Integrated analysis of DNA copy number and gene expression microarray data using gene sets (2009)
Menezes, Renée X, Boetzer, Marten, Sieswerda, Melle, Boer, Judith M
Abstract Background Genes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be...
Judith M. Boer, Wolfgang K. Huber, Holger Sültmann, Friederike Wilmer, Anja Von Heydebreck, Stefan Haas, ...
We investigated the changes in gene expression accompanying the development and progression of kidney cancer by use of 31,500-element complementary DNA arrays. We measured expression profiles for...
Frequent Itemsets for Genomic Profiling (2008)
Judith M. Boer, Walter A. Kosters
Abstract. Frequent itemset mining is a promising approach to the study of genomic profiling data. Here a dataset consists of real numbers describing the relative level in which a clone occurs in...
Pedotti, Paola, 't Hoen, Peter AC, Vreugdenhil, Erno, Schenk, Geert J, Vossen, Rolf HAM, Ariyurek, Yavuz, ...
Abstract Background The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the...
Ariyurek, Yavuz, Thygesen, Helene H., Vreugdenhil, Erno, De Menezes, Renée X., ...
The hippocampal expression profiles of wild-type mice and mice transgenic for δC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray...
Gene expression variation between mouse inbred strains (2004)
Turk, Rolf, 't Hoen, Peter AC, Sterrenburg, Ellen, De Menezes, Renée X, De Meijer, Emile J, Boer, Judith M, ...
Abstract Background In this study, we investigated the effect of genetic background on expression profiles. We analysed the transcriptome of mouse hindlimb muscle of five frequently used mouse inbred...
Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH (2004)
Cardoso, Joana, Molenaar, Lia, De Menezes, Renée X., Rosenberg, Carla, Morreau, Hans, Möslein, Gabriela, ...
Comparative genomic hybridization by means of BAC microarrays (array CGH) allows high-resolution profiling of copy-number aberrations in tumor DNA. However, specific genetic lesions associated with...
Svensson, B Anders T, Kreeft, Arja J, Den Dunnen, Johan T, Boer, Judith M
Abstract Global gene-expression analysis is carried out using different technologies that are either array- or sequence-tag-based. To compare experiments that are performed on these different...
Global gene-expression analysis is carried out using different technologies that are either array- or sequence-tag-based. To compare experiments that are performed on these different platforms, array...
A common reference for cDNA microarray hybridizations (2002)
Sterrenburg, Ellen, Turk, Rolf, Boer, Judith M., Van Ommen, Gertjan B., Den Dunnen, Johan T.
Comparisons of expression levels across different cDNA microarray experiments are easier when a common reference is co‐hybridized to every microarray. Often this reference consists of one...
Boer, Judith M., Huber, Wolfgang K., Sültmann, Holger, Wilmer, Friederike, Von Heydebreck, Anja, Haas, Stefan, ...
Boer, Judith M., Huber, Wolfgang K., Sültmann, Holger, Wilmer, Friederike, Von Heydebreck, Anja, Haas, Stefan, ...
Boer, Judith M., Huber, Wolfgang K., Sültmann, Holger, Wilmer, Friederike, Von Heydebreck, Anja, Haas, Stefan, ...
A common reference for cDNA microarray hybridizations
Sterrenburg, Ellen, Turk, Rolf, Boer, Judith M., Van Ommen, Gertjan B., Den Dunnen, Johan T.
Comparisons of expression levels across different cDNA microarray experiments are easier when a common reference is co-hybridized to every microarray. Often this reference consists of one...
Svensson, B Anders T, Kreeft, Arja J, Den Dunnen, Johan T, Boer, Judith M
To compare experiments that are performed on different platforms, array probes and sequence tags need to be linked. A web-based search engine GeneHopper has been developed to link different...
Boer, Judith M., Huber, Wolfgang K., Sültmann, Holger, Wilmer, Friederike, Von Heydebreck, Anja, Haas, Stefan, ...
We investigated the changes in gene expression accompanying the development and progression of kidney cancer by use of 31,500-element complementary DNA arrays. We measured expression profiles for...
Turk, Rolf, Boer, Judith M., Sterrenburg, Ellen, De Menezes, Renée X., ...
In two-colour microarrays, the ratio of signal intensities of two co-hybridized samples is used as a relative measure of gene expression. Ratio-based analysis becomes complicated and inefficient in...
Gene expression variation between mouse inbred strains
Turk, Rolf, 't Hoen, Peter AC, Sterrenburg, Ellen, De Menezes, Renée X, De Meijer, Emile J, Boer, Judith M, ...
Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH
Cardoso, Joana, Molenaar, Lia, De Menezes, Renée X., Rosenberg, Carla, Morreau, Hans, Möslein, Gabriela, ...
Comparative genomic hybridization by means of BAC microarrays (array CGH) allows high-resolution profiling of copy-number aberrations in tumor DNA. However, specific genetic lesions associated with...
A common reference for cDNA microarray hybridizations
Sterrenburg, Ellen, Turk, Rolf, Boer, Judith M., Van Ommen, Gertjan B., Den Dunnen, Johan T.
Comparisons of expression levels across different cDNA microarray experiments are easier when a common reference is co-hybridized to every microarray. Often this reference consists of one...
Svensson, B Anders T, Kreeft, Arja J, Den Dunnen, Johan T, Boer, Judith M
To compare experiments that are performed on different platforms, array probes and sequence tags need to be linked. A web-based search engine GeneHopper has been developed to link different...
Boer, Judith M., Huber, Wolfgang K., Sültmann, Holger, Wilmer, Friederike, Von Heydebreck, Anja, Haas, Stefan, ...
We investigated the changes in gene expression accompanying the development and progression of kidney cancer by use of 31,500-element complementary DNA arrays. We measured expression profiles for...
Turk, Rolf, Boer, Judith M., Sterrenburg, Ellen, De Menezes, Renée X., ...
In two-colour microarrays, the ratio of signal intensities of two co-hybridized samples is used as a relative measure of gene expression. Ratio-based analysis becomes complicated and inefficient in...
Gene expression variation between mouse inbred strains
Turk, Rolf, 't Hoen, Peter AC, Sterrenburg, Ellen, De Menezes, Renée X, De Meijer, Emile J, Boer, Judith M, ...
Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH
Cardoso, Joana, Molenaar, Lia, De Menezes, Renée X., Rosenberg, Carla, Morreau, Hans, Möslein, Gabriela, ...
Comparative genomic hybridization by means of BAC microarrays (array CGH) allows high-resolution profiling of copy-number aberrations in tumor DNA. However, specific genetic lesions associated with...
Can subtle changes in gene expression be consistently detected with different microarray platforms?
Pedotti, Paola, 't Hoen, Peter AC, Vreugdenhil, Erno, Schenk, Geert J, Vossen, Rolf HAM, Ariyurek, Yavuz, ...
Gaspar, Claudia, Cardoso, Joana, Franken, Patrick, Molenaar, Lia, Morreau, Hans, Möslein, Gabriela, ...
Expression profiling is a well established tool for the genome-wide analysis of human cancers. However, the high sensitivity of this approach combined with the well known cellular and molecular...
Ariyurek, Yavuz, Thygesen, Helene H., Vreugdenhil, Erno, De Menezes, Renée X., ...
The hippocampal expression profiles of wild-type mice and mice transgenic for δC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray...