-
1
-
-
33746361200
-
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations
-
Article 276 1513401 16749918
-
Okoniewski MJ Miller CJ Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations BMC Bioinformatics 2006, 7: Article 276 1513401 16749918
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Okoniewski, M.J.1
Miller, C.J.2
-
2
-
-
34248177279
-
How high is the level of technical noise in microarray data?
-
Article 9 1855048 17428341 10.1186/1745-6150-2-9
-
Klebanov L Yakovlev A How high is the level of technical noise in microarray data? Biol Direct 2007, 2:9. Article 9 1855048 17428341 10.1186/1745-6150-2-9
-
(2007)
Biol Direct
, vol.2
, pp. 9
-
-
Klebanov, L.1
Yakovlev, A.2
-
3
-
-
33748491517
-
The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
10.1038/nbt1239 16964229
-
Shi L Reid LH Jones WD Shippy R Warrington JA Baker SC Collins PJ de Longueville F Kawasaki ES Lee KY Lou Y Sun YA Willey JC Setterquist RA Fischer GM Tong W Dragan YP Dix DJ Frueh FW Goodsaid FM Herman D Jensen RV Johnson CD Lobenhofer EK Puri RK Sherf U Thierry-Mieg J Wang C Wilson M Wolber PK The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotechnol 2006, 24(9):1151-1161. 10.1038/nbt1239 16964229
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, 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
Lou, 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
Frueh, F.W.19
Goodsaid, F.M.20
Herman, D.21
Jensen, R.V.22
Johnson, C.D.23
Lobenhofer, E.K.24
Puri, R.K.25
Sherf, U.26
Thierry-Mieg, J.27
Wang, C.28
Wilson, M.29
Wolber, P.K.30
more..
-
5
-
-
25444485444
-
The effects of normalization on the correlation structure of microarray data
-
Article 120 1156869 15904488
-
Qiu X Brooks AI Klebanov L Yakovlev A The effects of normalization on the correlation structure of microarray data BMC Bioinformatics 2005, 6: Article 120 1156869 15904488
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Qiu, X.1
Brooks, A.I.2
Klebanov, L.3
Yakovlev, A.4
-
6
-
-
33847359223
-
Normality of gene expression revisited
-
10.1142/S0218339007002027
-
Chen L Klebanov L Yakovlev AY Normality of gene expression revisited J Biol Syst 2007, 15:1-39. 48 10.1142/S0218339007002027
-
(2007)
J Biol Syst
, vol.15
, pp. 39-48
-
-
Chen, L.1
Klebanov, L.2
Yakovlev, A.Y.3
-
7
-
-
34548471987
-
Comments on probabilistic models behind the concept of false discovery rate
-
10.1142/S0219720007002965
-
Qiu X Yakovlev A Comments on probabilistic models behind the concept of false discovery rate J Bioinformatics and Comput Biol 2007, 5(4):963-975. 10.1142/S0219720007002965
-
(2007)
J Bioinformatics and Comput Biol
, vol.5
, Issue.4
, pp. 963-975
-
-
Qiu, X.1
Yakovlev, A.2
-
8
-
-
25444494145
-
Correlation test to assess low-level processing of high-density oligonucleotide microarray data
-
Article 80 1084343 15799785
-
Ploner A Miller LD Hall P Bergh J Pawitan Y Correlation test to assess low-level processing of high-density oligonucleotide microarray data BMC Bioinformatics 2005, 6: Article 80 1084343 15799785
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Ploner, A.1
Miller, L.D.2
Hall, P.3
Bergh, J.4
Pawitan, Y.5
-
9
-
-
33646358230
-
A new type of stochastic dependence revealed in gene expression data
-
Article7 Epub 16646871
-
Klebanov L Jordan C Yakovlev A A new type of stochastic dependence revealed in gene expression data Stat Appl Genet Mol Biol 2006, 5(): Article7 Epub 16646871
-
(2006)
Stat Appl Genet Mol Biol
, vol.5
-
-
Klebanov, L.1
Jordan, C.2
Yakovlev, A.3
-
10
-
-
38549171270
-
Diverse correlation structures in microarray gene expression data
-
