Affiliation: University of Nijmegen
Country: The Netherlands
- The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene contentJos 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...
- Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residuesRoland 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...
- The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environmentJos 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...
- Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteriaJos 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...
- Visualization for genomics: the Microbial Genome ViewerRobert 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..
- Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifsJos Boekhorst
Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, The Netherlands
J Bacteriol 187:4928-34. 2005....
- Complete genome sequence of Lactobacillus plantarum WCFS1Michiel 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...
- Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant nicheRoland 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...
- Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteriaRoland Siezen
Wageningen Centre for Food Sciences WCFS, Wageningen, The Netherlands
BMC Genomics 7:126. 2006....
- Identification of homologs in insignificant blast hits by exploiting extrinsic gene propertiesJos 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...
- LocateP: genome-scale subcellular-location predictor for bacterial proteinsMiaomiao 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...