minna, J.D.11
Girard, L.12
Misek, D.E.13
Taylor, J.M.14
Hanash, S.15
Naoki, K.16
Hayes, D.N.17
Ladd-Acosta, C.18
Enkemann, S.A.19
Viale, A.20
Giordano, T.J.21
more..
-
28
-
-
18244378238
-
Independence and reproducibility across microarray platforms
-
Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J (2005) Independence and reproducibility across microarray platforms. Nat Methods 2:337-344
-
(2005)
Nat Methods
, vol.2
, pp. 337-344
-
-
Larkin, J.E.1
Frank, B.C.2
Gavras, H.3
Sultana, R.4
Quackenbush, J.5
-
29
-
-
18244384210
-
Multiplelaboratory comparison of micrarray platforms
-
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Grif fin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martínez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W (2005) Multiplelaboratory comparison of micrarray platforms. Nat Methods 2:345-350
-
(2005)
Nat Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Frank, B.C.6
Gabrielson, E.7
Garcia, J.G.8
Geoghegan, J.9
Germino, G.10
Griffin, C.11
Hilmer, S.C.12
Hoffman, E.13
Jedlicka, A.E.14
Kawasaki, E.15
Martínez-Murillo, F.16
Morsberger, L.17
Lee, H.18
Petersen, D.19
Quackenbush, J.20
Scott, A.21
Wilson, M.22
Yang, Y.23
Ye, S.Q.24
Yu, W.25
more..
-
30
-
-
0036356994
-
Assessment of the relationship between signal intensities and transcript concentration for affymetrix genechip arrays
-
Chudin E, Walker R, Kosaka A, Wu SX, Rabert D, Chang TK, Kreder DE (2002) Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays. Genome Biol 3:RESEARCH0005
-
(2002)
Genome Biol
, vol.3
-
-
Chudin, E.1
Walker, R.2
Kosaka, A.3
Wu, S.X.4
Rabert, D.5
Chang, T.K.6
Kreder, D.E.7
-
31
-
-
0141450348
-
Comparison and meta-analysis of microarray data: From the bench to the computer desk
-
Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M (2003) Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet 19:570-577
-
(2003)
Trends Genet
, vol.19
, pp. 570-577
-
-
Moreau, Y.1
Aerts, S.2
De Moor, B.3
De Strooper, B.4
Dabrowski, M.5
-
32
-
-
0036793318
-
Use of rna and genomics dna references for inferred comparisons in dna microarray analyses
-
Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J (2002) Use of RNA and genomics DNA references for inferred comparisons in DNA microarray analyses. Biotechiques 33:924-930
-
(2002)
Biotechiques
, vol.33
, pp. 924-930
-
-
Kim, H.1
Zhao, B.2
Snesrud, E.C.3
Haas, B.J.4
Town, C.D.5
Quackenbush, J.6
-
33
-
-
2342624566
-
Microarray reality checks in the context of a complex disease
-
Miklos GL, Maleszka R (2004) Microarray reality checks in the context of a complex disease. Nat Biotechnol 22:615-621
-
(2004)
Nat Biotechnol
, vol.22
, pp. 615-621
-
-
Miklos, G.L.1
Maleszka, R.2
-
34
-
-
27144548491
-
The external rna controls consortium: A progress report
-
The External RNA Controls Consortium
-
The External RNA Controls Consortium (2005) The external RNA controls consortium: a progress report. Nat Methods 2:731-734
-
(2005)
Nat Methods
, vol.2
, pp. 731-734
-
-
-
35
-
-
61349095462
-
Use of disganostic accuracy as a metric for evaluating laboratory pro ficiency with microarray assays using mixed-tissue rna reference samples
-
Pine PS, Boedigheimer M, Rosenzweig BA, Turpaz Y, He YD, delestarr G, Ganter B, Jarnagin K, Jones WD, Reid LH, Thompson KL (2008) Use of disganostic accuracy as a metric for evaluating laboratory pro ficiency with microarray assays using mixed-tissue RNA reference samples. Pharmacogenomics 9: 1753-1763
-
(2008)
Pharmacogenomics
, vol.9
, pp. 1753-1763
-
-
Pine, P.S.1
Boedigheimer, M.2
Rosenzweig, B.A.3
Turpaz, Y.4
He, Y.D.5
Delestarr, G.6
Ganter, B.7
Jarnagin, K.8
Jones, W.D.9
Reid, L.H.10
Thompson, K.L.11
-
37
-
-
29144535372
-
