-
1
-
-
23444456437
-
Effects of RNA degradation on gene expression analysis of human postmortem tissues
-
3552fje
-
Lee J, Hever A, Willhite D, Zlotnik A, Hevezi P. Effects of RNA degradation on gene expression analysis of human postmortem tissues. FASEB J 2005, 04:3552fje.
-
(2005)
FASEB J
, vol.4
-
-
Lee, J.1
Hever, A.2
Willhite, D.3
Zlotnik, A.4
Hevezi, P.5
-
2
-
-
33845600784
-
Impact of RNA degradation on gene expression profiles: Assessment of different methods to reliably determine RNA quality
-
10.1016/j.jbiotec.2006.07.032, 16945445
-
Copois V, Bibeau F, Bascoul-Mollevi C, Salvetat N, Chalbos P, Bareil C, Candeil L, Fraslon C, Conseiller E, Granci V, Mazière P, Kramar A, Ychou M, Pau B, Martineau P, Molina F, Rio MD. Impact of RNA degradation on gene expression profiles: Assessment of different methods to reliably determine RNA quality. J Biotechnol 2007, 127:549-559. 10.1016/j.jbiotec.2006.07.032, 16945445.
-
(2007)
J Biotechnol
, vol.127
, pp. 549-559
-
-
Copois, V.1
Bibeau, F.2
Bascoul-Mollevi, C.3
Salvetat, N.4
Chalbos, P.5
Bareil, C.6
Candeil, L.7
Fraslon, C.8
Conseiller, E.9
Granci, V.10
Mazière, P.11
Kramar, A.12
Ychou, M.13
Pau, B.14
Martineau, P.15
Molina, F.16
Rio, M.D.17
-
3
-
-
7044286287
-
Evaluation of quality-control criteria for microarray gene expression analysis
-
10.1373/clinchem.2004.033225, 15364885
-
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. 10.1373/clinchem.2004.033225, 15364885.
-
(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
-
4
-
-
41049086156
-
Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues
-
10.1186/1471-2164-9-91, 2268927, 18298816
-
Popova T, Mennerich D, Weith A, Quast K. Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues. BMC Genomics 2008, 9:91. 10.1186/1471-2164-9-91, 2268927, 18298816.
-
(2008)
BMC Genomics
, vol.9
, pp. 91
-
-
Popova, T.1
Mennerich, D.2
Weith, A.3
Quast, K.4
-
5
-
-
33644975004
-
RNA integrity and the effect on the real-time qRT-PCR performance
-
10.1016/j.mam.2005.12.003, 16469371
-
Fleige S, Pfaffl MW. RNA integrity and the effect on the real-time qRT-PCR performance. Molecular Aspects of Medicine 2006, 27:126-139. 10.1016/j.mam.2005.12.003, 16469371.
-
(2006)
Molecular Aspects of Medicine
, vol.27
, pp. 126-139
-
-
Fleige, S.1
Pfaffl, M.W.2
-
6
-
-
0345257783
-
Chipping away at the chip bias: RNA degradation in microarray analysis
-
Auer H, Lyianarachchi S, Newsom D, Klisovic MI, Marcucci G, Kornacker K. Chipping away at the chip bias: RNA degradation in microarray analysis. Nat Genetics 2003, 35(4):292-293.
-
(2003)
Nat Genetics
, vol.35
, Issue.4
, pp. 292-293
-
-
Auer, H.1
Lyianarachchi, S.2
Newsom, D.3
Klisovic, M.I.4
Marcucci, G.5
Kornacker, K.6
-
7
-
-
34748834154
-
Big results from small samples: evaluation of amplification protocols for gene expression profiling
-
2062549, 17595311
-
Viale A, Li J, Tiesman J, Hester S, Massimi A, Griffin C, Grills G, Khitrov G, Lilley K, Knudtson K, Ward B, Kornacker K, Chu C-, Auer H, Brooks AI. Big results from small samples: evaluation of amplification protocols for gene expression profiling. J Biomol Tech 2007, 18(3):150-161. 2062549, 17595311.
