-
1
-
-
4043119775
-
Applications of biochips: From diagnostics to personalized medicine
-
Jain KK: Applications of biochips: from diagnostics to personalized medicine. Curr Opin Drug Discov Devel 2004, 7(3):285-289.
-
(2004)
Curr. Opin. Drug Discov. Devel.
, vol.7
, Issue.3
, pp. 285-289
-
-
Jain, K.K.1
-
2
-
-
0037974525
-
Application of microarray technology in environmental and comparative physiology
-
Gracey AY, Cossins AR: Application of microarray technology in environmental and comparative physiology. Annu Rev Physiol 2003, 65:231-259.
-
(2003)
Annu. Rev. Physiol.
, vol.65
, pp. 231-259
-
-
Gracey, A.Y.1
Cossins, A.R.2
-
3
-
-
0034927555
-
Analysis of variance for gene expression microarray data
-
Kerr MK, Martin M, Churchill GA: Analysis of variance for gene expression microarray data. J Comput Biol 2000, 7(6):819-837.
-
(2000)
J. Comput. Biol.
, vol.7
, Issue.6
, pp. 819-837
-
-
Kerr, M.K.1
Martin, M.2
Churchill, G.A.3
-
4
-
-
0036900895
-
Fundamentals of experimental design for cDNA microarrays
-
Churchill GA: Fundamentals of experimental design for cDNA microarrays. Nat Genet 2002, Suppl 32:490-495.
-
(2002)
Nat. Genet.
, Issue.SUPPL. 32
, pp. 490-495
-
-
Churchill, G.A.1
-
5
-
-
0036319960
-
Design issues for cDNA microarray experiments
-
Yang YH, Speed T: Design issues for cDNA microarray experiments. Nat Rev Genet 2002, 3(8):579-88.
-
(2002)
Nat. Rev. Genet.
, vol.3
, Issue.8
, pp. 579-588
-
-
Yang, Y.H.1
Speed, T.2
-
6
-
-
0000884487
-
Experimental design for gene expression microarrays
-
Kerr MK, Churchill GA: Experimental design for gene expression microarrays. Biostatistics 2001, 2(2):183-201.
-
(2001)
Biostatistics
, vol.2
, Issue.2
, pp. 183-201
-
-
Kerr, M.K.1
Churchill, G.A.2
-
7
-
-
0142151385
-
Overcoming technical variation and biological variation in quantitative proteomics
-
Molloy MP, Brzezinski EE, Hang J, McDowell MT, VanBogelen RA: Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 2003, 3(10):1912-1919.
-
(2003)
Proteomics
, vol.3
, Issue.10
, pp. 1912-1919
-
-
Molloy, M.P.1
Brzezinski, E.E.2
Hang, J.3
McDowell, M.T.4
VanBogelen, R.A.5
-
8
-
-
0036793353
-
Assessing sources of variability in microarray gene expression data
-
Spruill SE, Lu J, Hardy S, Weir B: Assessing sources of variability in microarray gene expression data. BioTechniques 2002, 33:916-923.
-
(2002)
BioTechniques
, vol.33
, pp. 916-923
-
-
Spruill, S.E.1
Lu, J.2
Hardy, S.3
Weir, B.4
-
9
-
-
0037452790
-
Individuality and variation in gene expression patterns in human blood
-
Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, Brown PO: Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci 2003, 100:1896-1901.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 1896-1901
-
-
Whitney, A.R.1
Diehn, M.2
Popper, S.J.3
Alizadeh, A.A.4
Boldrick, J.C.5
Relman, D.A.6
Brown, P.O.7
-
10
-
-
0036789519
-
Variation in gene expression within and among natural populations
-
Oleksiak MF, Churchill GA, Crawford DL: Variation in gene expression within and among natural populations. Nat Genet 2002, 32(2):261-266.
-
(2002)
Nat. Genet.
