Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans (2009)
Kersbergen, Paula, Van Duijn, Kate, Kloosterman, Ate D, Den Dunnen, Johan T, Kayser, Manfred, De Knijff, Peter
Abstract Background The identification and use of Ancestry-Sensitive Markers (ASMs), i.e. genetic polymorphisms facilitating the genetic reconstruction of geographical origins of individuals, is far...
Kerstens, Hindrik HD, Crooijmans, Richard PMA, Veenendaal, Albertine, Dibbits, Bert W, Den Dunnen, Johan T, ...
Abstract Background The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide...
Mozaffari, Melika, Hoogeveen-Westerveld, Marianne, Kwiatkowski, David, Sampson, Julian, Ekong, Rosemary, Povey, Sue, ...
Abstract Background Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterised by the development of hamartomas in a variety of organs and tissues. The disease is caused by...
Amaral, Andreia J, Megens, Hendrik-Jan, Kerstens, Hindrik HD, Heuven, Henri CM, Dibbits, Bert, Crooijmans, Richard PMA, ...
Abstract Background Although the Illumina 1 G Genome Analyzer generates billions of base pairs of sequence data, challenges arise in sequence selection due to the varying sequence quality. Therefore,...
Pepers, Barry A, Schut, Menno H, Vossen, Rolf HAM, Den Dunnen, Johan T
Abstract Background Methodologies like phage display selection, in vitro mutagenesis and the determination of allelic expression differences include steps where large numbers of clones need to be...
Hestand, Matthew S, Van Galen, Michiel, Villerius, Michel P, Den Dunnen, Johan T, 't Hoen, Peter AC
Abstract Background The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and...
Pepers, Barry A, 't Hoen, Peter AC, Verwijmeren, Carola ACM, Den Dunnen, Johan T, Dorsman, Josephine C, ...
Abstract Background Huntington's disease is a progressive autosomal dominant neurodegenerative disorder that is caused by a CAG repeat expansion in the HD or Huntington's disease gene. Although micro...
Jelier, Rob, 't Hoen, Peter AC, Sterrenburg, Ellen, Den Dunnen, Johan T, Kors, Jan A, ...
Abstract Background Comparative analysis of expression microarray studies is difficult due to the large influence of technical factors on experimental outcome. Still, the identified differentially...
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...
Ivliev, Alexander E., Villerius, Michel P., Den Dunnen, Johan T., Brandt, Bernd W.
The major public microarray repositories Gene Expression Omnibus and ArrayExpress are growing rapidly. This enables meta-analysis studies, in which expression data from multiple individual studies...
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...
Vink, Geraldine R, Kriek, Marjolein, Schouten, Jan, Bakker, Bert, ...
Genomic deletions and duplications play an important role in the etiology of human disease. Versatile tests are required to detect these rearrangements, both in research and diagnostic settings....
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...
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...
Fluorescent labelling of cRNA for microarray applications (2003)
De Kort, Floor, Den Dunnen, Johan T.
Microarrays of oligonucleotide expression libraries can be hybridised with either cDNA, generated from mRNA during reverse transcription, or cRNA, generated in an Eberwine mRNA amplification...
Aartsma-Rus, Annemieke, Janson, Anneke A.M., Kaman, Wendy E., Bremmer-Bout, Mattie, Den Dunnen, Johan T., Baas, Frank, ...
The dystrophin deficiency leading to the severely progressing muscle degeneration in Duchenne muscular dystrophy (DMD) patients is caused by frame-shifting mutations in the DMD gene. We are...
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...
Dorsman, Josephine C., Pepers, Barry, Langenberg, Dennis, Kerkdijk, Henri, Ijszenga, Marije, Den Dunnen, Johan T., ...
Expansion of a Glutamine (Gln) repeat above a specific critical size in certain proteins gives rise to aggregation-prone proteins that cause neurodegenerative disorders, such as Huntington's disease....
Bremmer-Bout, Mattie, Janson, Anneke A.M., Ginjaar, Ieke B., Baas, Frank, Den Dunnen, Johan T., ...
Due to frame-shifting mutations in the DMD gene that cause dystrophin deficiency, Duchenne muscular dystrophy (DMD) patients suffer from lethal muscle degeneration. In contrast, mutations in the...
High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes (1995)
Florijn, Ralpha J., Bonden, A. J., Vrolijk, Hans, Wiegant, Joop, Vaandrager, Jan-Willem, Bass, Frank, ...
We have applied two-colour fluorescence in situ hybridization (FISH) to DNA fibers and combined it with digital imaging microscopy for the mapping of large cosmid contigs. The technique was validated...