Evolving gene/transcript de finitions signi ficantly alter the interpretation of genechip data
-
Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F (2005) Evolving gene/transcript de finitions signi ficantly alter the interpretation of GeneChip data. Nucleic Acids Res 33:e175
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Dai, M.1
Wang, P.2
Boyd, A.D.3
Kostov, G.4
Athey, B.5
Jones, E.G.6
Bunney, W.E.7
Myers, R.M.8
Speed, T.P.9
Akil, H.10
Watson, S.J.11
Meng, F.12
-
39
-
-
26444454986
-
A sequence-based identi fication of the genes detected by probesets on the affymetrix u133 plus 2.0 array
-
Harbig J, Sprinkle R, Enkemann SA (2005) A sequence-based identi fication of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 33:e31
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Harbig, J.1
Sprinkle, R.2
Enkemann, S.A.3
-
40
-
-
79959524146
-
A haplotype map of the human genome
-
Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P (2005) A haplotype map of the human genome. Nature 437: 1299-1320
-
(2005)
Nature
, vol.437
, pp. 1299-1320
-
-
Altshuler, D.1
Brooks, L.D.2
Chakravarti, A.3
Collins, F.S.4
Daly, M.J.5
Donnelly, P.6
-
41
-
-
1342263843
-
Guidelines for incorporating non-perfectly matched oligonucleotides into target-speci fic hybridization probes for a dna microarray
-
Lee I, Dombkowski AA, Athey BD (2004) Guidelines for incorporating non-perfectly matched oligonucleotides into target-speci fic hybridization probes for a DNA microarray. Nucleic Acids Res 32:681-690
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 681-690
-
-
Lee, I.1
Dombkowski, A.A.2
Athey, B.D.3
-
42
-
-
0141483023
-
Probe selection for high-density oligonucleotide arrays
-
Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM, Lu G, Fang J, Liu WM, Ryder T, Kaplan P, Kulp D, Webster TA (2003) Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci USA 100:11237-11242
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 11237-11242
-
-
Mei, R.1
Hubbell, E.2
Bekiranov, S.3
Mittmann, M.4
Christians, F.C.5
Shen, M.M.6
Lu, G.7
Fang, J.8
Liu, W.M.9
Ryder, T.10
Kaplan, P.11
Kulp, D.12
Webster, T.A.13
-
43
-
-
7444229744
-
Dysregulation of the fibroblast growth factor system in major depression
-
Evans SJ, Choudary PV, Neal CR, Li JZ, Vawter MP, Tomita H, Lopez JF, Thompson RC, Meng F, Stead JD, Walsh DM, Myers RM, Bunney WE, Watson SJ, Jones EG, Akil H (2004) Dysregulation of the fibroblast growth factor system in major depression. Proc Natl Acad Sci USA 101:15506-15511
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 15506-15511
-
-
Evans, S.J.1
Choudary, P.V.2
Neal, C.R.3
Li, J.Z.4
Vawter, M.P.5
Tomita, H.6
Lopez, J.F.7
Thompson, R.C.8
Meng, F.9
Stead, J.D.10
Walsh, D.M.11
Myers, R.M.12
Bunney, W.E.13
Watson, S.J.14
Jones, E.G.15
Akil, H.16
-
44
-
-
77951221352
-
A re-annotation pipeline for illumina beadarrays: Improving the interpretation of gene expression data
-
Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JF, Ritchie ME, Lynch AG, Tavare S (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res 38(3):e17
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.3
-
-
Barbosa-Morais, N.L.1
Dunning, M.J.2
Samarajiwa, S.A.3
Darot, J.F.4
Ritchie, M.E.5
Lynch, A.G.6
Tavare, S.7
-
45
-
-
85083608706
-
-
Affymetrix (b) Whole Transcript (WT) Sense Target Labeling Assay Manual, (c) Alternative Transcript Analysis Methods for Exon Arrays v1.1, (d) Exon Array Background Correction v1.0, (e) Exon Probeset Annotations and Transcript Cluster Groupings v1.0, (f) Gene Signal Estimates from Exon Arrays v1.0, (g) Quality Assessment of Exon Arrays v1.0', HumanExon1.0 ST Array Manuals and White Papers
-