, vol.32
, Issue.2
, pp. 261-266
-
-
Oleksiak, M.F.1
Churchill, G.A.2
Crawford, D.L.3
-
11
-
-
0842331389
-
Quantification of sources of variation and accuracy of sequence discrimination in a replicated microarray experiment
-
Brown JS, Kuhn D, Wisser R, Power E, Schnell R: Quantification of sources of variation and accuracy of sequence discrimination in a replicated microarray experiment. BioTechniques 2004, 36:324-332.
-
(2004)
BioTechniques
, vol.36
, pp. 324-332
-
-
Brown, J.S.1
Kuhn, D.2
Wisser, R.3
Power, E.4
Schnell, R.5
-
12
-
-
2942576225
-
Sources of variability and effect of experimental approach on expression profiling data interpretation
-
Bakay M, Chen YW, Borup R, Zhao P, Nagaraju K, Hoffman EP: Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformatics 2002, 3(1):4.
-
(2002)
BMC Bioinformatics
, vol.3
, Issue.1
, pp. 4
-
-
Bakay, M.1
Chen, Y.W.2
Borup, R.3
Zhao, P.4
Nagaraju, K.5
Hoffman, E.P.6
-
13
-
-
3242708508
-
Impact of pre-analytical handling on bone marrow mRNA gene expression
-
Breit S, Nees M, Schaefer U, Pfoersich M, Hagemeier C, Muckenthaler M, Kulozik AE: Impact of pre-analytical handling on bone marrow mRNA gene expression. Br J Haematol 2004,126(2):231-243.
-
(2004)
Br. J. Haematol.
, vol.126
, Issue.2
, pp. 231-243
-
-
Breit, S.1
Nees, M.2
Schaefer, U.3
Pfoersich, M.4
Hagemeier, C.5
Muckenthaler, M.6
Kulozik, A.E.7
-
14
-
-
1842680967
-
Reproducibility, sources of variability, pooling, and sample size: Important considerations for the design of high-density oligonucleotide array experiments
-
Han ES, Wu Y, McCarter R, Nelson JF, Richardson A, Hilsenbeck SG: Reproducibility, sources of variability, pooling, and sample size: important considerations for the design of high-density oligonucleotide array experiments. J Gerontol A Biol Sci Med Sci 2004, 59(4):306-315.
-
(2004)
J. Gerontol. A Biol. Sci. Med. Sci.
, vol.59
, Issue.4
, pp. 306-315
-
-
Han, E.S.1
Wu, Y.2
McCarter, R.3
Nelson, J.F.4
Richardson, A.5
Hilsenbeck, S.G.6
-
15
-
-
3042683137
-
Hybridization buffer systems impact the quality of filter array data
-
Liu J, Walker N, Waalkes MP: Hybridization buffer systems impact the quality of filter array data. J Pharmacol Toxicol Methods 2004, 50(1):67-71.
-
(2004)
J. Pharmacol. Toxicol. Methods
, vol.50
, Issue.1
, pp. 67-71
-
-
Liu, J.1
Walker, N.2
Waalkes, M.P.3
-
16
-
-
0242496185
-
A design and statistical perspective on microarray gene expression studies in nutrition: The need for playful creativity and scientific hard-mindedness
-
Page GP, Edwards JW, Barnes S, Weindruch R, Allison DB: A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness. Nutrition 2003, 19(11-12):997-1000.
-
(2003)
Nutrition
, vol.19
, Issue.11-12
, pp. 997-1000
-
-
Page, G.P.1
Edwards, J.W.2
Barnes, S.3
Weindruch, R.4
Allison, D.B.5
-
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: Evaluation of quality-control criteria for microarray gene expression analysis. Clin Chem 2004, 50(11):1994-2002.
-
(2004)
Clin. Chem.
, vol.50
, Issue.11
, 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
-
-
0141939435
-
The efficiency of pooling mRNA in microarray experiments
-
Kendziorski CM, Zhang Y, Lan H, Attie AD: The efficiency of pooling mRNA in microarray experiments. Biostatistics 2003, 4(3):465-477.