-
(2007)
J Biomol Tech
, vol.18
, Issue.3
, pp. 150-161
-
-
Viale, A.1
Li, J.2
Tiesman, J.3
Hester, S.4
Massimi, A.5
Griffin, C.6
Grills, G.7
Khitrov, G.8
Lilley, K.9
Knudtson, K.10
Ward, B.11
Kornacker, K.12
Chu C.-13
Auer, H.14
Brooks, A.I.15
-
8
-
-
33744549560
-
In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays
-
10.2353/jmoldx.2006.050077, 1867595, 16645204
-
Ma C, Lyons-Weiler M, Liang W, LaFramboise W, Gilbertson JR, Becich MJ, Monzon FA. In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays. J Mol Diagn 2006, 8(2):183-192. 10.2353/jmoldx.2006.050077, 1867595, 16645204.
-
(2006)
J Mol Diagn
, vol.8
, Issue.2
, pp. 183-192
-
-
Ma, C.1
Lyons-Weiler, M.2
Liang, W.3
LaFramboise, W.4
Gilbertson, J.R.5
Becich, M.J.6
Monzon, F.A.7
-
9
-
-
70349091098
-
On the causes of outliers in Affymetrix GeneChip data
-
10.1093/bfgp/elp027, 23196852
-
Upton GJG, Sanchez-Graillet O, Rowsell J, Arteaga-Salas JM, Graham NS, Stalteri MA, Memon FN, May ST, Harrison AP. On the causes of outliers in Affymetrix GeneChip data. Briefings in Functional Genomics & Proteomics 2009, 8(3):199-212. 10.1093/bfgp/elp027, 23196852.
-
(2009)
Briefings in Functional Genomics & Proteomics
, vol.8
, Issue.3
, pp. 199-212
-
-
Upton, G.J.G.1
Sanchez-Graillet, O.2
Rowsell, J.3
Arteaga-Salas, J.M.4
Graham, N.S.5
Stalteri, M.A.6
Memon, F.N.7
May, S.T.8
Harrison, A.P.9
-
10
-
-
36348997057
-
Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA
-
10.1186/1472-6750-7-57, 2082023, 17854504
-
Thompson K, Pine PS, Rosenzweig B, Turpaz Y, Retief J. Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA. BMC Biotechnol 2007, 7(1):57. 10.1186/1472-6750-7-57, 2082023, 17854504.
-
(2007)
BMC Biotechnol
, vol.7
, Issue.1
, pp. 57
-
-
Thompson, K.1
Pine, P.S.2
Rosenzweig, B.3
Turpaz, Y.4
Retief, J.5
-
11
-
-
10744228401
-
Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain
-
Tomita H, Vawter MP, Walsh DM, Evans SJ, Choudary PV, Li J, Overman KM, Atz ME, Myers RM, Jones EG, Watson SJ, Akil H, William E, Bunne J. Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biological Psychatry 2004, 55:346-352.
-
(2004)
Biological Psychatry
, vol.55
, pp. 346-352
-
-
Tomita, H.1
Vawter, M.P.2
Walsh, D.M.3
Evans, S.J.4
Choudary, P.V.5
Li, J.6
Overman, K.M.7
Atz, M.E.8
Myers, R.M.9
Jones, E.G.10
Watson, S.J.11
Akil, H.12
William, E.13
Bunne, J.14
-
12
-
-
34547650893
-
Quality control for microarray analysis of human brain samples: the impact of postmortem factors, RNA characteristics, and histopathology
-
10.1016/j.jneumeth.2007.06.001, 17628689
-
Weis S, Llenos IC, Dulay JR, Elashoff M, Martínez-Murillo F, Miller CL. Quality control for microarray analysis of human brain samples: the impact of postmortem factors, RNA characteristics, and histopathology. Journal of Neuroscience Methods 2007, 165(2):198-209. 10.1016/j.jneumeth.2007.06.001, 17628689.
-
(2007)
Journal of Neuroscience Methods
, vol.165
, Issue.2
, pp. 198-209
-
-
Weis, S.1
Llenos, I.C.2
Dulay, J.R.3
Elashoff, M.4
Martínez-Murillo, F.5
Miller, C.L.6
-
13
-
-
33645241407
-
The RIN: an RNA integrity number for assigning integrity values to RNA measurements
-
10.1186/1471-2199-7-3, 1413964, 16448564
-
Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 2006, 7(1):3. 10.1186/1471-2199-7-3, 1413964, 16448564.
-
(2006)
BMC Mol Biol
, vol.7
, Issue.1
, 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
-
14
-
-
9444231674
-
Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations
-
10.1186/1471-2164-4-44, 280674, 14606961
-
Spiess A-N, Mueller N, Ivell R. Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 2003, 4(1):44. 10.1186/1471-2164-4-44, 280674, 14606961.
