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University of Southern Denmark IMADA - Department of Mathematics and Computer Science

   
Fiona Nielsen
PhD student, Bioinformatics

Schedule autumn 2007



  Monday Tuesday Wednesday Thursday Friday
8-9          
9-10     Group meeting Henk
Molecular Biology
   
10-11      8:45-12:30
Machine Learning
   
11-12        
12-13   Group meeting Martijn
CMBI COMICS 
   
13-14          
14-15          
15-16          
16-17          
17-18          

Current Projects

  • Quality control, signal-to-noise measurement in ChIP-on-chip data w. Werner Vach
  • A genome-wide low noise high coverage oligonucleotide array for mouse w. Stefan Graef
  • A simultaneous alignment and clustering algorithm for microarray hybridisation signals w. Lene Favrholdt
  • Statistical tests for distributions of ChIP-on-chip detected genomic locations w. Maarten Kooyman

Pending Projects

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

Previous Projects

Protein Secondary Structure Prediction

Publications

Graef S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P. Optimized design and assessment of whole genome tiling arrays Bioinformatics. 2007 Jul 1;23(13):i195-204

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

  • no current travel plans

Contacts and Collaborators

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

Students

Maarten Kooyman

Others

Yes, I will help debug your scripts if: 1) I have time 2) you bring chocolate.

Supervisors

Henk Stunnenberg
Martijn Huynen

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