1994 …2020
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Personal profile

Description of research and teaching

Our research is focused on molecular biology and functional genomics of non-pathogenic (dairy starters, probiotic lactobacilli, propionibacteria) and pathogenic bacteria (streptococci, staphylococci) that are adapted to food-environment.

We exploit gene and omics-level approaches combined with microbiological and biochemical analyses to study cell-physiology in beneficial and pathogenic bacteria in diverse food systems and materials. The ultimate goal of these research projects is to provide novel information to gain maximal benefit of beneficial bacteria as well as to combat pathogens in foods.

Keywords

  • 416 Food Science
  • 412 Animal science, dairy science
  • 1183 Plant biology, microbiology, virology
  • 1182 Biochemistry, cell and molecular biology

International and National Collaboration Publications and projects within past five years.

Publications 1994 2018

  • 57 Article
  • 3 Conference contribution
  • 2 Chapter
  • 1 Doctoral Thesis

De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

Deptula, P., Laine, P. K., Roberts, R. J., Smolander, O-P., Vihinen, H., Piironen, V., Paulin, L., Jokitalo, E., Savijoki, K., Auvinen, P. & Varmanen, P., 16 Oct 2017, In : BMC Genomics. 18, 24 p., 790.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Uncovering Surface-Exposed Antigens of Lactobacillus rhamnosus by Cell Shaving Proteomics and Two-Dimensional Immunoblotting

Espino, E., Koskenniemi, K., Mato Rodriguez, L., Nyman, T., Reunanen, J., Koponen, J., Öhman, T. J., Siljamäki, P., Alatossava, T., Varmanen, P. K. & Savijoki, K., 2015, In : Journal of Proteome Research. 14, 2, p. 1010-1024 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains

Savijoki, K., Iivanainen, A., Siljamaki, P., Laine, P. K., Paulin, L., Karonen (os. Miettinen), T., Pyörälä, S., Kankainen, M., Nyman, T. A., Salomaki, T., Koskinen, P., Holm, L., Simojoki, H., Taponen, S., Sukura, A., Kalkkinen, N., Auvinen, P. & Varmanen, P., Aug 2014, In : Journal of Proteome Research. 13, 8, p. 3748-3762 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG

Koskenniemi, K., Laakso, K., Koponen, J., Kankainen, M., Greco, D., Auvinen, P., Savijoki, K., Nyman, T., Surakka, A., Salusjärvi, T., de Vos, W. M., Tynkkynen, S., Kalkkinen, N. & Varmanen, P. K., 2011, In : Molecular & Cellular Proteomics. 10, 2, 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Projects 2004 2020

Activities 2002 2018

Review of PhD-thesis

Pekka Varmanen (Pre-examiner)
2018

Activity: Examination typesMember of doctoral thesis committee / follow-up group

12th International Symposium on Lactic Acid Bacteria

Pekka Varmanen (Poster Presentation)
27 Aug 201731 Aug 2017

Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

Review of a research project -proposals

Pekka Varmanen (Participant)
2017

Activity: Other activity typesOther

Microbial biofilms: environmental, pharmaceutical, medical & industrial research in Finland

Pekka Varmanen (Speaker: Presenter)
26 Jan 2016

Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

Review of a research project -proposals

Pekka Varmanen (Participant)
2016

Activity: Other activity typesTypes for other activities - Other