-
(2003)
BMC Genomics
, vol.4
, Issue.1
, pp. 44
-
-
Spiess, A.-N.1
Mueller, N.2
Ivell, R.3
-
15
-
-
24644512209
-
Simpleaffy: a bioconductor package for affymetrix quality control and data analysis
-
10.1093/bioinformatics/bti605, 16076888
-
Wilson CL, Miller CJ. Simpleaffy: a bioconductor package for affymetrix quality control and data analysis. Bioinformatics 2005, 21(18):3683-3685. 10.1093/bioinformatics/bti605, 16076888.
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3683-3685
-
-
Wilson, C.L.1
Miller, C.J.2
-
16
-
-
1342288026
-
Affy-analysis of Affymetrix GeneChip data at the probe level
-
10.1093/bioinformatics/btg405, 14960456
-
Gautier L, Cope L, Bolstad BM, Irizarry RA. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20(3):307-315. 10.1093/bioinformatics/btg405, 14960456.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 307-315
-
-
Gautier, L.1
Cope, L.2
Bolstad, B.M.3
Irizarry, R.A.4
-
17
-
-
0037934649
-
Modeling of DNA microarray data by using physical properties of hybridization
-
10.1073/pnas.0832500100, 164628, 12808153
-
Held GA, Grinstein G, Tu Y. Modeling of DNA microarray data by using physical properties of hybridization. Proc Natl Acad Sci USA 2003, 100(13):7575-7580. 10.1073/pnas.0832500100, 164628, 12808153.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.13
, pp. 7575-7580
-
-
Held, G.A.1
Grinstein, G.2
Tu, Y.3
-
19
-
-
9944226811
-
The sensitivity of microarray oligonucleotide probes - variability and the effect of base composition
-
Binder H, Kirsten T, Loeffler M, Stadler P. The sensitivity of microarray oligonucleotide probes - variability and the effect of base composition. J Phys Chem B 2004, 108(46):18003-18014.
-
(2004)
J Phys Chem B
, vol.108
, Issue.46
, pp. 18003-18014
-
-
Binder, H.1
Kirsten, T.2
Loeffler, M.3
Stadler, P.4
-
20
-
-
33646182577
-
Thermodynamics of competitive surface adsorption on DNA microarrays
-
Binder H. Thermodynamics of competitive surface adsorption on DNA microarrays. J Phys Cond Mat 2006, 18(18):S491-S523.
-
(2006)
J Phys Cond Mat
, vol.18
, Issue.18
-
-
Binder, H.1
-
21
-
-
65849368630
-
Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips
-
10.1093/nar/gkp168, 2677891, 19295132
-
Lee Y-S, Chen C-H, Tsai C-N, Tsai C-L, Chao A, Wang T-H. Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips. Nucl Acids Res 2009, 37(8):e61. 10.1093/nar/gkp168, 2677891, 19295132.
-
(2009)
Nucl Acids Res
, vol.37
, Issue.8
-
-
Lee, Y.-S.1
Chen, C.-H.2
Tsai, C.-N.3
Tsai, C.-L.4
Chao, A.5
Wang, T.-H.6
-
22
-
-
0025257556
-
Amplified RNA synthesized from limited quantities of heterogeneous cDNA
-
10.1073/pnas.87.5.1663, 53542, 1689846
-
Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1990, 87(5):1663-1667. 10.1073/pnas.87.5.1663, 53542, 1689846.
-
(1990)
Proceedings Of The National Academy Of Sciences Of The United States Of America
, vol.87
, Issue.5
, pp. 1663-1667
-
-
Van Gelder, R.N.1
von Zastrow, M.E.2
Yool, A.3
Dement, W.C.4
Barchas, J.D.5
Eberwine, J.H.6
-
23
-
-
33847771442
-
The highways and byways of mRNA decay
-
10.1038/nrm2104, 17245413
-
Garneau NL, Wilusz J, Wilusz CJ. The highways and byways of mRNA decay. Nat Rev Mol Cell Biol 2007, 8(2):113-126. 10.1038/nrm2104, 17245413.
-
(2007)
Nat Rev Mol Cell Biol
, vol.8
, Issue.2
, pp. 113-126
-
-
Garneau, N.L.1
Wilusz, J.2
Wilusz, C.J.3
-
24
-
-
1142298544
-
Sensitivity, specificity, and the hybridization isotherms of DNA Chips
-
10.1016/S0006-3495(04)74150-8, 1303922, 14747310
-
Halperin A, Buhot A, Zhulina EB. Sensitivity, specificity, and the hybridization isotherms of DNA Chips. Biophys J 2004, 86(2):718-730. 10.1016/S0006-3495(04)74150-8, 1303922, 14747310.
