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Blaveri, E., Brewer, J. L., Roydasgupta, R., Fridlyand, J., DeVries, S., Koppie, T., Pejavar, S., Mehta, K., Carroll, P., Simko, J. P., and Waldman, F. M. (2005).
Bladder cancer stage and outcome by array-based comparative genomic hybridization.
Clin Cancer Res, 11:7012-7022.

de Leeuw, R. J., Davies, J. J., Rosenwald, A., Bebb, G., Gascoyne, R. D., Dyer, M. J. S., Staudt, L. M., Martinez-Climent, J. A., and Lam, W. L. (2004).
Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes.
Hum Mol Genet, 13:1827-1837.

Douglas, E. J., Fiegler, H., Rowan, A., Halford, S., Bicknell, D. C., Bodmer, W., Tomlinson, I. P. M., and Carter, N. P. (2004).
Array comparative genomic hybridization analysis of colorectal cancer cell lines and primary carcinomas.
Cancer Res, 64:4817-4825.

Gysin, S., Rickert, P., Kastury, K., and McMahon, M. (2005).
Analysis of genomic DNA alterations and mRNA expression patterns in a panel of human pancreatic cancer cell lines.
Genes Chromosomes Cancer, 44:37-51.

Hupé, P., Stransky, N., Thiery, J. P., Radvanyi, F., and Barillot, E. (2004).
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions.
Bioinformatics, 20:3413-3422.

Kaufman, L. and Rousseuw, P. (1990).
Finding Groups in Data- An Introduction to Cluster Analysis.
Wiley Series in Probability and Mathematical Sciences.

La Rosa, P., Viara, E., Hupé, P., Pierron, G., Liva, S., Neuvial, P., Brito, I., Lair, S., Servant, N., Robine, N., Manié, E., Brennetot, C., Jannoueix-Lerosey, I., Raynal, V., Gruel, N., Rouveirol, C., Stransky, N., Stern, M.-H., Delattre, O., Aurias, A., Radvanyi, F., and Barillot, E. (2006).
VAMP: Visualization and analysis of array-cgh, transcriptome and other molecular profiles.
Bioinformatics, 22:2066-2073.

Nakao, K., Mehta, K. R., Fridlyand, J., Moore, D. H., Jain, A. N., Lafuente, A., Wiencke, J. W., Terdiman, J. P., and Waldman, F. M. (2004).
High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization.
Carcinogenesis, 25:1345-1357.

Patil, M. A., Gutgemann, I., Zhang, J., Ho, C., Cheung, S.-T., Ginzinger, D., Li, R., Dykema, K. J., So, S., Fan, S.-T., Kakar, S., Furge, K. A., Buttner, R., and Chen, X. (2005).
Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma.
Carcinogenesis, 26:2050-2057.

Pollack, J. R., Sorlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lonning, P. E., Tibshirani, R., Botstein, D., Borresen-Dale, A.-L., and Brown, P. O. (2002).
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.
Proc Natl Acad Sci U S A, 99:12963-12968.

Rouveirol, C., Stransky, N., Hupé, P., La Rosa, P., Viara, E., Barillot, E., and Radvanyi, F. (2006).
Computation of recurrent minimal genomic alterations from CGH data.
Bioinformatics, 22.

Snijders, A. M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A. K., Huey, B., Kimura, K., S, S. L., Myambo, K., Palmer, J., Ylstra, B., Yue, J. P., Gray, J. W., Jain, A. N., Pinkel, D., and Albertson, D. G. (2001).
Assembly of microarrays for genome-wide measurement of DNA copy number.
Nat. Genet., 29:263-4.

Snijders, A. M., Schmidt, B. L., Fridlyand, J., Dekker, N., Pinkel, D., Jordan, R. C. K., and Albertson, D. G. (2005).
Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma.
Oncogene, 24:4232-4242.

Stransky, N., Vallot, C., Reyal, F., Bernard-Pierrot, I., de Medina, S. G. D., Segraves, R., de Rycke, Y., Elvin, P., Cassidy, A., Spraggon, C., Graham, A., Southgate, J., Asselain, B., Allory, Y., Abbou, C. C., Albertson, D. G., Thiery, J. P., Chopin, D. K., Pinkel, D., and Radvanyi, F. (2006).
Regional copy number-independent deregulation of transcription in cancer.
Nat Genet, 38:1386-1396.

Veltman, J. A., Fridlyand, J., Pejavar, S., Olshen, A. B., Korkola, J. E., DeVries, S., Carroll, P., Kuo, W.-L., Pinkel, D., Albertson, D., Cordon-Cardo, C., Jain, A. N., and Waldman, F. M. (2003).
Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.
Cancer Res, 63:2872-2880.

2007 - Institut Curie Bioinformatics unit