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B.D.C. van Schaik

Position
Research Associate
Main activities
Research
Specialisation
Bioinformatics, sequence analysis, next generation sequencing
Focus of research

Over the past decade we have gained considerable experience with the analysis of nucleotide sequences. Currently, most of our effort is devoted to the analysis of next generation sequencing data that is produced in the AMC sequencing facility (Roche 454 and ABI Solid). We are involved in a large range of projects that often require the development of dedicated methods for the analysis of the data. Examples of such projects include the determination of T-cell variation, virus discovery (metagenomics), identification of alternative splicing and identification of HIV microRNAs. http://www.bioinformaticslaboratory.nl/

Key publications
  • van Schaik Barbera, Klarenbeek Paul, Doorenspleet Marieke, van Kampen Antoine, Moody D. Branch, de Vries Niek, van Rhijn Ildiko Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire Journal of immunology (Baltimore, Md. 2014;193 (10):5338-5344 [PubMed]
  • van Schaik Barbera D. C., Santcroos Mark, Korkhov Vladimir, Jongejan Aldo, Willemsen Marcel, van Kampen Antoine H. C., Olabarriaga Silvia D. Challenges in DNA sequence analysis on a production gridin: A. Anonymous, editors. EGI Community Forum 2012 / EMI Second Technical Conference. s.n.; 2012. p. 1-19
  • van Houdt Jeroen K. J., Nowakowska Beata Anna, Sousa Sérgio B., van Schaik Barbera D. C., Seuntjens Eve, Avonce Nelson, Sifrim Alejandro, Abdul-Rahman Omar A., van den Boogaard Marie-José H., Bottani Armand, Castori Marco, Cormier-Daire Valérie, Deardorff Matthew A., Filges Isabel, Fryer Alan, Fryns Jean-Pierre, Gana Simone, Garavelli Livia, Gillessen-Kaesbach Gabriele, Hall Bryan D., Horn Denise, Huylebroeck Danny, Klapecki Jakub, Krajewska-Walasek Malgorzata, Kuechler Alma, Lines Matthew A., Maas Saskia, Macdermot Kay D., McKee Shane, Magee Alex, de Man Stella A., Moreau Yves, Morice-Picard Fanny, Obersztyn Ewa, Pilch Jacek, Rosser Elizabeth, Shannon Nora, Stolte-Dijkstra Irene, van Dijck Patrick, Vilain Catheline, Vogels Annick, Wakeling Emma, Wieczorek Dagmar, Wilson Louise, Zuffardi Orsetta, van Kampen Antoine H. C., Devriendt Koenraad, Hennekam Raoul, Vermeesch Joris Robert Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome Nature genetics 2012;44 (4):445-U261 [PubMed]
  • Luyf Angela C. M., van Schaik Barbera D. C., de Vries Michel, Baas Frank, van Kampen Antoine H. C., Olabarriaga Silvia D. Initial steps towards a production platform for DNA sequence analysis on the grid BMC bioinformatics 2010;11 (1):598 [PubMed]
All Publications
Research programmes

Prof. PhD A.H.C. van Kampen (Medical Bioinformatics)

The Bioinformatics Laboratory is engaged in different types of research and support projects. The main research efforts comprise (a) Bioinformatics, (b) Systems Genomics, and (c) Systems Medicine  


 

Faculty
MEng PhD P.D. Moerland
PhD F.M. van der Kloet
B.D.C. van Schaik

Postdocs
PhD A. Jongejan
PhD M.L. Pras-Raves

PhD Students
MSc A. Nigam
MSc M. Soleimani

Others
MSc P.F.G. de Geest
A.C.M. Luyf