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Tamminen M. Spaak J. Caduff L. Schiff H. Montealegre M. Lang R. Schmid S. and Julian T.

Communications Biology


Tamminen M. Betz A. Thali M. Matthews B. Suter M. and Narwani A.

Nature Communications

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Brito I. L. Yilmaz S. Huang K. Xu L. Jupiter S. D. Jenkins, A. P. Naisilisili W. Tamminen M. Smillie C. S. Wortman J. R. Birren B. W. Xavier R. J. Blainey P. C. Singh A. K. Gevers D. and Alm E.


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Spencer S. Tamminen M. Preheim S. Guo M. Briggs A. Brito I. Weitz D. Pitkänen L. Vigneault F. Virta M. and Alm E.

ISME Journal


Tamminen M. Virta M. Fani R. and Fondi M.

Molecular Biology and Evolution

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Ovaska, M., Tamminen, M., Lahdenperä, M., Vahtera, J., Rautava, S., Gonzales-Inca, C., Heiskanen, M. and Lagström, H. (2024) The role of early life factors and green living environment in the development of gut microbiota in infancy: population-based cohort study. SSRN.

Jeevannavar, A., Narwani, A., Matthews, B., Spaak, P., Brantschen, J., Mächler, E., Altermatt, F. and Tamminen, M. (2024)  Foundation species stabilize an alternative eutrophic state in nutrient- disturbed ponds via selection on microbial community. Frontiers in Microbiology.

Hogle, S., Tamminen, M. and Hiltunen, T. (2024) Complete genome sequences of 30 bacterial species from a synthetic community. Microbiology Resource Announcements.

Mathew, S., Jeevannavar, A., Helander, M., Tamminen, M., Puigbò, P., Rainio, M., Saikkonen, K. and Fuchs, B. (2024) Glyphosate residues in soil and phosphate fertilizer affect foliar endophytic microbial community composition and phytohormone levels in potato. Phytobiomes.


Helander, M., Jeevannavar, A., Kaakinen, K., Mathew, S.A., Saikkonen, K., Fuchs, B., Puigbò, P., Loukola, O.J., Tamminen, M. (2023) Glyphosate and a glyphosate-based herbicide affect bumblebee gut microbiota. FEMS Microbiology Ecology.

Schmid, S., Jeevannavar, A., Julian, T. and Tamminen, M. (2023) Portable BLAST-like algorithm library and its implementations for command line, Python, and R. PLoS One.

Jeevannavar, A., Florenza, J., Divne, A., Tamminen, M., Bertilsson, S. (2023) De novo assembled single-cell transcriptomes from aquatic phytoflagellates reveal a metabolically distinct cell population. bioRxiv.

Morrill A., Forbes M., Vesterinen E., Tamminen M., Sääksjärvi I. & Kaunisto K. (2023) Molecular characterisation of faecal bacterial assemblages among four species of syntopic Odonates. Microbial Ecology.


Smolander, N., Julian, T. and Tamminen, M. (2022) Prider - multiplexed primer design using linearly scaling approximation of set coverage. BMC Bioinformatics.

Tran-Minh, M., Tamminen, M., Tamminen-Sirkiä, J., Majumder, M., Tabassum, R. and Lahti, T. (2022) A quantitative online survey of self-perceived knowledge and knowledge gaps of medicines research and development among Finnish general public. BMJ Open.

Merbt, S., Kroll, A., Tamminen, M., Rühs, P., Wagner, B., Sambalova, O., Sgier, L., Abel, B., Tlili, A., Schirmer, K. and Behra, R. (2022) Influence of microplastics on microbial structure, function and mechanical properties of stream periphyton. Frontiers in Enviromental Science.


Tamminen, M., Spaak, J., Tlili, A., Eggen, R., Stamm, C. and Räsänen, K. (2021) Wastewater constituents impact biofilm microbial community in receiving streams. Science of the Total Environment.

Smolander, N. and Tamminen, M. (2021) Prider – multiplexed primer design using linearly scaling approximation of set coverage. bioRxiv.


Tamminen M., Spaak J., Caduff L., Schiff H., Montealegre M., Lang, R., Schmid S. and Julian T. (2020) Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates. Communications Biology.

Bernhard, J., Kratina, P., Pereira, A., Tamminen, M., Thomas, M. and Narwani, A. (2020) The evolution of competitive ability for essential resources. Philosophical Transactions B.

Tran Minh, M., Tamminen, M., Tamminen, J., Majumder, M., Tabassum, R., Anttonen, M. and Lahti, T. (2020) Finns are interested in learning about their personal genetic risks. Duodecim.

Burdon, F., Bai, Y., Reyes, M., Tamminen, M., Staudacher, P., Mangold, S., Singer, H., Rasanen, K., Joss, A., Tiegs, S., Jokela, J., Eggen, R. and Stamm, C. (2020) Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewater. Global Change Biology.


Bernhard, J., Kratina, P., Pereira, A., Tamminen, M., Thomas, M. and Narwani, A. (2019) The evolution of competitive ability for essential resources. bioRxiv.

Florenza, J., Tamminen, M. and Bertilsson, S. (2019) Uncovering microbial inter-domain interactions in complex communities. Philosophical Transactions B.

Nakanishi, S., Tamminen, M., Yokokawa, T., Sato-Takabe, Y., Ohta, K., Chou, H-Y., Muziasari, W., Virta, M. and Suzuki, S. (2019) Occurrence of sul and tet(M) genes in bacterial community in Japanese marine aquaculture environment throughout the year: profile comparison with Taiwanese and Finnish aquaculture waters. Science of the Total Environment.


