(Logo)   IMADA
University of Southern Denmark IMADA - Department of Mathematics and Computer Science

   
Fiona Nielsen
PhD student, Bioinformatics

Schedule spring 2007



  Monday Tuesday Wednesday Thursday Friday
8-9          
9-10     Group meeting Henk
Molecular Biology
8:45-12:30
Introduction to Pattern Recognition
 
10-11        
11-12        
12-13        
13-14   Group meeting Martijn
CMBI
     
14-15          
15-16          
16-17          
17-18          

Current Projects

  • A new algorithm for designing oligonucleotide microarrays for ChIP-on-chip
  • Quality control, signal-to-noise measurement in ChIP-on-chip data
  • A genome-wide low noise high coverage oligonucleotide array for mouse
  • A simultaneous alignment and clustering algorithm for microarray hybridisation signals
  • Statistical tests for distributions of ChIP-on-chip detected genomic locations

Pending Projects

  • Quantitation for MeDIP-chip
  • Peak detection in ChIP-on-chip data
  • Oligonucleotide array design for genome-wide CGH
  • Comparative genomics of sequence uniqueness properties

Previous Projects

Protein Secondary Structure Prediction

Reports

BK41 simulation of biological processes: Calcium activation of the transcription factor NFAT
Analysis of Large Datasets in Genomics and Proteomics: The Gibbs sampling algorithm for motif finding

Travel plans

  • February 14 to 16, EUCOMM course at the Welcome Trust conference centre in Hinxton, UK.
  • March 9 to 18, vacation, Norway
  • March 28 to April 1, CSHL conference on systems biology, New York
  • April 2 to 8, vacation, New York
  • June 29 to July 19, vacation, Denmark and Canada
  • July 20 to July 25, ISMB/ECCB conference, Austria
  • August 25 to September 3, vacation

Contacts and Collaborators

Lene Monrad Favrholdt
Joan Boyar
Susanne Mandrup
Stefan Graef
Paul Flicek
Werner Vach

Students

Maarten Kooyman

Supervisors

Henk Stunnenberg
Martijn Huynen