News

 Esther and Jan's paper on cacao fermentations published...

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Our paper describing how the kinetics of gene regulation affect the lag phase appeared in PLoS Biology....

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 Stijn Mertens was awarded the annual MSc thesis prize of the Royal Society of Brewing Schools....

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Tools

Tools and Data constructed by our lab:

  • SERV - "Sequence-Based Estimation of Repeat Variability". A tool to find tandem repeats in DNA sequences and estimate the variability of each repeat found. The higher the VARscore, the higher the estimated variability. Sequences with VARscores above 1 are usually polymorphic between species/strains.

For more information, see: Legendre, M., Pochet, N., Pak, T. and Verstrepen, K.J. (2007). Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research. PDF file.

  • Searchable Databases containing all tandem repeats located within genes and/or promoters of the following organisms: S. cerevisiae, A. thaliana, O. sativa, A. fumigatus.
  • PDF File containing all S. cerevisiae Open Reading Frames (ORFs) containing "non-fuzzy" internal tandem repeats. Reference: Verstrepen et al., Nature Genetics 37: 986-990 (2005). PDF file of this paper.

 

Protocols:

  • High-yield total RNA isolation from S. cerevisiae. (download PDF)
  • A simple yet efficient protocol for yeast transformation.  Works fine with industrial strains as well. (download PDF)
  • Quick genomic prep from yeast.  This prep yields semi-pure gDNA, perfect for diagnostic PCR. (download PDF)
  • RNA prep from yeast cells using the ABI6100 Nucleoprep machine. (download PDF)

 

Links:

  • Dot Plots - find repeats in a DNA sequence, or duplicated areas in two sequences.
  • Compare Two Excel Lists - handy program developed by the Whitehead Institute’s BARC team to compare two excel columns and find which elements are common and unique to each list.
  • OSPREY - automated visualization of gene/protein interaction networks.