-
1
-
-
0027547142
-
Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors
-
Kallioniemi,O.P., Kallioniemi,A., Sudar,D., Rutovitz,D., Gray,J.W., Waldman,F. and Pinkel,D. (1993) Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol., 4, 41-46.
-
(1993)
Semin Cancer Biol.
, vol.4
, pp. 41-46
-
-
Kallioniemi, O.P.1
Kallioniemi, A.2
Sudar, D.3
Rutovitz, D.4
Gray, J.W.5
Waldman, F.6
Pinkel, D.7
-
2
-
-
17344371740
-
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
-
Pinkel,D., Segraves,R., Sudar,D., Clark,S., Poole,I., Kowbel,D., Collins,C., Kuo,W.L., Chen,C., Zhai,Y. et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20, 207-211.
-
(1998)
Nat. Genet.
, vol.20
, pp. 207-211
-
-
Pinkel, D.1
Segraves, R.2
Sudar, D.3
Clark, S.4
Poole, I.5
Kowbel, D.6
Collins, C.7
Kuo, W.L.8
Chen, C.9
Zhai, Y.10
-
3
-
-
0030701970
-
Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances
-
Solinas-Toldo,S., Lampel,S., Stilgenbauer,S., Nickolenko,J., Benner,A., Dohner,H., Cremer,T. and Lichter,P. (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer, 20, 399-407.
-
(1997)
Genes Chromosomes Cancer
, vol.20
, pp. 399-407
-
-
Solinas-Toldo, S.1
Lampel, S.2
Stilgenbauer, S.3
Nickolenko, J.4
Benner, A.5
Dohner, H.6
Cremer, T.7
Lichter, P.8
-
4
-
-
34347339520
-
Methods and strategies for analyzing copy number variation using DNA microarrays
-
Carter,N.P. (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet., 39, S16-S21.
-
(2007)
Nat. Genet.
, vol.39
-
-
Carter, N.P.1
-
5
-
-
2342453338
-
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays
-
Zhao,X., Li,C., Paez,J.G., Chin,K., Jänne,P.A., Chen,T.H., Girard,L., Minna,J., Christiani,D., Leo,C. et al. (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res., 64, 3060-3071.
-
(2004)
Cancer Res.
, vol.64
, pp. 3060-3071
-
-
Zhao, X.1
Li, C.2
Paez, J.G.3
Chin, K.4
Jänne, P.A.5
Chen, T.H.6
Girard, L.7
Minna, J.8
Christiani, D.9
Leo, C.10
-
6
-
-
56649103903
-
CNVDetector: locating copy number variations using array CGH data
-
Chen,P.A., Liu,H.F. and Chao,K.M. (2008) CNVDetector: locating copy number variations using array CGH data. Bioinformatics, 24, 2773-2775.
-
(2008)
Bioinformatics
, vol.24
, pp. 2773-2775
-
-
Chen, P.A.1
Liu, H.F.2
Chao, K.M.3
-
7
-
-
25144489650
-
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data
-
Margolin,A.A., Greshock,J., Naylor,T.L., Mosse,Y., Maris,J.M., Bignell,G., Saeed,A.I., Quackenbush,J. and Weber,B.L. (2005) CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics, 21, 3308-3311.
-
(2005)
Bioinformatics
, vol.21
, pp. 3308-3311
-
-
Margolin, A.A.1
Greshock, J.2
Naylor, T.L.3
Mosse, Y.4
Maris, J.M.5
Bignell, G.6
Saeed, A.I.7
Quackenbush, J.8
Weber, B.L.9
-
8
-
-
22844435668
-
CGHPRO - a comprehensive data analysis tool for array CGH
-
Chen,W., Erdogan,F., Ropers,H.H., Lenzner,S. and Ullmann,R. (2005) CGHPRO - a comprehensive data analysis tool for array CGH. BMC Bioinformatics, 6, 85.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 85
-
-
Chen, W.1
Erdogan, F.2
Ropers, H.H.3
Lenzner, S.4
Ullmann, R.5
-
9
-
-
25444469387
-
Visualization-based discovery and analysis of genomic aberrations in microarray data
-
Myers,C.L., Chen,X. and Troyanskaya,O.G. (2005) Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinformatics, 6, 146
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 146
-
-
Myers, C.L.1
Chen, X.2
Troyanskaya, O.G.3
-
10
-
-
34547611743
-
ISACGH: a web-based environment for the analysis of array CGH and gene expression which includes functional profiling
-
Conde,L., Montaner,D., Burguet-Castell,J., Tárraga,J., Medina,I., Al-Shahrour,F. and Dopazo,J. (2007) ISACGH: a web-based environment for the analysis of array CGH and gene expression which includes functional profiling. Nucleic Acids Res., 35, W81-W85.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Conde, L.1
Montaner, D.2
Burguet-Castell, J.3
Tárraga, J.4
Medina, I.5
Al-Shahrour, F.6
Dopazo, J.7
-
11
-
-
40349108567
-
ADaCGH: a parallelized web-based application and R package for the analysis of aCGH data
-
Díaz-Uriarte,R. and Rueda,O.M. (2007) ADaCGH: a parallelized web-based application and R package for the analysis of aCGH data. PLoS ONE, 2, e737.
