MAQC Publications

 

 

 

Journal Issues Featuring MAQC

Nature Biotechnology — August 2010 Issue  Pharmacogenomics Journal — August 2010 Issue Nature Biotechnology — September 2006 Issue

 

 

 

 

 

 

 

 

 

 

Publications by Year

	2006	2008	2009	2010

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2006

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• Canales, R.D., Luo, Y., Willey, J.C., Austermiller, B., Barbacioru, C.C., Boysen, C., Hunkapiller, K., Jensen, R.V., Knight, C.R., Lee, K.Y. et al. Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol, 24(9):1115-1122, 2006.
• Guo, L., Lobenhofer, E., Wang, C., Shippy, R., Harris, S., Zhang, L., Mei, N., Chen, T., Herman, D., Goodsaid, F. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol, 24:1162-1169, 2006.
• Patterson, T.A., Lobenhofer, E.K., Fulmer-Smentek, S.B., Collins, P.J., Chu, T.M., Bao, W., Fang, H., Kawasaki, E.S., Hager, J., Tikhonova, I.R. et al. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol, 24(9):1140-1150, 2006.
• Shi, L., Reid, L.H., Jones, W.D., Shippy, R., Warrington, J.A., Baker, S.C., Collins, P.J., de Longueville, F., Kawasaki, E.S., Lee, K.Y. et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol, 24(9):1151-1161, 2006.
• Shippy, R., Fulmer-Smentek, S., Jensen, R.V., Jones, W.D., Wolber, P.K., Johnson, C.D., Pine, P.S., Boysen, C., Guo, X., Chudin, E. et al. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol, 24(9):1123-1131, 2006.
• Tong, W., Lucas, A.B., Shippy, R., Fan, X., Fang, H., Hong, H., Orr, M.S., Chu, T.M., Guo, X., Collins, P.J. et al. Evaluation of external RNA controls for the assessment of microarray performance. Nat Biotechnol, 24(9):1132-1139, 2006.

 

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2008

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• Shi, L., Jones, W.D., Jensen, R.V., Harris, S.C., Perkins, R.G., Goodsaid, F.M., Guo, L., Croner, L.J., Boysen, C., Fang, H. et al. The balance of reproducibility, sensitivity, and specificity of lists of differenctially expressed genes in microarray studies. BMC Bioinformatics, 9 Suppl 9:S10, 2008.
• Shi, L., Perkins, R.G., Fang, H., Tong, W. Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential. Curr Opin Biotechnol, 19(1):10-18, 2008.

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2009

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• Fan, X., Fang, H., Hong, H., Perkins, R.G., She, L., Tong, W. Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay. Anal Biochem, 385(2):203-207, 2009.
• Fan, X., Shi, L., Fang, H., Harris, S., Perkins, R.G., Tong, W. Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation. BMC Proc, 3 Suppl 2:S4, 2009.

