Fiona Nielsen
PhD student, Bioinformatics

Schedule autumn 2008

  Monday Tuesday Wednesday Thursday Friday
9-10     Lab meeting
Molecular Biology
GIPcatch meeting   
12-13   Group meeting

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
  • Probe selection for FISH quantitation of bacterial species w. Francisca Luesken and Bas Dutilh
  • Epigenetics of Mouse embryonic stem cells w. Hendrik Marks

Pending Projects

  • Comparative genomics of sequence uniqueness properties
  • Statistical noise estimation in ChIP data w. Lene Favrholdt

Previous Projects

  • PinkThing Statistical tests for distributions of ChIP-on-chip detected genomic locations w. Maarten Kooyman
  • Sequence Prediction Evaluator Segment comparison statistics w. Kristian K Nielsen and Lene Favrholdt

Protein Secondary Structure Prediction


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

Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, Nijman IJ, Koster J, Santo EE, Welboren W, Versteeg R, Cuppen E, van de Wetering M, Clevers H, Stunnenberg HG. Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. Mol Cell Biol. 2008 Apr;28(8):2732-44. Epub 2008 Feb 11.


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

  • October 6-8, HEROIC annual meeting, Vienna
  • October 29-November 2, RECOMB regulatory genomics, Boston
  • November 20-25, vacation, Manchester
  • December 15-16, Benelux Bioinformatics Conference, Maastricht, Netherlands

Contacts and Collaborators

Lene Monrad Favrholdt
Joan Boyar
Susanne Mandrup
Stefan Graef
Paul Flicek
Werner Vach
Rune Møllegaard Friborg, University of Copenhagen
Brian Vinter, University of Copenhagen
Francisca Luesken, Department of Microbiology, Nijmegen
Ulrike Jacobi, Molecular Biology, Nijmegen
Gert Jan Veenstra, Molecular Biology, Nijmegen


Maarten Kooyman, see also the PinkThing
Kasper Markus
Moniek Riemersma

GiPCATCH team: Mark Zandstra, Berry Lijklema, Julius Mucke, Richard Willems, Daan Pijper
Jens Kristian Kræmmer Nielsen


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


Henk Stunnenberg, Molecular Biology
Martijn Huynen, Centre for Molecular and Biomolecular Informatics (CMBI)