-
(2007)
PLoS ONE
, vol.2
-
-
Díaz-Uriarte, R.1
Rueda, O.M.2
-
12
-
-
33744901128
-
WebaCGH: an interactive online tool for the analysis and display of array comparative genomic hybridisation data
-
Frankenberger,C., Wu,X., Harmon,J., Church,D., Gangi,L.M., Munroe,D.J. and Urzúa,U. (2006) WebaCGH: an interactive online tool for the analysis and display of array comparative genomic hybridisation data. Appl. Bioinformatics, 5, 125-130.
-
(2006)
Appl. Bioinformatics
, vol.5
, pp. 125-130
-
-
Frankenberger, C.1
Wu, X.2
Harmon, J.3
Church, D.4
Gangi, L.M.5
Munroe, D.J.6
Urzúa, U.7
-
13
-
-
19544370909
-
ArrayCyGHt: a web application for analysis and visualization of array-CGH data
-
Kim,S.Y., Nam,S.W., Lee,S.H., Park,W.S., Yoo,N.J., Lee,J.Y. and Chung,Y.J. (2005) ArrayCyGHt: a web application for analysis and visualization of array-CGH data. Bioinformatics, 21, 2554-2555.
-
(2005)
Bioinformatics
, vol.21
, pp. 2554-2555
-
-
Kim, S.Y.1
Nam, S.W.2
Lee, S.H.3
Park, W.S.4
Yoo, N.J.5
Lee, J.Y.6
Chung, Y.J.7
-
14
-
-
41349085816
-
CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms
-
Lai,W., Choudhary,V. and Park,P.J. (2008) CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms. Bioinformatics, 24, 1014-1015.
-
(2008)
Bioinformatics
, vol.24
, pp. 1014-1015
-
-
Lai, W.1
Choudhary, V.2
Park, P.J.3
-
15
-
-
33747829588
-
CAPweb: a bioinformatics CGH array Analysis Platform
-
Liva,S., Hupé,P., Neuvial,P., Brito,I., Viara,E., La Rosa,P. and Barillot,E. (2006) CAPweb: a bioinformatics CGH array Analysis Platform. Nucleic Acids Res., 34, W477-W481.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Liva, S.1
Hupé, P.2
Neuvial, P.3
Brito, I.4
Viara, E.5
La Rosa, P.6
Barillot, E.7
-
16
-
-
33748673977
-
VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles
-
La Rosa,P., Viara,E., Hupé,P., Pierron,G., Liva,S., Neuvial,P., Brito,I., Lair,S., Servant,N., Robine,N. et al. (2006) VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics, 22, 2066-2073.
-
(2006)
Bioinformatics
, vol.22
, pp. 2066-2073
-
-
La Rosa, P.1
Viara, E.2
Hupé, P.3
Pierron, G.4
Liva, S.5
Neuvial, P.6
Brito, I.7
Lair, S.8
Servant, N.9
Robine, N.10
-
17
-
-
38549176691
-
Ensembl 2008
-
Flicek,P., Aken,B.L., Beal,K., Ballester,B., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cunningham,F., Cutts,T. et al. (2008) Ensembl 2008. Nucleic Acids Res., 36, D707-D714.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Flicek, P.1
Aken, B.L.2
Beal, K.3
Ballester, B.4
Caccamo, M.5
Chen, Y.6
Clarke, L.7
Coates, G.8
Cunningham, F.9
Cutts, T.10
-
18
-
-
33644872577
-
Limma: linear models for microarray data
-
Gentleman,R., Carey,V., Dudoit,S., Irizarry,R. and Huber,W. (eds), Springer, New York
-
Smyth,G.K. (2005) Limma: linear models for microarray data. In Gentleman,R., Carey,V., Dudoit,S., Irizarry,R. and Huber,W. (eds), Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, pp. 397-420.
