Matti Kankainen

Summary

Affiliation: University of Helsinki
Country: Finland

Publications

  1. pmc BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 13:33. 2012
  2. pmc Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae
    Laura Salusjärvi
    VTT, Technical Research Centre of Finland, P, O, Box 1000, FI 02044 VTT, Finland
    Microb Cell Fact 7:18. 2008
  3. pmc Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, P O Box 56, FIN 00014, Helsinki, Finland
    Proc Natl Acad Sci U S A 106:17193-8. 2009
  4. doi request reprint MPEA--metabolite pathway enrichment analysis
    Matti Kankainen
    VTT Technical Research Centre of Finland, Espooi, Finland
    Bioinformatics 27:1878-9. 2011
  5. pmc MATLIGN: a motif clustering, comparison and matching tool
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 8:189. 2007
  6. doi request reprint Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG
    Johanna Koponen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    J Proteomics 75:1357-74. 2012
  7. pmc POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 33:W427-31. 2005
  8. doi request reprint Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705
    Kirsi Savijoki
    Institute of Biotechnology, University of Helsinki, Finland
    J Proteome Res 10:3460-73. 2011
  9. doi request reprint Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium
    Kati Laakso
    Research and Development, Valio Ltd, Helsinki, Finland Department of Veterinary Biosciences Institute of Biotechnology Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
    Microb Biotechnol 4:746-66. 2011
  10. pmc POXO: a web-enabled tool series to discover transcription factor binding sites
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014 Helsinki, Finland
    Nucleic Acids Res 34:W534-40. 2006