Protein truncation test (PTT) for rapid detection of translation-terminating mutations (1993)
Roest, Pauline A.M., Roberts, Roland G., Sugino, Shigeto, Den Dunnen, Johan T.
Currently available techniques used to recognize point mutations in genetic disease are time consuming and are capable of screening only small pieces of DNA. Moreover, they detect all sequence...
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...
Fluorescent labelling of cRNA for microarray applications
De Kort, Floor, Den Dunnen, Johan T.
Microarrays of oligonucleotide expression libraries can be hybridised with either cDNA, generated from mRNA during reverse transcription, or cRNA, generated in an Eberwine mRNA amplification...
Gussoni, Emanuela, Bennett, Richard R., Muskiewicz, Kristina R., Meyerrose, Todd, Nolta, Jan A., Gilgoff, Irene, ...
Duchenne muscular dystrophy (DMD) is a severe progressive muscle-wasting disorder caused by mutations in the dystrophin gene. Studies have shown that bone marrow cells transplanted into lethally...
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...
Heus, Joris J., Van De Vosse, Esther, Den Dunnen, Johan T.
We have constructed a set of fragmentation vectors for the truncation of either the centromeric or the noncentromeric end of YACs containing a human DNA insert. These vectors carry ADE2 or HIS5 as...
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, ...
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...
Fluorescent labelling of cRNA for microarray applications
De Kort, Floor, Den Dunnen, Johan T.
Microarrays of oligonucleotide expression libraries can be hybridised with either cDNA, generated from mRNA during reverse transcription, or cRNA, generated in an Eberwine mRNA amplification...
Gussoni, Emanuela, Bennett, Richard R., Muskiewicz, Kristina R., Meyerrose, Todd, Nolta, Jan A., Gilgoff, Irene, ...
Duchenne muscular dystrophy (DMD) is a severe progressive muscle-wasting disorder caused by mutations in the dystrophin gene. Studies have shown that bone marrow cells transplanted into lethally...
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...
Heus, Joris J., Van De Vosse, Esther, Den Dunnen, Johan T.
We have constructed a set of fragmentation vectors for the truncation of either the centromeric or the noncentromeric end of YACs containing a human DNA insert. These vectors carry ADE2 or HIS5 as...
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, ...
Standard Mutation Nomenclature in Molecular Diagnostics : Practical and Educational Challenges
Ogino, Shuji, Gulley, Margaret L., Den Dunnen, Johan T., Wilson, Robert B.
To translate basic research findings into clinical practice, it is essential that information about mutations and variations in the human genome are communicated easily and unequivocally....
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, ...
Ivliev, Alexander E., Villerius, Michel P., Den Dunnen, Johan T., Brandt, Bernd W.
The major public microarray repositories Gene Expression Omnibus and ArrayExpress are growing rapidly. This enables meta-analysis studies, in which expression data from multiple individual studies...
Pepers, Barry A, 't Hoen, Peter AC, Verwijmeren, Carola ACM, Den Dunnen, Johan T, Dorsman, Josephine C, ...
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...
Kayser, Manfred, Liu, Fan, Rivadeneira, Fernando, Lao, Oscar, Van Duijn, Kate, ...
Human iris color was one of the first traits for which Mendelian segregation was established. To date, the genetics of iris color is still not fully understood and is of interest, particularly in...
Bruder, Carl E.G., Piotrowski, Arkadiusz, Andersson, Robin, Erickson, Stephen, Diaz De Ståhl, Teresita, ...
The exploration of copy-number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic makeup between twins derived from the same zygote...
Cost-effective HRMA pre-sequence typing of clone libraries; application to phage display selection
Pepers, Barry A, Schut, Menno H, Vossen, Rolf HAM, Den Dunnen, Johan T
Mozaffari, Melika, Hoogeveen-Westerveld, Marianne, Kwiatkowski, David, Sampson, Julian, Ekong, Rosemary, Povey, Sue, ...
Kerstens, Hindrik HD, Crooijmans, Richard PMA, Veenendaal, Albertine, Dibbits, Bert W, Den Dunnen, Johan T, ...
Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans
Kersbergen, Paula, Van Duijn, Kate, Kloosterman, Ate D, Den Dunnen, Johan T, Kayser, Manfred, De Knijff, Peter
Novel Protein-Protein Interactions Inferred from Literature Context
Botelho Bovo, Alessandro, De Morrée, Antoine, Van Mulligen, Erik M., Chichester, Christine, ...
We have developed a method that predicts Protein-Protein Interactions (PPIs) based on the similarity of the context in which proteins appear in literature. This method outperforms previously...