-
(2005)
Bioinformatics and Computational Biology Solutions using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
19
-
-
56049110212
-
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms
-
Diskin,S.J., Li,M., Hou,C., Yang,S., Glessner,J., Hakonarson,H., Bucan,M., Maris,J.M. and Wang,K. (2008) Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res., 36, e126.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Diskin, S.J.1
Li, M.2
Hou, C.3
Yang, S.4
Glessner, J.5
Hakonarson, H.6
Bucan, M.7
Maris, J.M.8
Wang, K.9
-
20
-
-
49549085311
-
A fast and flexible method for the segmentation of aCGH data
-
Ben-Yaacov,E. and Eldar,Y.C. (2008) A fast and flexible method for the segmentation of aCGH data. Bioinformatics, 24, i139-i145.
-
(2008)
Bioinformatics
, vol.24
-
-
Ben-Yaacov, E.1
Eldar, Y.C.2
-
21
-
-
3543105225
-
Circular binary segmentation for the analysis of array-based DNA copy number data
-
Olshen,A.B., Venkatraman,E.S., Lucito,R. and Wigler,M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
-
(2004)
Biostatistics
, vol.5
, pp. 557-572
-
-
Olshen, A.B.1
Venkatraman, E.S.2
Lucito, R.3
Wigler, M.4
-
22
-
-
12344259648
-
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions
-
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.
-
(2004)
Bioinformatics
, vol.20
, pp. 3413-3422
-
-
Hupé, P.1
Stransky, N.2
Thiery, J.P.3
Radvanyi, F.4
Barillot, E.5
-
23
-
-
22144458387
-
Denoising array-based comparative genomic hybridization data using wavelets
-
Hsu,L., Self,S.G., Grove,D., Randolph,T., Wang,K., Delrow,J.J., Loo,L. and Porter,P. (2005) Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics, 6, 211-226.
-
(2005)
Biostatistics
, vol.6
, pp. 211-226
-
-
Hsu, L.1
Self, S.G.2
Grove, D.3
Randolph, T.4
Wang, K.5
Delrow, J.J.6
Loo, L.7
Porter, P.8
-
24
-
-
9244229940
-
Hidden markov models approach to the analysis of array cgh data
-
Fridlyand,J., Snijders,A.M., Pinkel,D. and Albertson,D.G. (2004) Hidden markov models approach to the analysis of array cgh data. J. Multivariate Anal., 90, 132-153.
-
(2004)
J. Multivariate Anal.
, vol.90
, pp. 132-153
-
-
Fridlyand, J.1
Snijders, A.M.2
Pinkel, D.3
Albertson, D.G.4
-
25
-
-
33646163019
-
Biohmm: a heterogeneous hidden markov model for segmenting array cgh data
-
Marioni,J.C., Thorne,N.P. and Tavaré,S. (2006) Biohmm: a heterogeneous hidden markov model for segmenting array cgh data. Bioinformatics, 22, 1144-1146.
-
(2006)
Bioinformatics
, vol.22
, pp. 1144-1146
-
-
Marioni, J.C.1
Thorne, N.P.2
Tavaré, S.3
-
26
-
-
25444531432
-
A statistical approach for array cgh data analysis
-
Picard,P., Robin,S., Lavielle,M., Vaisse,C. and Daudin,J.J. (2005) A statistical approach for array cgh data analysis. BMC Bioinformatics, 6, 27.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 27
-
-
Picard, P.1
Robin, S.2
Lavielle, M.3
Vaisse, C.4
Daudin, J.J.5
-
27
-
-
27944455289
-
A comparison study: applying segmentation to array CGH data for downstream analyses
-
Willenbrock,H. and Fridlyand,J. (2005) A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics, 21, 4084-4091.
