Jos Boekhorst

Summary

Affiliation: University of Nijmegen
Country: The Netherlands

Publications

  1. ncbi The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content
    Jos Boekhorst
    Center for Molecular and Biomolecular Informatics, 6525ED, Nijmegen, The Netherlands
    Microbiology 150:3601-11. 2004
  2. ncbi Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues
    Roland J Siezen
    Center for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands
    Proteins 67:681-94. 2007
  3. ncbi The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment
    Jos Boekhorst
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Microbiology 152:3175-83. 2006
  4. ncbi Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria
    Jos Boekhorst
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, 6525ED, Nijmegen, The Netherlands
    Microbiology 152:273-80. 2006
  5. ncbi Visualization for genomics: the Microbial Genome Viewer
    Robert Kerkhoven
    Centre for Molecular and Biomolecular Informatics, University of Nijmegen, P O Box 9010, 6500 GL Nijmegen, The Netherlands
    Bioinformatics 20:1812-4. 2004
  6. ncbi Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs
    Jos Boekhorst
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, The Netherlands
    J Bacteriol 187:4928-34. 2005
  7. ncbi Complete genome sequence of Lactobacillus plantarum WCFS1
    Michiel Kleerebezem
    Wageningen Centre for Food Sciences, P O Box 557, 6700 AN Wageningen, The Netherlands
    Proc Natl Acad Sci U S A 100:1990-5. 2003
  8. ncbi Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche
    Roland J Siezen
    NIZO Food Research, P O Box 20, 6710 BA Ede, The Netherlands
    Appl Environ Microbiol 74:424-36. 2008
  9. ncbi Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria
    Roland Siezen
    Wageningen Centre for Food Sciences WCFS, Wageningen, The Netherlands
    BMC Genomics 7:126. 2006
  10. ncbi Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
    Jos Boekhorst
    Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, The Netherlands
    BMC Bioinformatics 8:356. 2007

Detail Information

Publications11

  1. ncbi The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content
    Jos Boekhorst
    Center for Molecular and Biomolecular Informatics, 6525ED, Nijmegen, The Netherlands
    Microbiology 150:3601-11. 2004
    ..The differences between L. plantarum and L. johnsonii, both in genome organization and gene content, are exceptionally large for two bacteria of the same genus, emphasizing the difficulty in taxonomic classification of lactobacilli...
  2. ncbi Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues
    Roland J Siezen
    Center for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands
    Proteins 67:681-94. 2007
    ..Over 100 proteins were predicted to be subtilases for the first time by our improved searching methods, thereby improving genome annotation...
  3. ncbi The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment
    Jos Boekhorst
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Microbiology 152:3175-83. 2006
    ..cmbi.ru.nl/secretome which could serve as a basis for targeted experimental studies into the function of extracellular proteins...
  4. ncbi Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria
    Jos Boekhorst
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, 6525ED, Nijmegen, The Netherlands
    Microbiology 152:273-80. 2006
    ..These findings strongly suggest that the MUB domain is an LAB-specific functional unit that performs its task in various domain contexts and could fulfil an important role in host-microbe interactions in the gastrointestinal tract...
  5. ncbi Visualization for genomics: the Microbial Genome Viewer
    Robert Kerkhoven
    Centre for Molecular and Biomolecular Informatics, University of Nijmegen, P O Box 9010, 6500 GL Nijmegen, The Netherlands
    Bioinformatics 20:1812-4. 2004
    ..Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. AVAILABILITY: The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV..
  6. ncbi Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs
    Jos Boekhorst
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, The Netherlands
    J Bacteriol 187:4928-34. 2005
    ....
  7. ncbi Complete genome sequence of Lactobacillus plantarum WCFS1
    Michiel Kleerebezem
    Wageningen Centre for Food Sciences, P O Box 557, 6700 AN Wageningen, The Netherlands
    Proc Natl Acad Sci U S A 100:1990-5. 2003
    ..These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome...
  8. ncbi Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche
    Roland J Siezen
    NIZO Food Research, P O Box 20, 6710 BA Ede, The Netherlands
    Appl Environ Microbiol 74:424-36. 2008
    ..Many of these genes were identified for the first time in Lactococcus lactis. In most cases good correspondence was found with the phenotypic characteristics of these two strains...
  9. ncbi Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria
    Roland Siezen
    Wageningen Centre for Food Sciences WCFS, Wageningen, The Netherlands
    BMC Genomics 7:126. 2006
    ....
  10. ncbi Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties
    Jos Boekhorst
    Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, The Netherlands
    BMC Bioinformatics 8:356. 2007
    ..However additional improvement could be made by exploiting sources of genomic information other than the primary sequence or tertiary structure...
  11. ncbi LocateP: genome-scale subcellular-location predictor for bacterial proteins
    Miaomiao Zhou
    Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
    BMC Bioinformatics 9:173. 2008
    ..As accurate and detailed SCL prediction on a genome scale is highly desired by experimental researchers, we decided to construct a new SCL prediction pipeline: LocateP...