Bioinformatics |
Computational methods are becoming an absolute requirement in the analysis of data in biology. Ongoing advances in high-throughput methods (DNA sequencing, microarray, mass spectrometry, ...) enable novel approaches also in the study of pathogens. The bioinformatic group at SwissTPH assists research groups in the design of experiments and the data analysis. Applied methods are predominantly based on state-of-the-art open source programs developed by the scientific community for the UNIX/linux computer operating system. Established approaches are supplemented by customized programs in perl, and by data analysis in the R environment.
The bioinformatic group furthermore coordinates activities in the -omics workgroup at SwissTPH, and participates in teaching of bioinformatic courses at the University of Basel. The group is currently involved in genome (re-)sequencing projects of genomes of:
- Parasitic worms (P. Mäser)
- Plasmodium as causative agent of malaria (H-P Beck)
- Neisseria bacteria causing meningitis (G. Pluschke)
and further contributes to the analysis of gene expression in Plasmodium (T. Voss).
The bioinformatics group has a leading role in the data analysis in investigation of a potential effect of EMF on epigenetic modifications (EU FP7 ARIMMORA). Finally the group directs projects to investigate epigenetic DNA methylation in prokaryotic pathogens.
Selected publications
Gaida A, Becker MM, Schmid CD, Bühlmann T, Louis EJ, and Beck H-P (2011) Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR). PLoS ONE 6, e17782. PM:21408186
Szalkowski AM, and Schmid CD (2010) Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts. Briefings in Bioinformatics 12, 626-633. PM:21059603
Schmid CD, and Bucher P (2010) MER41 repeat sequences contain inducible STAT1 binding sites. PLoS ONE 5, e11425. PM:20625510
Schmid CD, and Bucher P (2007) ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters. Cell 131, 831-832. PM:18045524
Schmid CD, Praz V, Delorenzi M, Perier R, and Bucher P (2004) The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res 32, D82-D85. PM:14681364