-
(2005)
Bioinformatics
, vol.21
, pp. 4084-4091
-
-
Willenbrock, H.1
Fridlyand, J.2
-
28
-
-
34248523183
-
CGHcall: calling aberrations for array CGH tumor profiles
-
van de Wiel,M.A., Kim,K.I., Vosse,S.J., van Wieringen,W.N., Wilting,S.M. and Ylstra,B. (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics, 23, 892-894.
-
(2007)
Bioinformatics
, vol.23
, pp. 892-894
-
-
van de Wiel, M.A.1
Kim, K.I.2
Vosse, S.J.3
van Wieringen, W.N.4
Wilting, S.M.5
Ylstra, B.6
-
29
-
-
43449100079
-
Comparative genome profiling across subtypes of low-grade B-cell lymphoma identifies type-specific and common aberrations that target genes with a role in B-cell neoplasia
-
Ferreira,B.I., García,J.F., Suela,J., Mollejo,M., Camacho,F.I., Carro,A., Montes,S., Piris,M.A. and Cigudosa,J.C. (2008) Comparative genome profiling across subtypes of low-grade B-cell lymphoma identifies type-specific and common aberrations that target genes with a role in B-cell neoplasia. Haematologica, 93, 670-679.
-
(2008)
Haematologica
, vol.93
, pp. 670-679
-
-
Ferreira, B.I.1
García, J.F.2
Suela, J.3
Mollejo, M.4
Camacho, F.I.5
Carro, A.6
Montes, S.7
Piris, M.A.8
Cigudosa, J.C.9
-
30
-
-
41149168760
-
Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing' s sarcoma
-
Ferreira,B.I., Alonso,J., Carrillo,J., Acquadro,F., Largo,C., Suela,J., Teixeira,M.R., Cerveira,N., Molares,A., Gómez-López,G. et al. (2008) Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing' s sarcoma. Oncogene, 27, 2084-2090.
-
(2008)
Oncogene
, vol.27
, pp. 2084-2090
-
-
Ferreira, B.I.1
Alonso, J.2
Carrillo, J.3
Acquadro, F.4
Largo, C.5
Suela, J.6
Teixeira, M.R.7
Cerveira, N.8
Molares, A.9
Gómez-López, G.10
-
31
-
-
33748276243
-
STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
-
Diskin,S.J., Eck,T., Greshock,J., Mosse,Y.P., Naylor,T., Stoeckert,C.J., Weber,B.L., Maris,J.M. and Grant,G.R. (2006) STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res., 16, 1149-1158.
-
(2006)
Genome Res.
, vol.16
, pp. 1149-1158
-
-
Diskin, S.J.1
Eck, T.2
Greshock, J.3
Mosse, Y.P.4
Naylor, T.5
Stoeckert, C.J.6
Weber, B.L.7
Maris, J.M.8
Grant, G.R.9
-
32
-
-
38849092212
-
GEAR: genomic enrichment analysis of regional DNA copy number changes
-
Kim,T.M., Jung,Y.C., Rhyu,M.G., Jung,M.H. and Chung,Y.J. (2008) GEAR: genomic enrichment analysis of regional DNA copy number changes. Bioinformatics, 24, 420-421.
-
(2008)
Bioinformatics
, vol.24
, pp. 420-421
-
-
Kim, T.M.1
Jung, Y.C.2
Rhyu, M.G.3
Jung, M.H.4
Chung, Y.J.5
-
33
-
-
43049143055
-
Mapping and sequencing of structural variation from eight human genomes
-
Kidd,J.M., Cooper,G.M., Donahue,W.F., Hayden,H.S., Sampas,N., Graves,T., Hansen,N., Teague,B., Alkan,C., Antonacci,F. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.
-
(2008)
Nature
, vol.453
, pp. 56-64
-
-
Kidd, J.M.1
Cooper, G.M.2
Donahue, W.F.3
Hayden, H.S.4
Sampas, N.5
Graves, T.6
Hansen, N.7
Teague, B.8
Alkan, C.9
Antonacci, F.10
-
34
-
-
2442666425
-
The Ensembl core software libraries
-
Stabenau,A., McVicker,G., Melsopp,C., Proctor,G., Clamp,M. and Birney,E. (2004) The Ensembl core software libraries. Genome Res., 14, 929-933.
-
(2004)
Genome Res.
, vol.14
, pp. 929-933
-
-
Stabenau, A.1
McVicker, G.2
Melsopp, C.3
Proctor, G.4
Clamp, M.5
Birney, E.6
|