Affymetrix (2005) (a) Exon Array Computational Tool Software User's Guide, (b) Whole Transcript (WT) Sense Target Labeling Assay Manual, (c) Alternative Transcript Analysis Methods for Exon Arrays v1.1, (d) Exon Array Background Correction v1.0, (e) Exon Probeset Annotations and Transcript Cluster Groupings v1.0, (f) Gene Signal Estimates from Exon Arrays v1.0, (g) Quality Assessment of Exon Arrays v1.0', http://www.affymetrix.com/products/arrays/speci fic/exon.affx, Human Exon 1.0 ST Array Manuals and White Papers
-
(2005)
Exon Array Computational Tool Software User's Guide
-
-
-
46
-
-
34548570202
-
Web-based genechip analysis system for large-scale collaborative projects
-
Dai M, Wang P, Jakupovic E, Watson SJ, Meng F (2007) Web-based GeneChip analysis system for large-scale collaborative projects. Bioinformatics 23:2185-2187
-
(2007)
Bioinformatics
, vol.23
, pp. 2185-2187
-
-
Dai, M.1
Wang, P.2
Jakupovic, E.3
Watson, S.J.4
Meng, F.5
-
47
-
-
33747520366
-
The effect of genechip gene de finitions on the microarray study of cancers
-
Lu X, Zhang X (2006) The effect of GeneChip gene de finitions on the microarray study of cancers. Bioessays 28:739-746
-
(2006)
Bioessays
, vol.28
, pp. 739-746
-
-
Lu, X.1
Zhang, X.2
-
48
-
-
33847679625
-
Improved precision and accuracy for microarrays using updated probe set de finitions
-
Sandberg R, Larsson O (2007) Improved precision and accuracy for microarrays using updated probe set de finitions. BMC Bioinform 8:48
-
(2007)
BMC Bioinform
, vol.8
, pp. 48
-
-
Sandberg, R.1
Larsson, O.2
-
49
-
-
4444291843
-
Detection of large-scale variation in the human genome
-
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C (2004) Detection of large-scale variation in the human genome. Nat Genet 36:949-951
-
(2004)
Nat Genet
, vol.36
, pp. 949-951
-
-
Iafrate, A.J.1
Feuk, L.2
Rivera, M.N.3
Listewnik, M.L.4
Donahoe, P.K.5
Qi, Y.6
Scherer, S.W.7
Lee, C.8
-
50
-
-
0012789869
-
Allelic variation in gene expression is common in the human genome
-
Lo HS, Wang Z, Hu Y, Yang HH, Gere S, Buetow KH, Lee MP (2003) Allelic variation in gene expression is common in the human genome. Genome Res 13:1855-1862
-
(2003)
Genome Res
, vol.13
, pp. 1855-1862
-
-
Lo, H.S.1
Wang, Z.2
Hu, Y.3
Yang, H.H.4
Gere, S.5
Buetow, K.H.6
Lee, M.P.7
-
51
-
-
34548786857
-
Gene expression in peripheral blood mononuclear cells from children with diabetes
-
Kaizer EC, Glaser CL, Chaussabel D, Banchereau J, Pascual V, White PC (2007) Gene expression in peripheral blood mononuclear cells from children with diabetes. J Clin Endocrinol Metab 92:3705-3711
-
(2007)
J Clin Endocrinol Metab
, vol.92
, pp. 3705-3711
-
-
Kaizer, E.C.1
Glaser, C.L.2
Chaussabel, D.3
Banchereau, J.4
Pascual, V.5
White, P.C.6
-
53
-
-
33745476107
-
Standardizing the standards
-
Quackenbush J (2006) Standardizing the standards. Mol Syst Biol 2:2006.0010
-
(2006)
Mol Syst Biol
, vol.2
, Issue.2006
, pp. 0010
-
-
Quackenbush, J.1
-
54
-
-
66149146644
-
Toward a public toxicogenomics capability for supporting predictive toxicology: Survey of current resources and chemical indexing of experiments in geo and arrayexpress
-
Williams-Devane CR, Wolf MA, Richard AM (2009) Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress. Toxicol Sci 109:358-371
-
(2009)
Toxicol Sci
, vol.109
, pp. 358-371
-
-
Williams-Devane, C.R.1
Wolf, M.A.2
Richard, A.M.3
-
55
-
-
70249098051
-
Postpublication sharing of data and tools
-
CASIMIR Consortium (2009) Postpublication sharing of data and tools. Nature 461:171-173
-
(2009)
Nature
, vol.461
, pp. 171-173
-
-
Casimir, C.1
-
57
-
-
0034069495
-
Gene ontology: Tool for the uni fication of biology
-
Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the uni fication of biology. The Gene Ontology Consortium. Nat Genet 25:25-32
-
(2000)
The Gene Ontology Consortium. Nat Genet
, vol.25
, pp. 25-32
-
-
Ashburner, M.1
Ball, C.2
Blake, J.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
58
-
-
68249085263
-
The gene ontology's reference genome project: A uni fied framework for functional annotation across species
-
Gaudet P, Chisholm R, Berardini T, Dimmer E, Engel SR, Fey P, Hill DP, Howe D, Hu JC, Huntley R, Khodiyar VK, Kishore R, Li D, Lovering RC, McCarthy F, Ni L, Petri V, Siegele DA, Tweedie S, Van Auken K, Wood V, Basu S, Carbon S, Dolan M, Mungall CJ, Dolinski K, Thomas P, Ashburner M, Blake JA, Cherry JM, Lewis SE, Balakrishnan R, Christie KR, Costanzo MC, Deegan J, Diehl AD, Drabkin H, Fisk DG, Harris M, Hirschman JE, Hong EL, Ireland A, Lomax J, Nash RS, Park J, Sitnikov D, Skrzypek MS, Apweiler R, Bult C, Eppig J, Jacob H, Parkhill J, Rhee S, Ringwald M, Sternberg P, Talmud P, Twigger S, Wester field M (2009) The Gene Ontology's Reference Genome Project: a uni fied framework for functional annotation across species. PLoS Comput Biol 5:e1000431
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Gaudet, P.1
Chisholm, R.2
Berardini, T.3
Dimmer, E.4
Engel, S.R.5
Fey, P.6
Hill, D.P.7
Howe, D.8
Hu, J.C.9
Huntley, R.10
Khodiyar, V.K.11
Kishore, R.12
Li, D.13
Lovering, R.C.14
McCarthy, F.15
Ni, L.16
Petri, V.17
Siegele, D.A.18
Tweedie, S.19
Van Auken, K.20
Wood, V.21
Basu, S.22
Carbon, S.23
Dolan, M.24
Mungall, C.J.25
Dolinski, K.26
Thomas, P.27
Ashburner, M.28
Blake, J.A.29
Cherry, J.M.30
Lewis, S.E.31
Balakrishnan, R.32
Christie, K.R.33
Costanzo, M.C.34
Deegan, J.35
Diehl, A.D.36
Drabkin, H.37
Fisk, D.G.38
Harris, M.39
Hirschman, J.E.40
Hong, E.L.41
Ireland, A.42
Lomax, J.43
Nash, R.S.44
Park, J.45
Sitnikov, D.46
Skrzypek, M.S.47
Apweiler, R.48
Bult, C.49
Eppig, J.50
Jacob, H.51
Parkhill, J.52
Rhee, S.53
Ringwald, M.54
Sternberg, P.55
Talmud, P.56
Twigger, S.57
Westerfield, M.58
more..
-
59
-
-
18344396568
-
Minimum information about a microarray experiment (miame)-toward standards for microarray data
-
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365-371
-
(2001)
Nat Genet
, vol.29
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
Ansorge, W.8
Ball, C.A.9
Causton, H.C.10
Gaasterland, T.11
Glenisson, P.12
Holstege, F.C.13
Kim, I.F.14
Markowitz, V.15
Matese, J.C.16
Parkinson, H.17
Robinson, A.18
Sarkans, U.19
Schulze-Kremer, S.20
Stewart, J.21
Taylor, R.22
Vilo, J.23
Vingron, M.24
more..
-
60
-
-
0037163144
-
Design and implementation of microarray gene expression markup language (mage-ml)
-
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 3:RESEARCH0046
-
(2002)
Genome Biol
, vol.3
-
-
Spellman, P.T.1
Miller, M.2
Stewart, J.3
Troup, C.4
Sarkans, U.5
Chervitz, S.6
Bernhart, D.7
Sherlock, G.8
Ball, C.9
Lepage, M.10
Swiatek, M.11
Marks, W.L.12
Goncalves, J.13
Markel, S.14
Iordan, D.15
Shojatalab, M.16
Pizarro, A.17
White, J.18
Hubley, R.19
Deutsch, E.20
Senger, M.21
Aronow, B.J.22
Robinson, A.23
Bassett, D.24
Stoeckert Jr., C.J.25
Brazma, A.26
more..
-
61
-
-
33845643077
-
A simple spreadsheet-based, miame-supportive format for microarray data: Mage-tab
-
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A (2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform 7:489
-
(2006)
BMC Bioinform
, vol.7
, pp. 489
-
-
Rayner, T.F.1
Rocca-Serra, P.2
Spellman, P.T.3
Causton, H.C.4
Farne, A.5
Holloway, E.6
Irizarry, R.A.7
Liu, J.8
Maier, D.S.9
Miller, M.10
Petersen, K.11
Quackenbush, J.12
Sherlock, G.13
Stoeckert Jr., C.J.14
White, J.15
Whetzel, P.L.16
Wymore, F.17
Parkinson, H.18
Sarkans, U.19
Ball, C.A.20
Brazma, A.21
more..