Klebanov L Yakovlev A Diverse correlation structures in microarray gene expression data Ann Appl Statist
-
Ann Appl Statist
-
-
Klebanov, L.1
Yakovlev, A.2
-
11
-
-
33745413936
-
Utility of correlation measures in analysis of gene expression
-
10.1016/j.nurx.2006.05.037 16815221
-
Almudevar A Klebanov LB Qiu X Salzman P Yakovlev AY Utility of correlation measures in analysis of gene expression NeuroRx 2006, 3(3):384-395. 10.1016/j.nurx.2006.05.037 16815221
-
(2006)
NeuroRx
, vol.3
, Issue.3
, pp. 384-395
-
-
Almudevar, A.1
Klebanov, L.B.2
Qiu, X.3
Salzman, P.4
Yakovlev, A.Y.5
-
12
-
-
34250173397
-
Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures
-
1890303 17509157 10.1186/1471-2105-8-157
-
Lu X Perkins DL Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures BMC Bioinformatics 2007, 8:157. 1890303 17509157 10.1186/1471-2105-8-157
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 157
-
-
Lu, X.1
Perkins, D.L.2
-
14
-
-
33750219625
-
Deconfounding microarray analysis
-
17019511
-
Jacobsen M Repsilber D Gutschmidt A Neher A Feldmann K Mollenkopf HJ Kaufmann SHE Ziegler A Deconfounding microarray analysis Methods Inf Med 2006, 45(5):557-563. 17019511
-
(2006)
Methods Inf Med
, vol.45
, Issue.5
, pp. 557-563
-
-
Jacobsen, M.1
Repsilber, D.2
Gutschmidt, A.3
Neher, A.4
Feldmann, K.5
Mollenkopf, H.J.6
Kaufmann, S.H.E.7
Ziegler, A.8
-
15
-
-
33749335282
-
The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease
-
10.1126/science.1132939 17008526
-
Lamb J Crawford ED Peck D Modell JW Blat IC Wrobel MJ Lerner J Brunet J-P Subramanian A Ross KN Reich M Hieronymus H Wei G Armstrong SA Haggarty SJ Clemons PA Ru Wei R Carr SA Lander ES Golub TR The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease Science 2006, 313:1929-1935. 10.1126/ science.1132939 17008526
-
(2006)
Science
, vol.313
, pp. 1929-1935
-
-
Lamb, J.1
Crawford, E.D.2
Peck, D.3
Modell, J.W.4
Blat, I.C.5
Wrobel, M.J.6
Lerner, J.7
Brunet, J.-P.8
Subramanian, A.9
Ross, K.N.10
Reich, M.11
Hieronymus, H.12
Wei, G.13
Armstrong, S.A.14
Haggarty, S.J.15
Clemons, P.A.16
Ru Wei, R.17
Carr, S.A.18
Lander, E.S.19
Golub, T.R.20
more..
-
16
-
-
33144462268
-
Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis
-
16478745
-
Sotiriou C Wirapati P Loi S Harris A Fox S Smeds J Nordgren H Farmer P Praz V Haibe-Kains B Desmedt C Larsimont D Cardoso F Peterse H Nuyten D Buyse M Van de Vijver MJ Bergh J Piccart M Delorenzi M Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis J Natl Cancer Inst 2006, 98(4):262-272. 16478745
-
(2006)
J Natl Cancer Inst
, vol.98
, Issue.4
, pp. 262-272
-
-
Sotiriou, C.1
Wirapati, P.2
Loi, S.3
Harris, A.4
Fox, S.5
Smeds, J.6
Nordgren, H.7
Farmer, P.8
Praz, V.9
Haibe-Kains, B.10
Desmedt, C.11
Larsimont, D.12
Cardoso, F.13
Peterse, H.14
Nuyten, D.15
Buyse, M.16
Van de Vijver, M.J.17
Bergh, J.18
Piccart, M.19
Delorenzi, M.20
more..
-
17
-
-
19044399684
-
Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling
-
10.1016/S1535-6108(02)00032-6 12086872
-
Yeoh EJ Ross ME Shurtleff SA Williams WK Patel D Mahfouz R Behm FG Raimondi SC Relling MV Patel A Cheng C Campana D Wilkins D Zhou X Li J Liu H Pui CH Evans WE Naeve C Wong L Downing JR Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling Cancer Cell 2002, 1(2):133-143. 10.1016/S1535-6108(02)00032-6 12086872
-
(2002)
Cancer Cell
, vol.1
, Issue.2
, pp. 133-143
-
-
Yeoh, E.J.1
Ross, M.E.2
Shurtleff, S.A.3
Williams, W.K.4
Patel, D.5
Mahfouz, R.6
Behm, F.G.7
Raimondi, S.C.8
Relling, M.V.9
Patel, A.10
Cheng, C.11
Campana, D.12
Wilkins, D.13
Zhou, X.14
Li, J.15
Liu, H.16
Pui, C.H.17
Evans, W.E.18
Naeve, C.19
Wong, L.20
Downing, J.R.21
more..
