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Items: 1 to 20 of 85

1.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD; MAQC Consortium..

Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665.

2.
3.

k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction.

Parry RM, Jones W, Stokes TH, Phan JH, Moffitt RA, Fang H, Shi L, Oberthuer A, Fischer M, Tong W, Wang MD.

Pharmacogenomics J. 2010 Aug;10(4):292-309. doi: 10.1038/tpj.2010.56.

4.

Microarrays in the clinic.

Tillinghast GW.

Nat Biotechnol. 2010 Aug;28(8):810-2. doi: 10.1038/nbt0810-810. No abstract available.

PMID:
20697405
5.

Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data.

Liu Q, Sung AH, Chen Z, Liu J, Huang X, Deng Y.

PLoS One. 2009 Dec 11;4(12):e8250. doi: 10.1371/journal.pone.0008250.

6.

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M.

Genome Biol. 2015 Jun 25;16:133. doi: 10.1186/s13059-015-0694-1.

7.

Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients.

Oberthuer A, Juraeva D, Li L, Kahlert Y, Westermann F, Eils R, Berthold F, Shi L, Wolfinger RD, Fischer M, Brors B.

Pharmacogenomics J. 2010 Aug;10(4):258-66. doi: 10.1038/tpj.2010.53.

8.

Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data.

Chen JJ, Hsueh HM, Delongchamp RR, Lin CJ, Tsai CA.

BMC Bioinformatics. 2007 Oct 25;8:412.

9.

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples.

Wen Z, Wang C, Shi Q, Huang Y, Su Z, Hong H, Tong W, Shi L.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S10. doi: 10.1186/1471-2105-11-S6-S10.

10.
11.
12.

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data.

Luo J, Schumacher M, Scherer A, Sanoudou D, Megherbi D, Davison T, Shi T, Tong W, Shi L, Hong H, Zhao C, Elloumi F, Shi W, Thomas R, Lin S, Tillinghast G, Liu G, Zhou Y, Herman D, Li Y, Deng Y, Fang H, Bushel P, Woods M, Zhang J.

Pharmacogenomics J. 2010 Aug;10(4):278-91. doi: 10.1038/tpj.2010.57.

13.

MAQC-II: analyze that!

[No authors listed]

Nat Biotechnol. 2010 Aug;28(8):761. doi: 10.1038/nbt0810-761b. No abstract available.

PMID:
20697381
14.

A new method for class prediction based on signed-rank algorithms applied to Affymetrix microarray experiments.

Rème T, Hose D, De Vos J, Vassal A, Poulain PO, Pantesco V, Goldschmidt H, Klein B.

BMC Bioinformatics. 2008 Jan 11;9:16. doi: 10.1186/1471-2105-9-16.

15.

Maximizing biomarker discovery by minimizing gene signatures.

Chang C, Wang J, Zhao C, Fostel J, Tong W, Bushel PR, Deng Y, Pusztai L, Symmans WF, Shi T.

BMC Genomics. 2011 Dec 23;12 Suppl 5:S6. doi: 10.1186/1471-2164-12-S5-S6.

16.

Development and validation of predictive molecular signatures.

Kohl M.

Curr Mol Med. 2010 Mar;10(2):173-9. Review.

PMID:
20196729
17.
18.

Rat toxicogenomic study reveals analytical consistency across microarray platforms.

Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P, Phillips KL, Xu J, Deng X, Sun YA, Tong W, Dragan YP, Shi L.

Nat Biotechnol. 2006 Sep;24(9):1162-9.

PMID:
17061323
19.

Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.

Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, Harkins TT, Thierry-Mieg D, Thierry-Mieg J, Jensen RV.

BMC Genomics. 2009 Jun 12;10:264. doi: 10.1186/1471-2164-10-264.

20.

Clinical implementation of the intrinsic subtypes of breast cancer.

Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PS.

Lancet Oncol. 2010 Aug;11(8):718-9; author reply 720-1. doi: 10.1016/S1470-2045(10)70176-5. No abstract available.

PMID:
20688274
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