-
62
-
-
33645277092
-
The mged ontology: A resource for semanticsbased description of microarray experiments
-
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr (2006) The MGED Ontology: a resource for semanticsbased description of microarray experiments. Bioinformatics 22:866-873
-
(2006)
Bioinformatics
, vol.22
, pp. 866-873
-
-
Whetzel, P.L.1
Parkinson, H.2
Causton, H.C.3
Fan, L.4
Fostel, J.5
Fragoso, G.6
Game, L.7
Heiskanen, M.8
Morrison, N.9
Rocca-Serra, P.10
Sansone, S.A.11
Taylor, C.12
White, J.13
Stoeckert Jr., C.J.14
-
63
-
-
4444297547
-
Standards for microarray data: An open letter
-
Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N (2004) Standards for microarray data: an open letter. Environ Health Perspect 112:A666-A667
-
(2004)
Environ Health Perspect
, vol.112
-
-
Ball, C.A.1
Brazma, A.2
Causton, H.3
Chervitz, S.4
Edgar, R.5
Hingamp, P.6
Matese, J.C.7
Parkinson, H.8
Quackenbush, J.9
Ringwald, M.10
Sansone, S.A.11
Sherlock, G.12
Spellman, P.13
Stoeckert, C.14
Tateno, Y.15
Taylor, R.16
White, J.17
Winegarden, N.18
-
64
-
-
19344365567
-
Submission of microarray data to public repositories
-
Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N (2004) Submission of microarray data to public repositories. PLoS Biol 2:E317
-
(2004)
PLoS Biol
, vol.2
-
-
Ball, C.A.1
Brazma, A.2
Causton, H.3
Chervitz, S.4
Edgar, R.5
Hingamp, P.6
Matese, J.C.7
Parkinson, H.8
Quackenbush, J.9
Ringwald, M.10
Sansone, S.A.11
Sherlock, G.12
Spellman, P.13
Stoeckert, C.14
Tateno, Y.15
Taylor, R.16
White, J.17
Winegarden, N.18
-
65
-
-
33846039701
-
Arrayexpress -A public database of microarray experiments and gene expression pro files
-
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A (2007) ArrayExpress -A public database of microarray experiments and gene expression pro files. Nucleic Acids Res 35:D747-D750
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Parkinson, H.1
Kapushesky, M.2
Shojatalab, M.3
Abeygunawardena, N.4
Coulson, R.5
Farne, A.6
Holloway, E.7
Kolesnykov, N.8
Lilja, P.9
Lukk, M.10
Mani, R.11
Rayner, T.12
Sharma, A.13
William, E.14
Sarkans, U.15
Brazma, A.16
-
66
-
-
0036081355
-
Gene expression omnibus: Ncbi gene expression and hybridization array data repository
-
Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
67
-
-
0347122079
-
Cibex: Center for information biology gene expression database
-
Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y (2003) CIBEX: center for information biology gene expression database. C R Biol 326:1079-1082
-
(2003)
C R Biol
, vol.326
, pp. 1079-1082
-
-
Ikeo, K.1
Ishi-i, J.2
Tamura, T.3
Gojobori, T.4
Tateno, Y.5
-
68
-
-
33748481775
-
Impact of microarray data quality on genomic data submissions to the fda
-
Frueh F (2006) Impact of microarray data quality on genomic data submissions to the FDA. Nat Biotechnol 24:1105-1107
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1105-1107
-
-
Frueh, F.1
-
69
-
-
33846703052
-
Global clinical data interchange standards are here!
-
Souza T, Kush R, Evans JP (2007) Global clinical data interchange standards are here! Drug Discov Today 12:174-181
-
(2007)
Drug Discov Today
, vol.12
, pp. 174-181
-
-
Souza, T.1
Kush, R.2
Evans, J.P.3
-
70
-
-
85083614291
-
-
U.S. Environmental Protection Agency DRAFT: Interim Guidance for Microarray-Based Assays: Data Submission, Quality, Analysis, Management, and Training Considerations
-
U.S. Environmental Protection Agency DRAFT: Interim Guidance for Microarray-Based Assays: Data Submission, Quality, Analysis, Management, and Training Considerations (2007). http://www.epa.gov/osa/spc/pdfs/epa-interim- guidance-for-microarray-based-assays-external-review-draft.pdf
-
(2007)
-
-
|