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2016

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

Fondi, M., Karkman, A., Tamminen, M. V., Bosi, E., Virta, M., Fani, R., Alm, E. & McInerney, J. O., May 2016, In : Genome Biology and Evolution. 8, 5, p. 1388-1400 13 p.

Research output: Contribution to journalArticleScientificpeer-review

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Evolving interactions between diazotrophic cyanobacterium and phage mediate nitrogen release and host competitive ability

Cairns, J., Coloma, S., Sivonen, K. & Hiltunen, T., Dec 2016, In : Royal Society Open Science. 3, 12, 12 p., 160839.

Research output: Contribution to journalArticleScientificpeer-review

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Fertilizing with Animal Manure Disseminates Antibiotic Resistance Genes to the Farm Environment

Ruuskanen, M., Muurinen, S. J., Meierjohan, A., Pärnänen, K. M. M., Tamminen, M. V., Lyra, C. D., Kronberg, L. & Virta, M. P. J., 2016, In : Journal of Environmental Quality. 45, 2, p. 488-493 6 p.

Research output: Contribution to journalArticleScientificpeer-review

High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant

Karkman, A., Johnson, T. A., Lyra, C., Stedtfeld, R. D., Tamminen, M., Tiedje, J. M. & Virta, M., Mar 2016, In : FEMS Microbiology Ecology. 92, 3, 7 p., 014.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Identification and characterization of a ribose 2′-O-methyltransferase encoded by the ronivirus branch of Nidovirales.

Zeng, C., Wu, A., Wang, Y., Xu, S., Tang, Y., Jin, X., Wang, S., Qin, L., Sun, Y., Fan, C., Snijder, E., Neuman, B., Chen, Y., Ahola, T. T. & Guo, D., 2016, In : Journal of Virology. 90, 15, p. 6675-6685 11 p.

Research output: Contribution to journalArticleScientificpeer-review

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Kaikki tarinat eivät ole samanarvoisia: Tiede edustaa ihmiskunnan pisimmälle hioutunutta ymmärrystä asioista

Cairns, J. & Muurinen, J., 1 Aug 2016, In : Helsingin Sanomat. 2016, 1.8.2016, 1 p.

Research output: Contribution to journalArticleGeneral public

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

Spencer, S. J., Tamminen, M. V., Preheim, S. P., Guo, M. T., Briggs, A. W., Brito, I. L., A Weitz, D., Pitkanen, L. K., Vigneault, F., Virta, M. P. J. & Alm, E. J., 2016, In : ISME Journal. 10, 2, p. 427-436 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Molecular insights into the function of the viral RNA silencing suppressor HCPro

Ivanov, K., Eskelin, K. J., Bašić, M., De, S., Lohmus, A., Varjosalo, M. T. & Mäkinen, K. M., 2016, In : Plant Journal. 85, 1, p. 30-45 16 p.

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Mu insertion in feuD triggers the increase in nisin immunity in Lactococcus lactis subsp lactis N8

Zhu, D., Li, R., Liu, F., Xu, H., Li, B., Yuan, Y., Saris, P. E. J. & Qiao, M., Feb 2016, In : Journal of Applied Microbiology. 120, 2, p. 402-412 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs

Rinta-Kanto, J. M., Sinkko, H-M., Rajala, T., Abu al Soud, W., Sørensen, S. J., Tamminen, M. V. & Timonen, S., 2016, In : FEMS Microbiology Ecology. 92, 7, 10 p., fiw087.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification

Mäkelä, M. R., Mansouri, S., Wiebenga, A., Rytioja, J., de Vries, R. P. & Hilden, K. S., 25 Dec 2016, In : New Biotechnology. 33, 6, p. 834-841 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Polvomaviruses as causative agents of diseases

Sadeghi, M., 2016, In : Duodecim.

Research output: Contribution to journalArticleScientificpeer-review

Protein composition of 6K2-induced membrane structures formed during Potato virus A infection

Lohmus, A., Varjosalo, M. & Mäkinen, K., Aug 2016, In : Molecular Plant Pathology. 17, 6, p. 943-958 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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RNA Replication and Membrane Modification Require the Same Functions of Alphavirus Nonstructural Proteins

Kallio, K., Hellström, K., Jokitalo, E. & Ahola, T., Feb 2016, In : Journal of Virology. 90, 3, p. 1687-1692 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow

Caucci, S., Karkman, A. V., Cacace, D., Rybicki, M., Timpel, P., Voolaid, V., Gurke, R., Virta, M. & Berendonk, T. U., May 2016, In : FEMS Microbiology Ecology. 92, 5, 10 p., fiw060.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

The Antiviral Alkaloid Berberine Reduces Chikungunya Virus-Induced Mitogen-Activated Protein Kinase Signaling

Varghese, F. S., Thaa, B., Amrun, S. N., Simarmata, D., Rausalu, K., Nyman, T. A., Merits, A., McInerney, G. M., Ng, L. F. P. & Ahola, T., Nov 2016, In : Journal of Virology. 90, 21, p. 9743-9757 15 p.