Tamminen, M., Betz, A., Thali, M., Matthews, B., Suter, M. and Narwani, A. (2018) Proteome evolution under essential resource limitation. Nature Communications.

Schmid S., Julian, T., Tamminen M. (2018) nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data. bioRxiv.

Cairns J., Jokela, R., Hultman, J., Tamminen, M., Virta, M. and Hiltunen, T. (2018) Construction and characterization of synthetic bacterial community for experimental ecology and evolution. Frontiers in Microbiology.

Cairns, J., Ruokolainen, L., Hultman, J., Tamminen, M., Virta, M. and Hiltunen, T. (2018) Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Communications Biology.

Hultman, J., Tamminen, M., Pärnänen, K., Cairns, J., Karkman, A. and Virta, M. (2018) Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent. FEMS Microbiology Ecology.

Rinta-Kanto, J., Pehkonen, K., Sinkko, H., Tamminen, M. and Timonen, S. (2018) Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms. Canadian Journal of Microbiology.


Briggs, A., Goldfless, S., Timberlake, S., Belmont, B., Clouser, C., Koppstein, D., Sok, D., Heiden, J., Tamminen, M., Kleinstein, S., Burton, D., Church, G. and Vigneault, F. (2017) Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion. bioRxiv.

Krismer, J., Tamminen, M., Fontana, S., Zenobi, R. and Narwani. A. (2017) Single-cell mass spectrometry reveals the importance of genetic diversity and plasticity for phenotypic variation in nitrogen limited Chlamydomonas. ISME Journal.


Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S.D., Jenkins, A.P., Naisilisili, W. Tamminen, M., Smillie, C.S., Wortman, J.R., Birren, B.W., Xavier, R.J., Blainey, P.C., Singh, A.K., Gevers, D., Alm, E.J. (2016) Mobile genes in the human microbiome are structured from global to individual scales. Nature.

Spencer, S.*, Tamminen, M.*, Preheim, S., Guo, M., Briggs, A., Brito, I., Weitz, D., Pitkänen, L., Vigneault, F., Virta, M., Alm, E. (2016) Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME Journal. *Equal contribution.

Pärnänen, K., Karkman, A., Tamminen, M., Lyra, C., Hultman, J., Paulin, L. and Virta, M. (2016) Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics. Scientific Reports.

Muziasari, W., Pärnänen, K., Johnson, T., Lyra, C., Karkman, A., Stedtfeld, R., Tamminen, M., Tiedje, J and Virta, M. (2016) Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments. FEMS Microbiology Ecology.

Karkman, A., Johnson, T., Lyra, C., Stedtfeld, R., Tamminen, M., Tiedje, J. and Virta, M (2016) High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiology Ecology.

Fondi, M., Karkman, A., Tamminen, M., Bosi, E., Virta, M., Fani, R., Alm, E. and McInerney, J. (2016) Every gene is everywhere but the environment selects: Global geo-localization of gene sharing in environmental samples through network analysis. Genome Biology and Evolution.

Rinta-Kanto, J., Sinkko, H., Rajala, T., Al-Soud, W., Sørensen, S., Tamminen, M. and Timonen, S. (2016) Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs. FEMS Microbiology Ecology.


Tamminen, M. & Virta, M. (2015) Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells. Frontiers in Microbiology.

Ruuskanen, M., Muurinen, J., Meierjohan, A., Pärnänen, K., Tamminen, M., Lyra, C., Kronberg, L., Virta, M. (2015) Fertilizing with animal manure disseminates antibiotic resistance genes to the farm environment. Journal of Environmental Quality.

2014 and before

Muziasari W., Managaki S., Pärnänen K., Karkman A., Lyra C., Tamminen, M., Suzuki, S. and Virta, M. (2014) Sulphonamide and trimethoprim resistance genes persist in sediments at Baltic sea aquaculture farms but are not detected in the surrounding environment. PLoS ONE.

Castrén, S., Pankakoski, M., Tamminen, M., Lipsanen, J., Ladouceur, R. and Lahti, T. (2013) Internet-based CBT intervention for gamblers in Finland: Experiences from the field. Scandinavian Journal of Psychology.

Tamminen, M., Virta, M., Fani, R. & Fondi, M. (2012) Analysis of plasmid relationships through gene sharing networks. Molecular Biology and Evolution.

Tamminen, M., Karkman, A., Lõhmus, A., Muziasari, W., Takasu, H., Wada, S., Suzuki, S. & Virta, M. (2011) Tetracycline resistance genes persist at aquaculture farms in the absence of selection pressure. Environmental Science and Technology.

Tamminen, M., Karkman, A., Corander, J., Paulin, L. & Virta, M. (2011) Differences in bacterial community composition in Baltic Sea sediment in response to fish farming. Aquaculture.

Pitkänen, L.K., Tamminen, M., Hynninen, A., Karkman, A., Corander, J., Kotilainen, A. & Virta, M. (2011) Fish farming affects the abundance and diversity of the mercury resistance gene merA in marine sediments. Microbes & Environments.

Karkman, A., Mattila, K., Tamminen, M. & Virta, M. (2011) Cold temperature decreases bacterial species richness in nitrogen-removing bioreactors treating inorganic mine waters. Biotechnology and Bioengineering.

Tamminen, M. & Virta, M. (2007) Quantification of ecotoxicological tests based on bioluminescence using Polaroid film. Chemosphere.

Doctoral thesis

Tamminen, M. (2011) Molecular characterization of sediment bacterial communities affected by fish farming. University of Helsinki. link


Tamminen, M., Julian, T., Spaak, J., Caduff, L., Schiff, H. (2019) Accurate and massively parallel quantification of nucleic acid. EP18756250

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