Collaborators

Detail Information

Publications22

  1. pmc BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 13:33. 2012
    ..This problem has created a pressing need for improvements in homology-based annotation...
  2. pmc Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae
    Laura Salusjärvi
    VTT, Technical Research Centre of Finland, P, O, Box 1000, FI 02044 VTT, Finland
    Microb Cell Fact 7:18. 2008
    ..abstract:..
  3. pmc Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, P O Box 56, FIN 00014, Helsinki, Finland
    Proc Natl Acad Sci U S A 106:17193-8. 2009
    ..The presence of mucus-binding pili on the surface of a nonpathogenic Gram-positive bacterial strain reveals a previously undescribed mechanism for the interaction of selected probiotic lactobacilli with host tissues...
  4. doi request reprint MPEA--metabolite pathway enrichment analysis
    Matti Kankainen
    VTT Technical Research Centre of Finland, Espooi, Finland
    Bioinformatics 27:1878-9. 2011
    ....
  5. pmc MATLIGN: a motif clustering, comparison and matching tool
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 8:189. 2007
    ..Efficient post-processing, for example, reduces the redundancy of the motifs predicted and enables them to be annotated...
  6. doi request reprint Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG
    Johanna Koponen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    J Proteomics 75:1357-74. 2012
    ..rhamnosus GG proteins with ProQ Diamond 2-DE gel staining. Proteins participating in central cellular pathways were shown to be phosphorylated, and the phosphorylation of glycolytic enzymes was found to be especially extensive...
  7. pmc POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 33:W427-31. 2005
    ..The program is freely available at http://ekhidna.biocenter.helsinki.fi/poco...
  8. doi request reprint Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705
    Kirsi Savijoki
    Institute of Biotechnology, University of Helsinki, Finland
    J Proteome Res 10:3460-73. 2011
    ..The present study provides the most comprehensive catalog of the Lactobacillus proteins to date and holds great promise for the discovery of novel probiotic effector molecules...
  9. doi request reprint Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium
    Kati Laakso
    Research and Development, Valio Ltd, Helsinki, Finland Department of Veterinary Biosciences Institute of Biotechnology Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
    Microb Biotechnol 4:746-66. 2011
    ..rhamnosus GG has a highly flexible and adaptable metabolism and that the growth stage during which bacterial cells are harvested and consumed should be taken into consideration to gain the maximal benefit from probiotic bacteria...
  10. pmc POXO: a web-enabled tool series to discover transcription factor binding sites
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014 Helsinki, Finland
    Nucleic Acids Res 34:W534-40. 2006
    ..The performance of POXO is demonstrated by analysing expression data from pathogen treated Arabidopsis thaliana. In this example, POXO detected activated gene sets and suggested transcription factors responsible for their regulation...
  11. pmc Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana
    Matti Kankainen
    Institute of Biotechnology, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 34:e124. 2006
    ..Thus, in comparison to analyses of manually selected gene lists, the systematic analysis of every cluster can reveal unexpected biological phenomena and produce much more comprehensive biological insights to the experiment of interest...
  12. pmc Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG
    Kerttu Koskenniemi
    Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
    Mol Cell Proteomics 10:M110.002741. 2011
    ..The significance of these findings in terms of the functionality of a probiotic bacterium is discussed...
  13. pmc Genome sequence of Lactobacillus crispatus ST1
    Teija Ojala
    Division of Genetics, Department of Biosciences, P O Box 56, FIN 00014 University of Helsinki, Finland
    J Bacteriol 192:3547-8. 2010
    ..Here, we report the genome sequence of L. crispatus ST1, a chicken isolate displaying strong adherence to vaginal epithelial cells...
  14. doi request reprint LOCP--locating pilus operons in gram-positive bacteria
    Ilya Plyusnin
    Institute of Biotechnology, University of Helsinki, P O Box 56 Viikinkaari 5, FIN 00014 University of Helsinki, Finland
    Bioinformatics 25:1187-8. 2009
    ..Thus, the tool helps us to focus the laboratory research on genes behind this important and indicative feature, and to screen for strains containing them...
  15. pmc Probiotic Lactobacillus rhamnosus downregulates FCER1 and HRH4 expression in human mast cells
    Anna Oksaharju
    Wihuri Research Institute, Helsinki 00140, Finland
    World J Gastroenterol 17:750-9. 2011
    ..To investigate the effects of four probiotic bacteria and their combination on human mast cell gene expression using microarray analysis...
  16. pmc Mucosal adhesion properties of the probiotic Lactobacillus rhamnosus GG SpaCBA and SpaFED pilin subunits
    Ingemar von Ossowski
    Department of Veterinary Biosciences, Veterinary Microbiology and Epidemiology, P O Box 66, FIN 00014 University of Helsinki, Finland
    Appl Environ Microbiol 76:2049-57. 2010
    ....
  17. pmc Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli
    Riikka Kylväjä
    Division of General Microbiology, Department of Biosciences, University of Helsinki, Viikinkaari 9C, University of Helsinki, Finland
    BMC Microbiol 11:117. 2011
    ....
  18. pmc POBO, transcription factor binding site verification with bootstrapping
    Matti Kankainen
    Structural Genomics Group, Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 32:W222-9. 2004
    ..POBO is freely available from http://ekhidna.biocenter.helsinki.fi:9801/pobo...
  19. doi request reprint Proteome analysis of Lactobacillus rhamnosus GG using 2-D DIGE and mass spectrometry shows differential protein production in laboratory and industrial-type growth media
    Kerttu Koskenniemi
    Department of Basic Veterinary Sciences, University of Helsinki, Finland
    J Proteome Res 8:4993-5007. 2009
    ..The present study demonstrates the fundamental effects of culture conditions on the proteome of LGG, which are likely to affect the functionality and characteristics of its use as a probiotic...
  20. pmc Nonpathogenic Lactobacillus rhamnosus activates the inflammasome and antiviral responses in human macrophages
    Minja Miettinen
    Valio R and D, Helsinki, Finland
    Gut Microbes 3:510-22. 2012
    ..Our results indicate that nonpathogenic bacteria are able to activate the inflammasome. In addition, our results suggest that L. rhamnosus may prime the antiviral potential of human macrophages...
  21. doi request reprint Identification of regulatory elements in the AGT1 promoter of ale and lager strains of brewer's yeast
    Virve Vidgren
    VTT Technical Research Centre of Finland, PO Box 1000, FI 02044 VTT, Finland
    Yeast 28:579-94. 2011
    ..Both AGT1 promoters were repressed by glucose but their derepression was different, possibly due to a distinct distribution of Mig1 elements in these two promoters...
  22. pmc DANCER: a program for digital anatomical reconstruction of gene expression data
    Matti Kankainen
    Laboratory of Functional Genomics and Bioinformatics, Department of Neurobiology, A I Virtanen Institute for Molecular Sciences, University of Kuopio, PO Box 1627, FIN 70211, Kuopio, Finland
    Nucleic Acids Res 31:e132. 2003
    ..This program should help to provide visualization and interpretation of data derived from gene expression experiments. DANCER may be freely downloaded...