Barbera D. C. van Schaik  |  Bioinformatician

Bioinformatics Laboratory – Epidemiology and Data Science

Location AMC | Room J1b-218-1 | PO box 22660, 1100 DD Amsterdam

T: +31 20 566 68 80  |  E: b.d.vanschaik [at] amsterdamumc.nl

Absent: Friday

www.amsterdamumc.nl  | www.amc.nl | bioinformatics.amc.nl

I’m broadly interested in DNA research and techniques that aid the analysis, and enjoy teaching these topics to students and other researchers. I have worked on topics ranging from transcriptomics and alternative splicing to virus discovery, comparing bacterial genomes, and searching for variants in whole exome data. Currently I work in the field of immunogenomics.

Projects

  • Immunogenomics
    • Analysis pipeline for adaptive immune receptor repertoire sequencing (AIRRseq) data (current)
    • Quality control methods for AIRR sequencing data
    • Reconstruction of B cell lineages
    • Discovery of invariant T cells
  • e-Science
    • Optimization of sequence alignment on a grid infrastructure
    • Porting the GoNL analysis pipeline to the Dutch life science grid
    • Grid-based BLAST gateway
  • Exome and whole genome sequencing
  • Assembly and comparison of bacterial genomes
    • Pneumococcal meningitis
  • Alternative splicing
    • Identification of alternative exon use
  • Virus discovery
    • VIDISCA-454 sequence analysis
  • Human transcriptome map
    • Discovery of high and low expressed regions of the genome
  • USAGE – Gene expression analysis on SAGE data
    • Addition of statistical methods to the USAGE application

Profile on networks

Personal stuff

In my spare time I go to concerts and festivals, cook (all cuisines), grow vegetables in my garden and make things (sewing, electronics, laser cutting, welding, 3d-printing, a house). Occasionally, I write about my hobbies and I maintain a database with Indonesian recipes: http://rabarbera.nl/