CyberArrayAnalysis: Microarray related papers

A. Experimental designs and cross platform comparisons

Kendziorski, C., Irizarry, R.A., Chen, K.S., Haag, J.D. and Gould, M.N. “On the utility of pooling biological samples in microarray experiments”, Proc Natl Acad Sci U.S.A., 2005. 102(12): 4252-4257

Kenzelmann, M., Klaren, R., Hergenhahn, M., Bonrouhi, M., Grone, H.J., Schmid, W. and Schutz, G. “High-accuracy amplification of nanogram total RNA amounts for gene profiling”, Genomics, 2004. 83: 550–558

Larkin, J.E., Frank, B.C., Gavras, H., Sultana, R.and Quackenbush, J. “Independence and reproducibility across microarray platforms”, Nature Methods, 2005. 2(5): 337-344

Irizarry, R.A., Warren, D., Spencer, F., Kim, I.F., Biswal, S., Frank, B.C., Gabrielson, E., Garcia, J.G., Geoghegan, J., Germino, G., Griffin, C., Hilmer, S.C., Hoffman, E., Jedlicka, A.E., Kawasaki, E., Martinez-Murillo, F., Morsberger, L., Lee, H., Petersen, D., Quackenbush, J., Scott, A., Wilson, M., Yang, Y., Ye, S.Q. and Yu, W. “Multiple-laboratory comparison of microarray platforms”, Nature Methods, 2005 2(5): 345-350

Sundaresh, S., Hung, S-p., Hatfield, G.W. and Baldi, P. “How noisy and replicable are DNA microarray data?”, International Journal Bioinformatics Research and Applications, 2005. 1(1): 31-50

B. Pre-processing GeneChip tools and statistical analysis

Choe, S.E., Boutros, M., Michelson, A.M., Church, G.M. and Halfon, M.S. ”Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset”, Genome Biology, 2005. 6(2): R16

Baldi, P. and Long, A.D. “A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes”, Bioinformatics, 2001 17(6): 509-519

Hatfield, G.W., Hung, S-p. and Baldi, P. “Differential analysis of DNA microarray gene expression data”, Molecular Microbiology, 2003. 47(4): 871-877

C. Data mining: papers on Caryoscope, DAVID 2.0 and Cytoscape

Awad, I.A., Rees, C.A., Hernandez-Boussard, T., Ball, C.A. and Sherlock, G. “Caryoscope: an open source Java application for viewing microarray data in a genomic context”, BMC Bioinformatics, 2004. 5(1): 151
Dennis. G. Jr, Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A. “DAVID: Database for Annotation, Visualization, and Integrated Discovery”, Genome Biology, 2003. 4(5):P3
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. “Cytoscape: a software environment for integrated models of biomolecular interaction networks”, Genome Research, 2003. 13(11):2498-2504


	A. Experimental designs and cross platform comparisons Kendziorski, C., Irizarry, R.A., Chen, K.S., Haag, J.D. and Gould, M.N. “On the utility of pooling biological samples in microarray experiments”, Proc Natl Acad Sci U.S.A., 2005. 102(12): 4252-4257 Kenzelmann, M., Klaren, R., Hergenhahn, M., Bonrouhi, M., Grone, H.J., Schmid, W. and Schutz, G. “High-accuracy amplification of nanogram total RNA amounts for gene profiling”, Genomics, 2004. 83: 550–558 Larkin, J.E., Frank, B.C., Gavras, H., Sultana, R.and Quackenbush, J. “Independence and reproducibility across microarray platforms”, Nature Methods, 2005. 2(5): 337-344 Irizarry, R.A., Warren, D., Spencer, F., Kim, I.F., Biswal, S., Frank, B.C., Gabrielson, E., Garcia, J.G., Geoghegan, J., Germino, G., Griffin, C., Hilmer, S.C., Hoffman, E., Jedlicka, A.E., Kawasaki, E., Martinez-Murillo, F., Morsberger, L., Lee, H., Petersen, D., Quackenbush, J., Scott, A., Wilson, M., Yang, Y., Ye, S.Q. and Yu, W. “Multiple-laboratory comparison of microarray platforms”, Nature Methods, 2005 2(5): 345-350 Sundaresh, S., Hung, S-p., Hatfield, G.W. and Baldi, P. “How noisy and replicable are DNA microarray data?”, International Journal Bioinformatics Research and Applications, 2005. 1(1): 31-50 B. Pre-processing GeneChip tools and statistical analysis Choe, S.E., Boutros, M., Michelson, A.M., Church, G.M. and Halfon, M.S. ”Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset”, Genome Biology, 2005. 6(2): R16 Baldi, P. and Long, A.D. “A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes”, Bioinformatics, 2001 17(6): 509-519 Hatfield, G.W., Hung, S-p. and Baldi, P. “Differential analysis of DNA microarray gene expression data”, Molecular Microbiology, 2003. 47(4): 871-877 C. Data mining: papers on Caryoscope, DAVID 2.0 and Cytoscape Awad, I.A., Rees, C.A., Hernandez-Boussard, T., Ball, C.A. and Sherlock, G. “Caryoscope: an open source Java application for viewing microarray data in a genomic context”, BMC Bioinformatics, 2004. 5(1): 151 Dennis. G. Jr, Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A. “DAVID: Database for Annotation, Visualization, and Integrated Discovery”, Genome Biology, 2003. 4(5):P3 Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. “Cytoscape: a software environment for integrated models of biomolecular interaction networks”, Genome Research, 2003. 13(11):2498-2504
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