Utrecht University > Biology > Bioinformatics > Group members > Jos Boekhorst

Personalia

Jos Boekhorst
Name Jos Boekhorst
Position Postdoc
Research topics Comparative Phosphoproteomics
Evolutionary Systemsbiology
Affiliations Bioinformatics group, Utrecht University
Address Padualaan 8
3584 CH Utrecht
the Netherlands
Location Room Z532
Phone +31 30 253 3004
Fax +31 30 251 3655
Email J.Boekhorst(at)uu(dot)nl

Research

I am currently working on the comparative analysis of phosphoproteomics data. The reversible phosphorylation of proteins plays a crucial in eukaryotic cells. Processes ranging from protein complex formation to enzyme activity and regulatory cascades are controlled through addition of phosphate groups. Investigating the tens of thousands phosphorylation events in e.g. human cells has proven challenging. Although recent advances in high-throughput (HTP) mass spectrometry (MS) experiments have lead to a dramatic increase in the amount of phosphorylation data available, the biological role of most of these sites is unclear. Determining the phenotypic effect of a phosphorylation event, for example through mutating a residue to a residue that cannot be phosphorylated, is a laborious process. I am developing methods for extracting biological insight through the comparative analysis of phosphoproteomics data.

I am also involved in two projects that utilize next-generation sequencing strategies to analyze closely related strains of bacteria and identify genomic features underlying phenotypic diversity.

Education

Please contact me if you wish to receive a copy of my CV.

Publications

Fokkens L, Botelho S. M., Boekhorst J, Snel B. (2010) Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. BMC Bioinformatics  
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.  
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  
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.  
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 link to manuscript
Zhou, M., Boekhorst, J., Francke, C. & Siezen, R. J.(2008). LocateP: Genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 9, 173.
 
Boekhorst, J. & Snel, B. (2007). Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics 8, 356.
link to manuscript
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., Renckens, B. & Boekhorst, J. (2007). Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues. Proteins 67(3):681-94.  
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
Siezen, R. J., Boekhorst, J., Muscariello, L., Molenaar, D., Renckens, B. & Kleerebezem, M. (2006). Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. BMC Genomics 7, 126.  
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.  
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
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.  
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.  
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.  
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.  
my publications in Pubmed: "Boekhorst+J"[Author]
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