-
(2004)
Biophys J
, vol.86
, Issue.2
, pp. 718-730
-
-
Halperin, A.1
Buhot, A.2
Zhulina, E.B.3
-
25
-
-
0037388263
-
Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays
-
10.1093/nar/gkg283, 152799, 12655013
-
Hekstra D, Taussig AR, Magnasco M, Naef F. Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucl Acids Res 2003, 31(7):1962-1968. 10.1093/nar/gkg283, 152799, 12655013.
-
(2003)
Nucl Acids Res
, vol.31
, Issue.7
, pp. 1962-1968
-
-
Hekstra, D.1
Taussig, A.R.2
Magnasco, M.3
Naef, F.4
-
26
-
-
33745787067
-
Adsorption models of hybridisation and post-hybridisation behaviour on oligonucleotide microarrays
-
Burden C, Pittlekow Y, Wilson S. Adsorption models of hybridisation and post-hybridisation behaviour on oligonucleotide microarrays. J Phys Condens Matter 2006, 18:5545-5565.
-
(2006)
J Phys Condens Matter
, vol.18
, pp. 5545-5565
-
-
Burden, C.1
Pittlekow, Y.2
Wilson, S.3
-
27
-
-
33646170830
-
GeneChip microarrays - signal intensities, RNA concentrations and probe sequences
-
Binder H, Preibisch S. GeneChip microarrays - signal intensities, RNA concentrations and probe sequences. J Phys Cond Mat 2006, 18:S537-S566.
-
(2006)
J Phys Cond Mat
, vol.18
-
-
Binder, H.1
Preibisch, S.2
-
28
-
-
33744542889
-
Relationship between gene expression and observed intensities in DNA microarrays-a modeling study
-
10.1093/nar/gkl122, 1472623, 16723429
-
Held GA, Grinstein G, Tu Y. Relationship between gene expression and observed intensities in DNA microarrays-a modeling study. Nucl Acids Res 2006, 34:e70. 10.1093/nar/gkl122, 1472623, 16723429.
-
(2006)
Nucl Acids Res
, vol.34
-
-
Held, G.A.1
Grinstein, G.2
Tu, Y.3
-
30
-
-
65249142261
-
Non-specific hybridization scaling of microarray expression estimates - a physico-chemical approach for chip-to-chip normalization
-
10.1021/jp808118m, 19708217
-
Binder H, Bruecker J, Burden CJ. Non-specific hybridization scaling of microarray expression estimates - a physico-chemical approach for chip-to-chip normalization. J Phys Chem B 2009, 113:2874-2895. 10.1021/jp808118m, 19708217.
-
(2009)
J Phys Chem B
, vol.113
, pp. 2874-2895
-
-
Binder, H.1
Bruecker, J.2
Burden, C.J.3
-
31
-
-
1542290446
-
Expression profiling - best practices for data generation and interpretation in clinical trials
-
Group TTABPW
-
Group TTABPW. Expression profiling - best practices for data generation and interpretation in clinical trials. Nat Rev Genet 2004, 5(3):229-237.
-
(2004)
Nat Rev Genet
, vol.5
, Issue.3
, pp. 229-237
-
-
-
32
-
-
70549098725
-
Quality control in microarray assessment of gene expression in human airway epithelium
-
10.1186/1471-2164-10-493, 2774870, 19852842
-
Raman T, O'Connor T, Hackett N, Wang W, Harvey B-G, Attiyeh M, Dang D, Teater M, Crystal R. Quality control in microarray assessment of gene expression in human airway epithelium. BMC Genomics 2009, 10(1):493. 10.1186/1471-2164-10-493, 2774870, 19852842.
-
(2009)
BMC Genomics
, vol.10
, Issue.1
, pp. 493
-
-
Raman, T.1
O'Connor, T.2
Hackett, N.3
Wang, W.4
Harvey, B.-G.5
Attiyeh, M.6
Dang, D.7
Teater, M.8
Crystal, R.9
-
33
-
-
52649112095
-
" Hook" calibration of GeneChip-microarrays: theory and algorithm
-
10.1186/1748-7188-3-12, 2546411, 18759985
-
Binder H, Preibisch S. " Hook" calibration of GeneChip-microarrays: theory and algorithm. Algorithms for Molecular Biology 2008, 3:12. 10.1186/1748-7188-3-12, 2546411, 18759985.