-
(2003)
Biostatistics
, vol.4
, Issue.3
, pp. 465-477
-
-
Kendziorski, C.M.1
Zhang, Y.2
Lan, H.3
Attie, A.D.4
-
19
-
-
0039910654
-
Power and money: Designing statistically powerful studies while minimizing financial costs
-
Allison DB, Allison RL, Faith MS, Paultre F, Pi-Sunyer FX: Power and money: designing statistically powerful studies while minimizing financial costs. Psychological Methods 1997, 2:20-33.
-
(1997)
Psychological Methods
, vol.2
, pp. 20-33
-
-
Allison, D.B.1
Allison, R.L.2
Faith, M.S.3
Paultre, F.4
Pi-Sunyer, F.X.5
-
20
-
-
28744458859
-
BioConductor: Open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, 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 AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: BioConductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80.
-
(2004)
Genome Biol.
, vol.5
, Issue.10
-
-
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..
-
21
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci 2001, 98:31-36.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
22
-
-
0036947892
-
Robust estimators for expression analysis
-
Hubbell E, Liu W, Mei R: Robust estimators for expression analysis. Bioinformatics 2002, 12:1585-92.
-
(2002)
Bioinformatics
, vol.12
, pp. 1585-1592
-
-
Hubbell, E.1
Liu, W.2
Mei, R.3
-
23
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4(2):249-264.
-
Biostatistics
, vol.4
, Issue.2
, 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
-
24
-
-
2442601878
-
A model based background adjustment for oligonucleotide expression arrays
-
Technical Report, John Hopkins University, Department of Biostatistics Working Papers, Baltimore, MD
-
Wu Z, Irizarry R, Gentleman R, Murillo F, Spencer F: A model based background adjustment for oligonucleotide expression arrays. Technical Report, John Hopkins University, Department of Biostatistics Working Papers, Baltimore, MD 2004.
-
(2004)
-
-
Wu, Z.1
Irizarry, R.2
Gentleman, R.3
Murillo, F.4
Spencer, F.5
-
25
-
-
19944429996
-
Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays
-
Dobbin KK, Beer DG, Meyerson 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: Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clin Cancer Res 2005, 11(2 Pt 1):565-572.
-
(2005)
Clin. Cancer Res.
, vol.11
, Issue.2 PART 1
, pp. 565-572
-
-
Dobbin, K.K.1
Beer, D.G.2
Meyerson, 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..
-
26
-
-
24144445705
-
Improved statistical tests for differential gene expression by shrinking variance components estimates
-
Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA: Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 2005, 6(1):59-75.
-
(2005)
Biostatistics
, vol.6
, Issue.1
, pp. 59-75
-
-
Cui, X.1
Hwang, J.T.2
Qiu, J.3
Blades, N.J.4
Churchill, G.A.5
-
27
-
-
0037187833
-
A mixture model approach for the analysis of microarray gene expression data
-
Allison DB, Gadbury GL, Heo M, Fernandez JR, Lee C, Prolla TA, Weindruch R: A mixture model approach for the analysis of microarray gene expression data. Comput Stati Data Anal 2002, 39:1-20.
-
(2002)
Comput. Stati. Data Anal.
, vol.39
, pp. 1-20
-
-
Allison, D.B.1
Gadbury, G.L.2
Heo, M.3
Fernandez, J.R.4
Lee, C.5
Prolla, T.A.6
Weindruch, R.7
-
28
-
-
17844379157
-
A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms
-
Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G: A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech 2004, 15(4):276-284.
