Online material for probe design related studies

This site contains supplementary information and data sets from research publications by the Systems biology of gene expression group at CBS.

Thermodynamic probe intensity correction for oligonucleotide microarrays
Georg M. Bruun , Rasmus Wernersson, Agnieszka S. Juncker , Hanni Willenbrock and Henrik Bjørn Nielsen
Nucleic Acids Res. 2007 (Mar 2)

Array design:
Excel-file describing the naming convension and the selection criteria used in OligoWiz 2: NimbleGenArray_final.xls
Cross-reference table mapping descriptive names to the CDF probe names:
CDF-file: RWSCER01a530205N

Raw data:
CEL-file: CCY-15_T030.CEL

Processed data:
Combined information (probeid, probe description, DNA sequence, DNA annotation, raw intensity, corrected intensity):

Software implementation:
TAR archive containing a C implementation of the model: PD_final.tgz (For UNIX like systems). Please see the "README" file for further instructions.

An implementation as an R package is currently being developed.

Probe selection for DNA microarrays using OligoWiz
Rasmus Wernersson, Agnieszka S Juncker and Henrik Bjørn Nielsen
Nature Protocols (2007) vol. 2, no. 11, p. 2677-91

OligoWiz 2.0 - integrating sequence feature annotation into design of microarray probes
Rasmus Wernersson and Henrik Bjørn Nielsen.
Nucleic Acids Research, 2005, Vol. 33, Web Server issue W611-W615

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.
Henrik Bjørn Nielsen, Rasmus Wernersson and Steen Knudsen.
Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496


H. Bjørn Nielsen,