Publications

In preparation

Tamminen M., Spaak J., Caduff L., Schiff H., Montealegre M., Schmid S, Julian T. Highly multiplexed target quantification by barcoded ligation-based assays.

Schmid S., Julian, T., Tamminen M. nsearch: An open source C++ library for processing next-generation sequencing data.

Tamminen M., Schmid S., Schiff H., Spaak J., Caduff L., Julian T. epride. A local alignment-based clustering and primer design tool for complex sequence pools.

Submitted

Tamminen, M., Betz, A., Thali, M., Matthews, B., Suter, M. and Narwani, A. Proteome evolution under essential resource limitation.

Tamminen, M., Spaak, J., Tlili, A., Eggen, R., Stamm, C. and Räsänen, K. Context dependency of biofilm community diversity in wastewater impacted streams: insight from next generation sequencing.

Single cell techniques

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 1: 35. link

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 94: fiy038. link

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 link

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 11: 988-998. link

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 535: 435–439. link

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 10: 427-436. link *Equal contribution. More details available at link

Tamminen, M. & Virta, M. (2015) Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells. Frontiers in Microbiology: 6:195 link

Antibiotic resistance

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 6, Article number 35790. link

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 92 (4): fiw052. link

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 92 (3): fiw014. link

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 45: 488-493. link

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 9 (3): e92702. link

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 45: 386-391 link

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 313: 15-23 link

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 26: 205-2011 link

Sequence meta-analyses

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 8: 1388-1400. link

Tamminen, M., Virta, M., Fani, R. & Fondi, M. (2012) Analysis of plasmid relationships through gene sharing networks. Molecular Biology and Evolution 29: 1225-1240 link

Other topics

Rinta-Kanto, J., Pehkonen, K., Sinkko, H., Tamminen, M. and Timonen, S. (2018) Diverse and abundant populations of archaea and bacteria colonize fruiting bodies of common forest mushrooms. Canadian Journal of Microbiology. Accepted for publication.

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 92 (7): fiw087. link

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 54: 230-235 link

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 108: 2876-2883 link

Tamminen, M. & Virta, M. (2007) Quantification of ecotoxicological tests based on bioluminescence using Polaroid film. Chemosphere 66: 1329-1335 link

Doctoral thesis

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