Research output: Contribution to journalArticleScientificpeer-review

The cyclochlorotine mycotoxin is produced by the nonribosomal peptide synthetase CctN in Talaromyces islandicus ('Penicillium islandicum')

Schafhauser, T., Kirchner, N., Kulik, A., Huijbers, M. M. E., Flor, L., Caradec, T., Fewer, D. P., Gross, H., Jacques, P., Jahn, L., Jokela, J., Leclere, V., Ludwig-Mueller, J., Sivonen, K., van Berkel, W. J. H., Weber, T., Wohlleben, W. & van Pee, K-H., Nov 2016, In : Environmental Microbiology. 18, 11, p. 3728-3741 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose

Kuuskeri, J., Häkkinen, M., Laine, P., Smolander, O-P., Tamene, F., Miettinen, S., Nousiainen, P., Kemell, M., Auvinen, P. & Lundell, T., 5 Sep 2016, In : Biotechnology for Biofuels. 9, 22 p., 192.

Research output: Contribution to journalArticleScientificpeer-review

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Towards the reconstitution of a two-enzyme cascade for resveratrol synthesis on potyvirus particles

Besong Epse Ndika, J. E., Wahlsten, M., Cardinale, D., Pille, J., Walter, J., Michon, T. & Mäkinen, K. M., 10 Feb 2016, In : Frontiers in plant science. 7, 12 p., 89.

Research output: Contribution to journalArticleScientificpeer-review

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Versatile Trans-Replication Systems for Chikungunya Virus Allow Functional Analysis and Tagging of Every Replicase Protein

Utt, A., Quirin, T., Saul, S., Hellstrom, K., Ahola, T. & Merits, A., 10 Mar 2016, In : PLoS One. 11, 3, 27 p., 0151616.

Research output: Contribution to journalArticleScientificpeer-review

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Open Access
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Virus Etiology of Airway Illness in the Elderly

Sadeghi, M., 2016, In : Journal of the American Geriatrics Society.

Research output: Contribution to journalArticleScientificpeer-review

2015

Anatoxin-a producing Tychonema (Cyanobacteria) in European waterbodies.

Shams, S., Capelli, C., Cerasino, L., Ballot, A., Dietrich, D. R., Sivonen, K. & Salmaso, N., 2015, In : Water Research. 69, p. 68-79 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Antifungal activity improved by coproduction of cyclodextrins and anabaenolysins in Cyanobacteria

Shishido, T. K., Jokela, J., Kolehmainen, C-T., Fewer, D. P., Wahlsten, M., Wang, H., Rouhiainen, L., Rizzi, E., De Bellis, G., Permi, P. & Sivonen, K., 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 44, p. 13669-13674 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Antifungal Compounds from Cyanobacteria

Shishido, T. K., Humisto, A., Jokela, J., Liu, L., Wahlsten, M., Tamrakar, A., Fewer, D. P., Permi, P., Andreote, A. P. D., Fiore, M. F. & Sivonen, K., 2015, In : Marine Drugs. 13, 4, p. 2124-2140 17 p.

Research output: Contribution to journalArticleScientificpeer-review

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Attachment of Escherichia coli to Listeria monocytogenes for Pediocin-Mediated Killing

Liu, S., Takala, T. M., Reunanen, J., Saris, O. & Saris, P. E. J., Feb 2015, In : Current Microbiology. 70, 2, p. 195-198 4 p.

Research output: Contribution to journalArticleScientificpeer-review

Biochemical characterization of recombinant oxalate decarboxylases of the white rot fungus Dichomitus squalens

Sietiö, O-M., Mäkelä, M. R. & Hilden, S. K., 2015, In : Current Biotechnology. p. 98-104 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass

Benoit, I., Culleton, H., Zhou, M., DiFalco, M., Aguilar-Osorio, G., Battaglia, E., Bouzid, O., Brouwer, C. P. J. M., El-Bushari, H. B. O., Coutinho, P. M., Gruben, B. S., Hildén, S. K., Houbraken, J., Jimenez Barboza, L. A., Levasseur, A., Majoor, E., Mäkelä, M. R., Narang, H-M., Trejo-Aguilar, B., van den Brink, J. & 7 othersvanKuyk, P. A., Wiebenga, A., McKie, V., McCleary, B., Tsang, A., Henrissat, B. & de Vries, R. P., 1 Aug 2015, In : Biotechnology for Biofuels. 8, 14 p., 107.