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2010

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• Chierici, M., Miclaus, K., Vega, S., and Furlanello, C. An interactive effect of batch size and composition contributes to discordant results in GWAS with the CHIAMO genotyping algorithm. Pharmacogenomics J, 10: 355-363, 2010.
• Fan, X., Lobenhofer, E. K., Chen, M., Shi, W., Huang, J., Luo, J., Zhang, J., Walker, S. J., Chu, T. M., Li, L., Wolfinger, R., Bao, W., Paules, R. S., Bushel, P. R., Li, J., Shi, T., Nikolskaya, T., Nikolsky, Y., Hong, H., Deng, Y., Cheng, Y., Fang, H., Shi, L., and Tong, W. Consistency of predictive signature genes and classifiers generated using different microarray platforms. Pharmacogenomics J, 10: 247-257, 2010.
• Hong, H., Shi, L., Su, Z., Ge, W., Jones, W. D., Czika, W., Miclaus, K., Lambert, C. G., Vega, S. C., Zhang, J., Ning, B., Liu, J., Green, B., Xu, L., Fang, H., Perkins, R., Lin, S. M., Jafari, N., Park, K., Ahn, T., Chierici, M., Furlanello, C., Zhang, L., Wolfinger, R. D., Goodsaid, F., and Tong, W. Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples. Pharmacogenomics J, 10: 364-374, 2010.
• Huang, J., Shi, W., Zhang, J., Chou, J. W., Paules, R. S., Gerrish, K., Li, J., Luo, J., Wolfinger, R. D., Bao, W., Chu, T. M., Nikolsky, Y., Nikolskaya, T., Dosymbekov, D., Tsyganova, M. O., Shi, L., Fan, X., Corton, J. C., Chen, M., Cheng, Y., Tong, W., Fang, H., and Bushel, P. R. Genomic indicators in the blood predict drug-induced liver injury. Pharmacogenomics J, 10: 267-277, 2010.
• 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., and Zhang, J. A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. Pharmacogenomics J, 10: 278-291, 2010.
• MAQC-II: analyze that! Nat Biotechnol, 28: 761, 2010.
• Miclaus, K., Chierici, M., Lambert, C., Zhang, L., Vega, S., Hong, H., Yin, S., Furlanello, C., Wolfinger, R., and Goodsaid, F. Variability in GWAS analysis: the impact of genotype calling algorithm inconsistencies. Pharmacogenomics J, 10: 324-335, 2010.
• Miclaus, K., Wolfinger, R., Vega, S., Chierici, M., Furlanello, C., Lambert, C., Hong, H., Zhang, L., Yin, S., and Goodsaid, F. Batch effects in the BRLMM genotype calling algorithm influence GWAS results for the Affymetrix 500K array. Pharmacogenomics J, 10: 336-346, 2010.
• Oberthuer, A., Juraeva, D., Li, L., Kahlert, Y., Westermann, F., Eils, R., Berthold, F., Shi, L., Wolfinger, R. D., Fischer, M., and Brors, B. Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients. Pharmacogenomics J, 10: 258-266, 2010.
• Parry, R. M., Jones, W., Stokes, T. H., Phan, J. H., Moffitt, R. A., Fang, H., Shi, L., Oberthuer, A., Fischer, M., Tong, W., and Wang, M. D. k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction. Pharmacogenomics J, 10: 292-309, 2010.
• Shi, W., Bessarabova, M., Dosymbekov, D., Dezso, Z., Nikolskaya, T., Dudoladova, M., Serebryiskaya, T., Bugrim, A., Guryanov, A., Brennan, R. J., Shah, R., Dopazo, J., Chen, M., Deng, Y., Shi, T., Jurman, G., Furlanello, C., Thomas, R. S., Corton, J. C., Tong, W., Shi, L., and Nikolsky, Y. Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. Pharmacogenomics J, 10: 310-323, 2010.
• Shi, L., Campbell, G., Jones, W. D., Campagne, F., Wen, Z., Walker, S. J., Su, Z., Chu, T. M., Goodsaid, F. M., Pusztai, L., Shaughnessy, J. D., Jr., Oberthuer, A., Thomas, R. S., Paules, R. S., Fielden, M., Barlogie, B., Chen, W., Du, P., Fischer, M., Furlanello, C., Gallas, B. D., Ge, X., Megherbi, D. B., Symmans, W. F., Wang, M. D., Zhang, J., Bitter, H., Brors, B., Bushel, P. R., Bylesjo, M., Chen, M., Cheng, J., Chou, J., Davison, T. S., Delorenzi, M., Deng, Y., Devanarayan, V., Dix, D. J., Dopazo, J., Dorff, K. C., Elloumi, F., Fan, J., Fan, S., Fan, X., Fang, H., Gonzaludo, N., Hess, K. R., Hong, H., Huan, J., Irizarry, R. A., Judson, R., Juraeva, D., Lababidi, S., Lambert, C. G., Li, L., Li, Y., Li, Z., Lin, S. M., Liu, G., Lobenhofer, E. K., Luo, J., Luo, W., McCall, M. N., Nikolsky, Y., Pennello, G. A., Perkins, R. G., Philip, R., Popovici, V., Price, N. D., Qian, F., Scherer, A., Shi, T., Shi, W., Sung, J., Thierry-Mieg, D., Thierry-Mieg, J., Thodima, V., Trygg, J., Vishnuvajjala, L., Wang, S. J., Wu, J., Wu, Y., Xie, Q., Yousef, W. A., Zhang, L., Zhang, X., Zhong, S., Zhou, Y., Zhu, S., Arasappan, D., Bao, W., Lucas, A. B., Berthold, F., Brennan, R. J., Buness, A., Catalano, J. G., 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, J. C., Gatto, L., Ge, W., Goldstein, D. R., Guo, L., Halbert, D. N., Han, J., Harris, S. C., Hatzis, C., Herman, D., Huang, J., Jensen, R. V., Jiang, R., Johnson, C. D., Jurman, G., Kahlert, Y., Khuder, S. A., Kohl, M., Li, J., Li, M., Li, Q. Z., Li, S., Liu, J., Liu, Y., Liu, Z., Meng, L., Madera, M., Martinez-Murillo, F., Medina, I., Meehan, J., Miclaus, K., Moffitt, R. A., Montaner, D., Mukherjee, P., Mulligan, G. J., Neville, P., Nikolskaya, T., Ning, B., Page, G. P., Parker, J., Parry, R. M., Peng, X., Peterson, R. L., Phan, J. H., Quanz, B., Ren, Y., Riccadonna, S., Roter, A. H., Samuelson, F. W., Schumacher, M. M., Shambaugh, J. D., Shi, Q., Shippy, R., Si, S., Smalter, A., Sotiriou, C., Soukup, M., Staedtler, F., Steiner, G., Stokes, T. H., Sun, Q., Tan, P. Y., Tang, R., Tezak, Z., Thorn, B., Tsyganova, M., Turpaz, Y., Vega, S. C., Visintainer, R., von Frese, J., Wang, C., Wang, E., Wang, J., Wang, W., Westermann, F., Willey, J. C., Woods, M., Wu, S., Xiao, N., Xu, J., Xu, L., Yang, L., Zeng, X., Zhang, M., Zhao, C., Puri, R. K., Scherf, U., Tong, W. and Wolfinger, R. D. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol, 28: 827-838, 2010.
• Slikker, W., Jr. Of genomics and bioinformatics. Pharmacogenomics J, 10: 245-246, 2010.
• Tillinghast, G. W. Microarrays in the clinic. Nat Biotechnol, 28: 810-812, 2010.
• Zhang, L., Yin, S., Miclaus, K., Chierici, M., Vega, S., Lambert, C., Hong, H., Wolfinger, R. D., Furlanello, C., and Goodsaid, F. Assessment of variability in GWAS with CRLMM genotyping algorithm on WTCCC coronary artery disease. Pharmacogenomics J, 10: 347-354, 2010.

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