Next: 8. Annexes
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Contents
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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.
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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.
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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.
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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.
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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.
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Kaufman, L. and Rousseuw, P. (1990).
- Finding Groups in Data- An Introduction to Cluster Analysis.
Wiley Series in Probability and Mathematical Sciences.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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