Research output: Contribution to journalArticleScientificpeer-review

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Construction of thyA deficient Lactococcus lactis using the Cre-loxP recombination system

Zhu, D., Zhao, K., Xu, H., Zhang, X., Bai, Y., Saris, P. E. J. & Qiao, M., Sep 2015, In : Annals of Microbiology. 65, 3, p. 1659-1665 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Coronavirus nsp10/nsp16 Methyltransferase Can Be Targeted by nsp10-Derived Peptide In Vitro and In Vivo To Reduce Replication and Pathogenesis

Wang, Y., Sun, Y., Wu, A., Xu, S., Pan, R., Zeng, C., Jin, X., Ge, X., Shi, Z., Ahola, T., Chen, Y. & Guo, D., Aug 2015, In : Journal of Virology. 89, 16, p. 8416-8427 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Correlative light and electron microscopy enables viral replication studies at the ultrastructural level

Hellstrom, K., Vihinen, H., Kallio, K., Jokitalo, E. & Ahola, T., 15 Nov 2015, In : Methods. 90, p. 49-56 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Cotranslational Coat Protein-Mediated Inhibition of Potyviral RNA Translation

Besong Epse Ndika, J. E., Ivanov, K., Hafren, A. J., Michon, T. & Mäkinen, K. M., Apr 2015, In : Journal of Virology. 89, 8, p. 4237-4248 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Cyanobacteria as a Source for Novel Anti-Leukemic Compounds

Humisto, A., Herfindal, L., Jokela, J., Karkman, A., Bjørnstad, R., Choudhury, R. R. & Sivonen, K., 2015, In : Current Pharmaceutical Biotechnology. 17, 1, p. 78-91 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Cyanobacterial toxic and bioactive peptides in freshwater bodies of Greece: Concentrations, occurrence patterns, and implications for human health.

Gkelis, S., Lanaras, T. & Sivonen, A. K., 2015, In : Marine Drugs. 13, 10, p. 6319-6335 26 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Differential Phosphatidylinositol-3-Kinase-Akt-mTOR Activation by Semliki Forest and Chikungunya Viruses Is Dependent on nsP3 and Connected to Replication Complex Internalization

Thaa, B., Biasiotto, R., Eng, K., Neuvonen, M., Gotte, B., Rheinemann, L., Mutso, M., Utt, A., Varghese, F., Balistreri, G., Merits, A., Ahola, T. & McInerney, G. M., Nov 2015, In : Journal of Virology. 89, 22, p. 11420-11437 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Discovery of bacterial polyhydroxyalkanoate synthase (PhaC)-encoding genes from seasonal Baltic Sea ice and cold estuarine waters

Pärnänen, K., Karkman, A., Virta, M., Eronen-Rasimus, E. & Kaartokallio, H., Jan 2015, In : Extremophiles. 19, 1, p. 197-206 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Draft genome sequence of Calothrix 336/3, novel H2 producing cyanobacterium isolated from Finnish lake

Isojärvi, J., Shunmugam, S., Sivonen, A. K., Allahverdiyeva, Y., Aro, E-M. & Battchikova, N., 2015, In : Genome Announcements. 3, 1, 2 p., e01474-14.

Research output: Contribution to journalArticleScientific

Open Access
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Draft genome sequence of Talaromyces islandicus ("Penicillium islandicum") WF-38-12, a neglected mold with significant biotechnological potential

Schafhauser, T., Wibberg, D., Rueckert, C., Winkler, A., Flor, L., van Pee, K-H., Fewer, D. P., Sivonen, K., Jahn, L., Ludwig-Mueller, J., Caradec, T., Jacques, P., Huijbers, M. M. E., van Berkel, W. J. H., Weber, T., Wohlleben, W. & Kalinowski, J., 10 Oct 2015, In : Journal of Biotechnology. 211, p. 101-102 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Electrochemical Atomic Force Microscopy Imaging of Redox-Immunomarked Proteins on Native Potyviruses: From Subparticle to Single-Protein Resolution

Nault, L., Taofifenua, C., Anne, A., Chovin, A., Demaille, C., Besong, J., Cardinale, D., Carette, N., Michon, T. & Walter, J., May 2015, In : ACS Nano. 9, 5, p. 4911-4924 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Formation of Potato virus A-induced RNA granules and viral translation are interrelated processes required for optimal virus accumulation

Hafren, A. J., Lohmus, A. & Mäkinen, K. M., 7 Dec 2015, In : PLoS Pathogens. 11, 12, 28 p., e1005314.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Fungal colonisation and moisture uptake of torrefied wood, charcoal, and thermally treated pellets during storage

