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2002-2006 Ph.D. position at the University of Groningen.

During my PhD project, I had two main research lines. One involved a large project funded by IOP Senter called 'Comparative and predictive transcriptomics of Gram-positive bacteria for enhanced food functionality, quality and safety'. The goal of this project was to generate predictive knowledge on the regulatory gene networks and metabolic pathways of four fully-sequenced, well-characterized, food relevant and evolutionarily related Gram-positive bacteria. The work resulted in several publications listed below

  1. Kok J*, Buist G, Zomer AL, van Hijum SA, Kuipers OP.; Comparative and functional genomics of lactococci.; FEMS Microbiol Rev. 2005 Jun 2; FEMS Microbiol Rev. 2005 Aug;29(3):411-33.
  2. Zomer AL*, Buist G, Larsen R, Kok J, Kuipers OP.; Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363; J Bacteriol. 2007 Feb;189(4):1366-81.
  3. Martínez B*, Zomer AL*, Rodríguez A, Kok J, Kuipers OP.; Cell envelope stress induced by the bacteriocin Lcn972 is sensed by the lactococcal two component system CesSR. Molecular Microbiology; 2007 Apr;64(2):473-86.
  4. Zomer AL*; Adaptation of Lactococcus lactis to its environment : a genomics approach: http://irs.ub.rug.nl/ppn/304591076

Additionally I was involved in sequencing, assembling and annotating the genome of Lactococcus lactis MG1363, the lactococcal strain most intensively studied throughout the world and one of the main model organisms for lactic acid bacteria. To facilitate assembly several bioinformatics tools where developed and the genome was published.

  1. van Hijum SA, Zomer AL, Kuipers OP, Kok J.; Projector: automatic contig mapping for gap closure purposes.; Nucleic Acids Res. 2003 Nov 15;31(22):e144.
  2. van Hijum SA, Zomer AL, Kuipers OP, Kok J.; Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.; Nucleic Acids Res. 2005 Jul 1;33:W560-W566
  3. Wegmann U*, O'Connell-Motherway M*, Zomer A*, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP, van Sinderen D, Kok J.; The complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363; J Bacteriol. 2007 Apr;189(8):3256-70.
  4. Ventura M, Zomer A, Canchaya C, O'Connell-Motherway M, Kuipers O, Turroni F, Ribbera A, Foroni E, Buist G, Wegmann U, Shearman C, Gasson MJ, Fitzgerald GF, Kok J, van Sinderen D.  Comparative Analyses of Prophage-Like Elements Present in Two Lactococcus lactis Strains. Appl Environ Microbiol. 2007 Dec;73(23):7771-80.

Other duties included maintaining the microarray facility at the Molecular Genetics Group, designing  and spotting microarrays, supervision of students and setting up Bioinformatics courses. Some of the work was published (see below).

  1. Kuipers OP*, de Jong A, Baerends RJ, van Hijum SA, Zomer AL, Karsens HA, den Hengst CD, Kramer NE, Buist G, Kok J.; Transcriptome analysis and related databases of Lactococcus lactis.; Antonie Van Leeuwenhoek. 2002 Aug;82(1-4):113-22.
  2. van Hijum SA*, Baerends RJ, Zomer AL, Karsens HA, Martin-Requena V, Trelles O, Kok J, Kuipers OP. Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons. BMC Bioinformatics. 2008 Feb 11;9:93.

 

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