·European Meeting on Next Generation Sequencing in Leiden ·MGC course "Next generation sequence (NGS) data analysis"

Publications of work we were involved in

• 2010
• Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies. Hestand MS, Klingenhoff A, Scherf M, Ariyurek Y, Ramos Y, van Workum W, Suzuki M, Werner T, van Ommen GJ, den Dunnen JT, Harbers M, 't Hoen PA (2010). Nucleic Acids Res. 2010 Jul 7.
• Terminal osseous dysplasia is caused by a single recurrent mutation in the FLNA gene. Sun Y, Almomani R, Aten E, Celli J, van der Heijden J, Venselaar H, Robertson SP, Baroncini A, Franco B, Basel-Vanagaite L, Horii E, Drut R, Ariyurek Y, den Dunnen JT, Breuning MH (2010). Am J Hum Genet. 2010 Jul 9;87(1):146-53.
• Accurate quantification of dystrophin mRNA and exon skipping levels in Duchenne Muscular Dystrophy. Spitali P, Heemskerk H, Vossen RH, Ferlini A, den Dunnen JT, 't Hoen PA, Aartsma-Rus A (2010). Lab Invest. 2010 May 10.
• High-throughput genotyping of mannose-binding lectin variants using high-resolution DNA-melting analysis. Vossen RH, van Duijn M, Daha MR, den Dunnen JT, Roos A (2010). Hum Mutat. 2010 Apr;31(4):E1286-93.
• Sensitive and specific KRAS somatic mutation analysis on whole-genome amplified DNA from archival tissues. van Eijk R, van Puijenbroek M, Chhatta AR, Gupta N, Vossen RH, Lips EH, Cleton-Jansen AM, Morreau H, van Wezel T (2010). J Mol Diagn. 2010 Jan;12(1):27-34.
• Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. Yolande F.M. Ramos, Matthew S. Hestand et al (2010). Nucleic Acids Research 2010 Apr 30, doi:10.1093/nar/gkq184.
• 2009
• Deep sequencing to reveal new variants in pooled DNA samples. Out AA, van Minderhout IJ, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, van Galen M, Taschner PE, Tops CM, Breuning MH, van Ommen GJ, den Dunnen JT, Devilee P, Hes FJ (2009). Hum Mutat. 2009 Dec;30(12):1703-12.
• Cost-effective HRMA pre-sequence typing of clone libraries; application to phage display selection. Pepers BA, Schut MH, Vossen RH, van Ommen GJ, den Dunnen JT, van Roon-Mom WM (2009). BMC Biotechnol. 2009 May 22;9:50.
• A molecular blueprint of gene expression in hippocampal subregions CA1, CA3, and DG is conserved in the brain of the common marmoset. Datson NA, Morsink MC, Steenbergen PJ, Aubert Y, Schlumbohm C, Fuchs E, de Kloet ER (2009). Hippocampus. 2009 Aug;19(8):739-52.
• High-resolution melting analysis (HRMA): more than just sequence variant screening. Vossen RH, Aten E, Roos A, den Dunnen JT (2009). Hum Mutat. 2009 Jun;30(6):860-6. Review.
• 2008
• Methods to detect CNVs in the human genome. Aten E, White SJ, Kalf ME, Vossen RH, Thygesen HH, Ruivenkamp CA, Kriek M, Breuning MH, den Dunnen JT (2008). Cytogenet Genome Res. 2008;123(1-4):313-21.
• CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. Hestand et al (2008). BMC Bioinformatics. 2008 Nov 26;9(1):495.
• Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Peter A. C. 't Hoen et al (2008). Nucleic Acids Research 2008; doi: 10.1093/nar/gkn705.
• Induced pluripotency with endogenous and inducible genes. D. Duinsbergen et al (2008). Exp. Cell Res. doi:10.1016/j.yexcr.2008.06.024.
• Microarray Retriever: a web-based tool for searching and large scale retrieval of public microarray data. Ivliev et al (2008). Accepted for NAR Webserver Issue 2008 (PDF).
• Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene. Kayser M et al (2008). Am J Hum Genet. 2008 Feb;82(2):411-23. Epub 2008 Jan 25.
• Can subtle changes in gene expression be consistently detected with different microarray platforms?. Pedotti P et al (2008). BMC Genomics 9: 124.
• Pyrophosphorolysis detects B-RAF mutations in primary uveal melanoma. Maat W et al (2008). Invest Ophthalmol Vis Sci. 2008 Jan;49(1):23-7.
• 2007
• Effects of urinary and recombinant gonadotrophins on gene expression profiles during the murine peri-implantation period. Sibug RM et al (2007). Hum Reprod. 2007 Jan;22(1):75-82. Epub 2006 Oct 19.
• 2006
• Analysis of Gene Expression Using Gene Sets Discriminates Cancer Patients with and without Late Radiation Toxicity. J.P. Svensson et al (2006) PLoS Med 2006 Oct; 3(10):e422.
• 2005
• Gene expression profiling in response to the histone deacetylase inhibitor BL1521 in neuroblastoma. A.J. de Ruijter et al. (2005) Exp. Cell Res. 2005; 309:451-467
• 2004
• Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia. P.J.M. Valk et al. (2004) N Engl J Med 2004;350:1617-28 (Editorial, Perspective).
• Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs. 't Hoen et al. (2004) Nucl Acids Res 32, e41.
• 2003
• GeneHopper: a web-based search engine to link gene expression platforms through GenBank accession numbers. Svensson et al. (2003). Genome Biology 2003, 4:R35.
• Fluorescent amino-allyl labelling of cRNA for microarray applications. 't Hoen et al. (2003). Nucl.Acids Res.31: e20.1-e20.8
• 2002
• Comprehensive detection of genomic duplications and deletions in the DMD gene, by use of multiplex amplifiable probe hybridization. White S et al (2002). Am J Hum Genet. 2002 Aug;71(2):365-74. Epub 2002 Jul 8.




Terms & conditions
©2007-2010 LGTC