Research Output per year
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
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 journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-review
BluB/CobT2 fusion enzyme activity reveals mechanisms responsible for production of active form of vitamin B 12 by Propionibacterium freudenreichii
Deptula, P., Kylli, P. T., Chamlagain, B. S., Holm, L. U. T., Kostiainen, R. K., Piironen, V. I., Savijoki, K. K. & Varmanen, P. K., 23 Nov 2015, In : Microbial Cell Factories. 14, 12 p., 186 .Research output: Contribution to journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-review
Projects 2004 2020
BIOB12: Vitamin B12-bioenriched wheat bran ingredients for food applications (BIOB12)
Piironen, V. I., Chamlagain, B. S., Edelmann, J. M., Varmanen, P. K. & Katina, K. K.
01/07/2018 → 30/06/2019
Project: Research project › _Research
Utaretulehdus ja antibioottiresistenssi − mikä on kalvovesikkeleiden rooli?
Siljamäki, P. M., Savijoki, K. K., Varmanen, P. K., Taponen, S. S. & Nyman, T.
01/05/2018 → 31/12/2020
Project: Research project › Laboratory operations
Bugsy: Leikkausalueen patogeenien tunnistus metagenomiikan menetelmiä hyödyntäen (Bugsy)
Kankainen, M. J., Holm, L. U. T., Kankuri, E. M., Varmanen, P. K., Savijoki, K. K., Ojala-Kankainen, T. A., Medlar, A. J. & Vuola, J. A.
01/09/2015 → 31/08/2019
Project: Research project
BIOFORCE: Bio-enriched bran ingredients - in situ synthesis of vitamin B12 and folate with propionibacteria and lactic acid bacteria
Piironen, V. I., Varmanen, P. K., Chamlagain, B. S., Edelmann, J. M. & Katina, K. K.
01/03/2017 → 31/03/2018
Project: Research project
Contribution of cereal-based fermented foods to Folate intake in European and African countries FolEA
Kariluoto, M. S., Piironen, V. I., Freese, R. I., Saris, P. E. J. & Varmanen, P. K.
01/09/2014 → 31/08/2017
Project: Research project
Activities 2002 2018
Review of PhD-thesis
Pekka Varmanen (Pre-examiner)2018
Activity: Examination types › Member of doctoral thesis committee / follow-up group
Review of a research project -proposals
Pekka Varmanen (Participant)2017
Activity: Other activity types › Other
12th International Symposium on Lactic Acid Bacteria
Pekka Varmanen (Poster Presentation)27 Aug 2017 → 31 Aug 2017
Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
Microbial biofilms: environmental, pharmaceutical, medical & industrial research in Finland
Pekka Varmanen (Speaker: Presenter)26 Jan 2016
Activity: Participating in or organising an event types › Organisation and participation in conferences, workshops, courses, seminars
Review of a research project -proposals
Pekka Varmanen (Participant)2016
Activity: Other activity types › Types for other activities - Other
Press / Media
A novel bacterial species named after the Finnish Nobelist A.I. Virtanen
Paulina Deptula, Pekka Kristian Varmanen, Petri Olli Viljami Auvinen & Vieno Irene Piironen
30/08/2018
1 media contribution
Press/Media: Press / Media
Fermentointi tuottaa leipään B-vitamiinia
Vieno Irene Piironen & Pekka Kristian Varmanen
12/01/2017
1 media contribution
Press/Media: Press / Media
Tutkijat kehittivät tavan tuottaa tärkeää B12-vitamiinia – ilouutinen kasvissyöjille
Vieno Irene Piironen & Pekka Kristian Varmanen
10/01/2017
1 media contribution
Press/Media: Press / Media
Vegaanit pois pilleripakosta – uusi menetelmä kehittää vain eläinkunnan tuotteista saatua vitamiinia kasvisravintoon
Vieno Irene Piironen & Pekka Kristian Varmanen
09/01/2017
1 media contribution
Press/Media: Press / Media