Judith Boer

Research interests Short vita Recent publications Talks Selected abstracts Links Contact

Research interests

Tumor profiling using expression, copy number and methylation arrays
Microarray technology implementation and development
Microarray data analysis

Short vita

Born

18^th of August, 1967 in Haarlem, the Netherlands

Education

Study Biomedical Sciences, Leiden University, the Netherlands (1985-1990)

PhD Cell Biology and Genetics, Erasmus University, Rotterdam, the Netherlands (1991-1993)

Continuation of PhD at St. Jude Children's Research Hospital, Memphis TN, USA (1993-1997)

Jobs

Postdoc at the German Cancer Research Center, Heidelberg, Germany (1997-1999)

Postdoc at the Leiden University Medical Center, the Netherlands (since 2000)
Assistant professor at the Leiden University Medical Center (since 2005)

Selected publications

de Menezes RX, Boetzer M, Sieswerda M, van Ommen GJB, Boer JM. Integrated analysis of DNA copy number and gene expression microarray data using gene sets. Submitted.
van Doorn R, van Kester MS, Dijkman R, Vermeer MH, Mulder AA, Szuhai K, Knijnenburg J, Boer JM, Willemze R, Tensen CP (2009). Oncogenomic analysis of mycosis fungoides reveals major differences with Sézary syndrome. Blood 113(1):127-36.
't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT (2008). Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 36(21):e141.
Gaspar C, Cardoso J, Franken P, Molenaar L, Morreau H, Möslein G, Sampson J, Boer JM, de Menezes RX, Fodde R (2008). Cross-species comparison of human and mouse adenomatous polyps reveals conserved mechanisms in APC-driven intestinal tumorigenesis. Am J Pathol. 172(5):1363-80.
't Hoen PA, de Meijer EJ, Boer JM, Vossen RH, Turk R, Maatman RG, Davies KE, van Ommen GJ, van Deutekom JC, den Dunnen JT (2008). Generation and characterization of transgenic mice with the full-length human DMD gene. J Biol Chem 283(9):5899-907.
Pedotti P, 't Hoen PAC, Vreugdenhil E, Schenk GJ, Vossen RHAM, Ariyurek Y, de Hollander M, Kuiper R, van Ommen GJB, den Dunnen JT, Boer JM, de Menezes RX (2008). Can subtle changes in gene expression be consistently detected with different microarray platforms? BMC Genomics 9(1):124.
Passtoors WM, Beekman M, Gunn D, Boer JM, Heijmans BT, Westendorp RGJ, Zwaan BJ, Slagboom PE (2008). Genomic studies in ageing research: the need to integrate genetic and gene expression approaches. J Int Med Journal of Internal Medicine 263:153-166.
Cardoso J, Boer JM, Morreau H, Fodde R. Expression and genomic profiling of colorectal cancer. Biochim Biophys Acta - Reviews on Cancer, 2007 Jan;1775(1):103-37.
van Roon EH, van Puijenbroek M, Morreau H, Boer JM (2006). Identification of DNA methylation markers for detection and classification of colon cancer. Eur J Hum Gen 14 Suppl 1: C76 (Abstract).
Boer JM (2006). Microarrays in colorectal cancer. In: Ganten D & Ruckpaul K (eds). Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine Springer, Berlin Heidelberg New York: 1081-8.
Cardoso J, Molenaar L, de Menezes RX, van Leerdam M, Rosenberg C, Moslein G, Sampson J, Morreau H, Boer JM, Fodde R (2006). Chromosomal instability in MYH- and APC-mutant adenomatous polyps. Cancer Res 66(5):2514-9.
de Graaf JM, de Menezes RX, Boer JM, Kosters WA. Frequent itemsets for genomic profiling. CompLife 2005, Lecture Notes in Computer Science 3695: 104-116.
Cardoso J, Molenaar L, de Menezes RX, Rosenberg C, Morreau H, Moslein G, Fodde R, Boer JM (2004). Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH. Nucleic Acids Res 32(19):e146.
Valk PJ, Verhaak RG, Beijen MA, Erpelinck CA, Barjesteh van Waalwijk van Doorn-Khosrovani S, Boer JM, Beverloo HB, Moorhouse MJ, van der Spek PJ, Lowenberg B, Delwel R (2004). Prognostically useful gene-expression profiles in acute myeloid leukemia.
N Engl J Med 350:1617-28.
't Hoen PAC, Turk R, Boer JM, Sterrenburg E, de Menezes RX, van Ommen GJB, den Dunnen JT (2004). Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs. Nucleic Acids Res: 32: e41.
Boer JM, de Meijer EJ, Mank EM, van Ommen GJB, and den Dunnen JT (2002). Expression profiling in stably regenerating skeletal muscle of dystrophin-deficient mdx mice. Neuro Musc Disord 12: S118-124.
Boer JM, Huber W, Sültmann H, Wilmer F, von Heydebreck A, Haas S, Korn B, Gunawan B, Vente A, Füzesi L, Vingron M, Poustka A (2001). Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500 element cDNA array. Genome Res 11: 1861-70.

Recent invited lectures

Dec '07 Keys Postdoc Meeting, KeyGene, Wageningen, Netherlands: Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH.
Sept '06 3^rd Annual Centre for Medical Systems Biology Symposium, Rotterdam, Netherlands: Identification of DNA methylation markers for detection and classification of colon cancer by epigenetic profiling.
March '06 Symposium Statistical Methods for Microarray Data, Leiden, Netherlands: Towards integrated analysis of gene expression and copy number data for hereditary colorectal polyposis.
March ’04 Utrecht Genetics Seminars, the Netherlands: Molecular classification of familial colorectal cancer by expression and genomic profiling

Recent conference presentations

Nov '07 Benelux Bioinformatics Conference, Leuven, Belgium: Integrated statistical analysis to identify associations between DNA copy number and gene expression in human tumor microarray data. (poster)
Oct '07 Symposium on Epigenetics and Pharmacogenomics, Ghent, Belgium: Identification of DNA methylation markers for detection and classification of colon cancer by epigenetic profiling. (poster)
April '07 Netherlands Bioinformatics Conference, Amsterdam, Netherlands: SIM: Statistical Integrated Model of copy number and expression microarray data. (poster)
Sept '06 Cold Spring Harbor Laboratory/Wellcome Trust Genome Informatics Meeting, Hinxton, UK: Integrated analysis of DNA copy number and gene expression in cancer genomes. (poster)
May '06 European Society for Human Genetics, Amsterdam, Netherlands: Identification of DNA methylation markers for detection and classification of colon cancer by epigenetic profiling. (oral)
Sept. '05 Microarray Gene Expression Data Society 8, Bergen, Norway: MYH-associated polyposis (MAP): a chromosomal instability syndrome? (oral)
April '04 HGM2004, Berlin, Germany: Molecular classification of familial colorectal cancer by expression and genomic profiling. (oral)

Links

Center for Human and Clinical Genetics

Leiden Genome Technology Center

Microarray Analysis Group

Address

Dr. Judith M. Boer
Center for Human and Clinical Genetics
Leiden University Medical Center (LUMC)
Research Building, Einthovenweg 20
Room S-04-003
Phone: 071-526 9422
Fax: 071-526 82 85
E-mail: j.m.boer@lumc.nl
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Postal address:
Postzone S-04-P
Postbus 9600
2300 RC Leiden
The Netherlands

Judith Boer - Last modified: August 11, 2008