-
18
-
-
29144535372
-
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
-
1283542 16284200 10.1093/nar/gni179
-
Dai M Wang P Boyd AD Kostov G Athey B Jones EG Bunney WR Myers RM Speed TP Akil H Watson SJ Meng F Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data Nucl Acids Res 2005, 33(20):e175. 1283542 16284200 10.1093/nar/gni179
-
(2005)
Nucl Acids Res
, vol.33
, Issue.20
-
-
Dai, M.1
Wang, P.2
Boyd, A.D.3
Kostov, G.4
Athey, B.5
Jones, E.G.6
Bunney, W.R.7
Myers, R.M.8
Speed, T.P.9
Akil, H.10
Watson, S.J.11
Meng, F.12
-
19
-
-
38549125417
-
-
http://brainarray.mbni.med.umich.edu
-
-
-
-
20
-
-
23844551199
-
Stochastic models inspired by hybridization theory for short oligonucleotide arrays
-
10.1089/cmb.2005.12.882
-
Wu Z Irizarry RA Stochastic models inspired by hybridization theory for short oligonucleotide arrays J Comp Biol 2005, 12(6):882-893. 10.1089/ cmb.2005.12.882
-
(2005)
J Comp Biol
, vol.12
, Issue.6
, pp. 882-893
-
-
Wu, Z.1
Irizarry, R.A.2
-
21
-
-
0041530047
-
Comment on 'Resampling-based multiple testing for DNA microarray data analysis' by Ge, Dudoit, and Speed
-
10.1007/BF02595811
-
Storey JD Comment on 'Resampling-based multiple testing for DNA microarray data analysis' by Ge, Dudoit, and Speed Test 2003, 12:1-77. 10.1007/BF02595811
-
(2003)
Test
, vol.12
, pp. 1-77
-
-
Storey, J.D.1
-
22
-
-
13944282215
-
Microarray analysis shows that some microRNAs down-regulate large numbers of target mRNAs
-
10.1038/nature03315
-
Lim LP Lau NC Garrett-Engele P Grimson A Schelter JM Castle J Bartel DP Linsley PS Johnson JM Microarray analysis shows that some microRNAs down-regulate large numbers of target mRNAs Nature 2005, 433:769773. 10.1038/nature03315
-
(2005)
Nature
, vol.433
, pp. 769773
-
-
Lim, L.P.1
Lau, N.C.2
Garrett-Engele, P.3
Grimson, A.4
Schelter, J.M.5
Castle, J.6
Bartel, D.P.7
Linsley, P.S.8
Johnson, J.M.9
-
23
-
-
28444469246
-
Silencing of microRNAs in vivo with antagomirs
-
10.1038/nature04303 16258535
-
Krutzfeldt J Rajewsky N Braich R Rajeev KG Tuschl T Manoharan M Stoffel M Silencing of microRNAs in vivo with antagomirs Nature 2005, 438:685-689. 10.1038/nature04303 16258535
-
(2005)
Nature
, vol.438
, pp. 685-689
-
-
Krutzfeldt, J.1
Rajewsky, N.2
Braich, R.3
Rajeev, K.G.4
Tuschl, T.5
Manoharan, M.6
Stoffel, M.7
-
24
-
-
38549145312
-
-
http://www.ncbi.nlm.nih.gov/geo/
-
-
-
-
25
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
doi:10.1371/journal.pgen.0030161 10.1371/journal.pgen.0030161
-
Leek JT Storey JD Capturing heterogeneity in gene expression studies by surrogate variable analysis PLoS Genetics 2007, 3(9):e161. doi:10.1371/ journal.pgen.0030161 10.1371/journal.pgen.0030161
-
(2007)
PLoS Genetics
, vol.3
, Issue.9
-
-
Leek, J.T.1
Storey, J.D.2
|