Explore

Jos Boekhorst

share this page
Jos Boekhorst
get in touch
I started my career in bioinformatics with the annotation and comparative analysis of bacterial genome sequences. My PhD research showed me the power of bioinformatics: it allows scientists to generate new insights from high-throughput biological data, and provides powerful tools for generating leads for experimental validation. NIZO food research employs excellent experimental scientists, and the combination of their expertise with bioinformatics techniques is particularly powerful, as it enables me to work with exiting new data produced through cutting-edge experimental techniques.
I am working on a wide variety of topics, ranging from the analysis of bacterial genome sequences to the determination of the composition of complex microbial communities. These projects all have in common that I work together with experts from the field to increase the value of products of NIZO customers.

Keywords: genome annotation, comparative genomics, integrative bioinformatics, evolutionary systemsbiology, (comparative) proteomics, microbial community composition, phylogenomics 

 My LinkedIn profile: http://www.linkedin.com/in/josboekhorst 

 Publications in peer-reviewed scientific journals:

Bart M.J., van Gent M., van der Heide H.G.J., Boekhorst J., Hermans P., Parkhill J., Mooi F.R. (2010) Comparative genomics of prevaccination and modern Bordetella pertussis strains. BMC Genomics 11:627  
Boekhorst, J., van Breukelen, B., Heck, A. J. R. & Snel, B. (2008). Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biology 9:R144 link to manuscript
Boekhorst, J. & Snel, B. (2007). Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics 8, 356. link to manuscript
Boekhorst, J., Wels, M., Kleerebezem, M. & Siezen, R. J. (2006). The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology 152, 3175-3183. link to manuscript
Boekhorst, J., Helmer, Q., Kleerebezem, M. & Siezen, R. J. (2006). Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria. Microbiology 152, 273-280. link to manuscript
Boekhorst, J., de Been, M. W., Kleerebezem, M. & Siezen, R. J. (2005). Genome-Wide Detection and Analysis of Cell Wall-Bound Proteins with LPxTG-Like Sorting Motifs. J Bacteriol 187, 4928-4934. link to manuscript
Boekhorst, J., Siezen, R. J., Zwahlen, M. C., Vilanova, D., Pridmore, R. D., Mercenier, A., Kleerebezem, M., de Vos, W. M., Brussow, H. & Desiere, F. (2004). The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology 150, 3601-3611. link to manuscript

Boersema, P.J., Foong, L.Y., Ding, V.M., Lemeer. S, van Breukelen, B., Philp, R., Boekhorst, J., Snel, B., den Hertog, J., Choo, A.B., Heck, A.J. (2009). In depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immuno-affinity purification and stable isotope dimethyl labeling. Molecular and Cellular Proteomics.

  

Booijink C.C.G.M., Boekhorst J., Zoetendal E.G., Smidt H., Kleerebezem M., de Vos W.M. (2010). Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Applied and Environmental Microbiology.

  

Ding VM, Boersema PJ, Foong LY, Preisinger C, Koh G, Natarajan S, Lee DY, Boekhorst J, Snel B, Lemeer S, Heck AJ, Choo A. (2011). Tyrosine phosphorylation profiling in fgf-2 stimulated human embryonic stem cells. PLoS One 17;6(3):e17538.

  

Fokkens L., Botelho S.M., Boekhorst J., Snel B. (2010). Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. BMC Bioinformatics 11:86

  

Gross, G., Snel, J., Boekhorst, J., Smits, M. A. & Kleerebezem, M. (2009). Biodiversity of mannose-specific adhesion in Lactobacillus plantarum revisited: strain-specific domain composition of the mannose-adhesin. Beneficial Microbes.

  
Kerkhoven, R., van Enckevort, F. H., Boekhorst, J., Molenaar, D. & Siezen, R. J. (2004). Visualization for genomics: the Microbial Genome Viewer. Bioinformatics 20, 1812-1814.  
Kim, Y. H., Kapfer, D. M., Boekhorst, J., Lubsen, N. H., Bachinger, H. P., Shearer, T. R., David, L. L., Feix, J. B. & Lampi, K. J. (2002). Deamidation, but not truncation, decreases the urea stability of a lens structural protein, betaB1-crystallin. Biochemistry 41, 14076-14084.  
Kleerebezem, M., Boekhorst, J., van Kranenburg, R., Molenaar, D., Kuipers, O. P., Leer, R., Tarchini, R., Peters, S. A., Sandbrink, H. M., Fiers, M. W., Stiekema, W., Lankhorst, R. M., Bron, P. A., Hoffer, S. M., Groot, M. N., Kerkhoven, R., de Vries, M., Ursing, B., de Vos, W. M. & Siezen, R. J. (2003). Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A 100, 1990-1995.  
van Schaik W., Top J., Riley D.R., Boekhorst J., Vrijenhoek J.E., Schapendonk C.M., Hendrickx A.P., Nijman I.J., Bonten M.J., Tettelin H., Willems R.J. (2010).Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island BMC genomics 11:239.  
Siezen, R. J., Starrenburg, M. J., Boekhorst, J., Renckens, B., Molenaar, D. & van Hylckama Vlieg, J. E. (2007). Genome-scale genotype-phenotype matching of two Lactococcus lactis plant isolates identifies adaptation mechanisms to the plant niche. Appl Environ Microbiol.  
Siezen, R. J., Boekhorst, J., Muscariello, L., Molenaar, D., Renckens, B. & Kleerebezem, M. (2006a). Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics 7, 126.  
Siezen, R. J., Renckens, B. & Boekhorst, J. (2007). Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues. Proteins 67(3):681-94.  
Smid, E. J., van Enckevort, F. J., Wegkamp, A., Boekhorst, J., Molenaar, D., Hugenholtz, J., Siezen, R. J. & Teusink, B. (2005). Metabolic models for rational improvement of lactic acid bacteria as cell factories. J Appl Microbiol 98, 1326-1331.  
van Kranenburg, R., Kleerebezem, M., van Hylckama Vlieg, J., Ursing, B., Boekhorst, J., Ayad, E., Smit, G. & Siezen, R. (2002). Flavour formation from amino acids by lactic acid bacteria: predictions from genome sequence analysis. International Dairy Journal 12, 111-121.  
Wels M, Bongers RS, Boekhorst J, Molenaar D, Sturme M, de Vos WM, Siezen RJ, Kleerebezem M. (2009). Large Intergenic Cruciform-like Supermotifs in the Lactobacillus plantarum Genome. J Bacteriol  
Zhou, M., Boekhorst, J., Francke, C. & Siezen, R. J.(2008). LocateP: Genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 9, 173.

Explore

Connect

Co-create