-
(2008)
Algorithms for Molecular Biology
, vol.3
, pp. 12
-
-
Binder, H.1
Preibisch, S.2
-
34
-
-
52649161839
-
" Hook" calibration of GeneChip-microarrays: chip characteristics and expression measures
-
10.1186/1748-7188-3-11, 2543012, 18759984
-
Binder H, Krohn K, Preibisch S. " Hook" calibration of GeneChip-microarrays: chip characteristics and expression measures. Algorithms for Molecular Biology 2008, 3:11. 10.1186/1748-7188-3-11, 2543012, 18759984.
-
(2008)
Algorithms for Molecular Biology
, vol.3
, pp. 11
-
-
Binder, H.1
Krohn, K.2
Preibisch, S.3
-
35
-
-
70449592079
-
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation
-
10.1371/journal.pone.0007479, 2759528, 19834616
-
Salisbury J, Hutchison KW, Wigglesworth K, Eppig JJ, Graber JH. Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PLoS One 2009, 4(10):e7479. 10.1371/journal.pone.0007479, 2759528, 19834616.
-
(2009)
PLoS One
, vol.4
, Issue.10
-
-
Salisbury, J.1
Hutchison, K.W.2
Wigglesworth, K.3
Eppig, J.J.4
Graber, J.H.5
-
36
-
-
33846986793
-
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
-
10.1186/1471-2105-8-13, 1784106, 17224057
-
Stalteri M, Harrison A. Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 2007, 8(1):13. 10.1186/1471-2105-8-13, 1784106, 17224057.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.1
, pp. 13
-
-
Stalteri, M.1
Harrison, A.2
-
37
-
-
75449110420
-
Physico-chemical modelling of target depletion during hybridisation on oligonulceotide microarrays
-
Burden C, Binder H. Physico-chemical modelling of target depletion during hybridisation on oligonulceotide microarrays. Phys Biol 2010, 7:016004.
-
(2010)
Phys Biol
, vol.7
, pp. 016004
-
-
Burden, C.1
Binder, H.2
-
38
-
-
77955290840
-
Impact of RNA degradation on gene expression profiling
-
10.1186/1755-8794-3-36, 2927474, 20696062
-
Opitz L, Salinas-Riester G, Grade M, Jung K, Jo P, Emons G, Ghadimi B, Beissbarth T, Gaedcke J. Impact of RNA degradation on gene expression profiling. BMC Medical Genomics 2010, 3(1):36. 10.1186/1755-8794-3-36, 2927474, 20696062.
-
(2010)
BMC Medical Genomics
, vol.3
, Issue.1
, pp. 36
-
-
Opitz, L.1
Salinas-Riester, G.2
Grade, M.3
Jung, K.4
Jo, P.5
Emons, G.6
Ghadimi, B.7
Beissbarth, T.8
Gaedcke, J.9
-
39
-
-
33750412618
-
An application for assessing quality of RNA hybridized to Affymetrix GeneChips
-
10.1093/bioinformatics/btl459, 16935927
-
Archer KJ, Guennel T. An application for assessing quality of RNA hybridized to Affymetrix GeneChips. Bioinformatics 2006, 22(21):2699-2701. 10.1093/bioinformatics/btl459, 16935927.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2699-2701
-
-
Archer, K.J.1
Guennel, T.2
-
40
-
-
33645560786
-
Assessing quality of hybridized RNA in affymetrix GeneChip experiments using mixed-effects models
-
Archer KJ, Dumur CI, Joel SE, Ramakrishnan V. Assessing quality of hybridized RNA in affymetrix GeneChip experiments using mixed-effects models. Biostat 2006, 7(2):198-212.
-
(2006)
Biostat
, vol.7
, Issue.2
, pp. 198-212
-
-
Archer, K.J.1
Dumur, C.I.2
Joel, S.E.3
Ramakrishnan, V.4
-
41
-
-
75449093509
-
Calibration of microarray gene-expression data
-
New York: Humana Press, Grützmann R, Pilarski C, 575
-
Binder H, Preibisch S, Berger H. Calibration of microarray gene-expression data. In: Methods in Molecular Biology 2009, 376-407. New York: Humana Press, Grützmann R, Pilarski C, 575.
-
(2009)
In: Methods in Molecular Biology
, pp. 376-407
-
-
Binder, H.1
Preibisch, S.2
Berger, H.3
|