Barbera D.C. van Schaik

Blog (BioLab members only)

Sequence analysis

After studying analytical chemistry at the HLO in Alkmaar (1995-1999) I started my bioinformatics training at the AMC under the supervision of Antoine van Kampen. Next I worked on a joint genome analysis project of the department of Human Genetics and the Bioinformatics Laboratory and several other DNA sequence analysis and data integration projects as scientific programmer.

Since 2007 I am full time appointed at the Bioinformatics Laboratory as junior researcher in the sequence analysis group. I apply existing methods to DNA sequence data and develop new methods in collaboration with researchers from several laboratories at the AMC. Furthermore I am involved in national bioinformatics projects. The e-bioscience group develops methodologies to scale up data analyses and the sequence analysis group applies these methods to deal with the exponentially growing amount of sequence data. Next to development and analysis I give education about bioinformatics to students and researchers.

Projects

• Exome and whole genome sequencing
• Genome of the Netherlands
• Assembly and comparison of bacterial genomes
• Alternative splicing
• Virus discovery
• T- and B-cell variation
• Human transcriptome map
• Usage - Gene expression analysis on SAGE data

Sequence analysis at the Bioinformatics Laboratory

Publications

2011

• Y. Mohammed, S. Shahand, V. Korkhov, A. Luyf, B. van Schaik, M. Caan, A. van Kampen, M. Palmblad, and S. Olabarriaga. Data Decomposition in Biomedical e-Science Applications. In Proceedings of the 7th IEEE International Conference on e-Science, 2011.
• Ritz K, van Schaik BDC, Jakobs ME, Aronica E, Tijssen MA, van Kampen AHC, Baas F (2011) Looking ultra deep: Short identical sequences and transcriptional slippage. Genomics 2011 May 23. Epub ahead of print pubmed
• Piet JR, Huis In 't Veld RA, van Schaik BDC, van Kampen AHC, Baas F, van de Beek D, Pannekoek Y, van der Ende A. (2011) Genome Sequence of Neisseria meningitidis serogroup B strain H44/76. Journal of Bacteriology.
• de Vries M, Deijs M, Canuti M, van Schaik BDC, Faria NR, van de Garde MD, Jachimowski LC, Jebbink MF, Jakobs M, Luyf AC, Coenjaerts FE, Claas EC, Molenkamp R, Koekkoek SM, Lammens C, Leus F, Goossens H, Ieven M, Baas F, van der Hoek L. A sensitive assay for virus discovery in respiratory clinical samples. PLoS One., 24;6(1):e16118.
• Ritz K, van Schaik BDC, Jakobs ME, van Kampen AHC, Aronica E, Tijssen MA, Baas F. (2011) SGCE isoform characterization and expression in human brain: implications for myoclonus-dystonia pathogenesis. Eur J Hum Genet, 19(4):438-44.

2010

• Luyf AC, van Schaik BDC, de Vries M, Baas F, van Kampen AHC, Olabarriaga SD. Initial steps towards a production platform for DNA sequence analysis on the grid. BMC Bioinformatics. 11(1), 598. (Note: Luyf AC, van Schaik BD =first authors)
• PL Klarenbeek, PP Tak, BDC van Schaik, AH Zwinderman, ME Jakobs, Z Zhang, AHC van Kampen, RAW van Lier, F Baas, N de Vries (2010) Human T cell memory consists mainly of unexpanded clones. Epub ahead of print (PubMed)

2009

• van Hooff SR, Koster J, Hulsen T, van Schaik BDC, Roos M, van Batenburg MF, Versteeg R, van Kampen AHC (2009). The construction of genome-based transcriptional units. OMICS, 13(2):105-14.

2003

• Versteeg R, van Schaik BDC, van Batenburg MF, Roos M, Monajemi R, Caron HN, Bussemaker HJ, van Kampen AHC (2003) The Human Transcriptome Map reveals extremes in gene density, intron length, GC content and repeat pattern for domains of highly and weakly expressed genes. Genome Research, 13, 1998-2004. [Pubmed]

2002

• Godfried MB, Veenstra M, van Sluis P, Boon K, van Asperen R, Hermus M-C, van Schaik BDC, Voûte TPA, Schwab M, Versteeg R, Caron HN (2002) The N-myc and c-myc downstream pathways include the chromosome 17q genes nm23-H1 and nm23-H2. Oncogene 21: 13. 2097-2101 (pubmed)

2001

• Spieker N, van Sluis P, Beitsma M, Boon K, van Schaik BDC, van Kampen AHC, Caron H and Versteeg R (2001) The MEIS1 Oncogene Is Highly Expressed in Neuroblastoma and Amplified in Cell Line IMR32. Genomics 71(2), 214-221. [Pubmed]
• Caron HN, van Schaik BDC, van der Mee M, van Sluis P, Hermus M-C, van Asperen R, Riggins G, Heisterkamp SH, Baas F, Boon K, Voûte PA, van Kampen AHC and Versteeg R (2001) The Human Transcriptome Map reveals a clustering of highly expressed genes in chromosomal domains, Science, 291, 1289-1292. [Pubmed]

2000

• van Kampen AHC, van Schaik BDC, Pauws E, Michiels EMC, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JAM, Baas F and van der Mee M (2000) USAGE: a web-based approach for the analysis of SAGE data. Bioinformatics, 16(10), 899-905. [Pubmed]

Profile on networks

• AMC
• LinkedIn
• NBIC BioAssist
• MyExperiment

Personal stuff

In my spare time I like to visit concerts and festivals, cook (all cuisines), grow vegetables on my balcony, read books (fantasy, popular science/philosophy, Dutch literature) and make stuff with my sewing machine. I have a website with all the usual homepage-thingies on it plus a database with Indonesian recipes: http://www.van-schaik.org/

Contact information

Bioinformatics Laboratory
Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB)
Phone: (+31) 20 - 566 47 11
http://www.bioinformaticslaboratory.nl/

Academic Medical Center / University of Amsterdam
PO Box 22660 (J1B.205)
1100 DD Amsterdam
The Netherlands

monday-thursday, friday (even weeks)
b.d.vanschaik@amc.uva.nl