-
(2004)
J. Biomol. Tech.
, vol.15
, Issue.4
, pp. 276-284
-
-
Woo, Y.1
Affourtit, J.2
Daigle, S.3
Viale, A.4
Johnson, K.5
Naggert, J.6
Churchill, G.7
-
29
-
-
23844483247
-
A study of inter-lab and inter-platform agreement of DNA microarray data
-
Wang H, He X, Band M, Wilson C, Liu L: A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 2005, 6(1):71.
-
(2005)
BMC Genomics
, vol.6
, Issue.1
, pp. 71
-
-
Wang, H.1
He, X.2
Band, M.3
Wilson, C.4
Liu, L.5
-
30
-
-
84885690522
-
Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data
-
Shedden K, Chen W, Kuick R, Ghosh D, Macdonald J, Cho KR, Giordano TJ, Gruber SB, Fearon ER, Taylor JM, Hanash S: Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.
-
-
-
Shedden, K.1
Chen, W.2
Kuick, R.3
Ghosh, D.4
Macdonald, J.5
Cho, K.R.6
Giordano, T.J.7
Gruber, S.B.8
Fearon, E.R.9
Taylor, J.M.10
Hanash, S.11
-
31
-
-
0043089918
-
Transformation and normalization of oligonucleotide microarray data
-
Geller SC, Gregg JP, Hagerman P, Rocke DM: Transformation and normalization of oligonucleotide microarray data. Bioinformatics 2003, 19(14):1817-1823.
-
(2003)
Bioinformatics
, vol.19
, Issue.14
, pp. 1817-1823
-
-
Geller, S.C.1
Gregg, J.P.2
Hagerman, P.3
Rocke, D.M.4
-
32
-
-
13244299122
-
Comparing transformation methods for DNA microarray data
-
Thygesen HH, Zwinderman AH. Comparing transformation methods for DNA microarray data. BMC Bioinformatics 2004, 5(1):77.
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.1
, pp. 77
-
-
Thygesen, H.H.1
Zwinderman, A.H.2
-
33
-
-
9144268360
-
Contributing Members of the Toxicogenomics Research Consortium: Empirical evaluation of data transformations and ranking statistics for microarray analysis
-
Qin LX, Kerr KF; Contributing Members of the Toxicogenomics Research Consortium: Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res 2004, 32(18):5471-5479.
-
(2004)
Nucleic Acids Res.
, vol.32
, Issue.18
, pp. 5471-5479
-
-
Qin, L.X.1
Kerr, K.F.2
-
34
-
-
18844447998
-
Statistical development and evaluation of microarray gene expression data filters
-
Pounds S, Cheng C: Statistical development and evaluation of microarray gene expression data filters. J Comput Biol 2005,12(4):482-495.
-
(2005)
J. Comput. Biol.
, vol.12
, Issue.4
, pp. 482-495
-
-
Pounds, S.1
Cheng, C.2
-
35
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:2.
-
(2003)
Bioinformatics
, vol.19
, pp. 2
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
36
-
-
18244389201
-
Standardizing global gene expression analysis between laboratories and across platforms
-
Toxicogenomics Research Consortium
-
Toxicogenomics Research Consortium: Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2005, 2(5):351-356.
-
(2005)
Nat. Methods
, vol.2
, Issue.5
, pp. 351-356
-
-
-
37
-
-
18244378238
-
Independence and reproducibility across microarray platforms
-
Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. Nat Methods 2005, 2(5):337-344.
-
(2005)
Nat. Methods
, vol.2
, Issue.5
, pp. 337-344
-
-
Larkin, J.E.1
Frank, B.C.2
Gavras, H.3
Sultana, R.4
Quackenbush, J.5
-
38
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W: Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2(5):345-350.
-
(2005)
Nat. Methods
, vol.2
, Issue.5
, 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
Martinez-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..
-
39
-
-
0030305457
-
A language for data analysis and graphics
-
Ihaka R, Gentleman R: A language for data analysis and graphics. J Comp Graph Stat 1996, 5(3):299-314.
-
(1996)
J. Comp. Graph. Stat.
, vol.5
, Issue.3
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
|