Kymäläinen, M., Mäkelä, M. R., Hilden, K. & Kukkonen, J., Nov 2015, In : European Journal of Wood and Wood Products. 73, 6, p. 709-717 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Genetic characterisation and expression of leucocin B, a class IId bacteriocin from Leuconostoc carnosum 4010

Wan, X., Saris, P. E. J. & Takala, T. M., 2015, In : Research in Microbiology. 166, 6, p. 494-503 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Genomic insights into the distribution, genetic diversity and evolution of polyketide synthases and nonribosomal peptide synthetases

Wang, H., Sivonen, A. K. & Fewer, D. P., 21 Nov 2015, In : Current Opinion in Genetics & Development. 35, p. 79-85 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Identification of geosmin and 2-methylisoborneol in cyanobacteria and molecular detection methods for the producers.

Suurnäkki, S., Gomes-Saez, G. V., Rantala-Ylinen, A., Jokela, J., Fewer, D. P. & Sivonen, K., 2015, In : Water Research. 68, p. 56-66 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Isolation of strong constitutive promoters from Lactococcus lactis subsp. lactis N8

Zhu, D., Liu, F., Xu, H., Bai, Y., Zhang, X., Saris, P. E. J. & Qiao, M., Aug 2015, In : FEMS Microbiology Letters. 362, 16, 6 p., fnv107.

Research output: Contribution to journalArticleScientificpeer-review

Lemon-shaped halo archaeal virus His1 with uniform tail but variable capsid structure

Hong, C., Pietilä, M. K., Fu, C. J., Schmid, M. F., Bamford, D. H. & Chiu, W., 24 Feb 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 8, p. 2449-2454 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Microbial, chemical and sensory properties of shalgams made using different production methods

Tanguler, H., Saris, P. E. & Erten, H., 2015, In : Journal of the Science of Food and Agriculture. 95, 5, p. 1008-1015 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Microorganisms associated with amylolytic starters and traditional fermented alcoholic beverages of North Western Himalayas in India

Thakur, N., Savitri, Saris, P. E. J. & Bhalla, T. C., 2015, In : Food Bioscience. 11, p. 92 - 96 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Minimum Information about a Biosynthetic Gene cluster

Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., de Bruijn, I., Chooi, Y. H., Claesen, J., Coates, R. C., Cruz-Morales, P., Duddela, S., Duesterhus, S., Edwards, D. J., Fewer, D. P., Garg, N., Geiger, C., Gomez-Escribano, J. P., Greule, A., Hadjithomas, M. & 134 othersHaines, A. S., Helfrich, E. J. N., Hillwig, M. L., Ishida, K., Jones, A. C., Jones, C. S., Jungmann, K., Kegler, C., Kim, H. U., Koetter, P., Krug, D., Masschelein, J., Melnik, A. V., Mantovani, S. M., Monroe, E. A., Moore, M., Moss, N., Nuetzmann, H-W., Pan, G., Pati, A., Petras, D., Reen, F. J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N. J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A. K., Balibar, C. J., Balskus, E. P., Barona-Gomez, F., Bechthold, A., Bode, H. B., Borriss, R., Brady, S. F., Brakhage, A. A., Caffrey, P., Cheng, Y-Q., Clardy, J., Cox, R. J., De Mot, R., Donadio, S., Donia, M. S., van der Donk, W. A., Dorrestein, P. C., Doyle, S., Driessen, A. J. M., Ehling-Schulz, M., Entian, K-D., Fischbach, M. A., Gerwick, L., Gerwick, W. H., Gross, H., Gust, B., Hertweck, C., Hofte, M., Jensen, S. E., Ju, J., Katz, L., Kaysser, L., Klassen, J. L., Keller, N. P., Kormanec, J., Kuipers, O. P., Kuzuyama, T., Kyrpides, N. C., Kwon, H-J., Lautru, S., Lavigne, R., Lee, C. Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Mendez, C., Metsa-Ketela, M., Micklefield, J., Mitchell, D. A., Moore, B. S., Moreira, L. M., Mueller, R., Neilan, B. A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M. S., Ostash, B., Payne, S. M., Pernodet, J-L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J. M., Salas, J. A., Schmitt, E. K., Scott, B., Seipke, R. F., Shen, B., Sherman, D. H., Sivonen, K., Smanski, M. J., Sosio, M., Stegmann, E., Suessmuth, R. D., Tahlan, K., Thomas, C. M., Tang, Y., Truman, A. W., Viaud, M., Walton, J. D., Walsh, C. T., Weber, T., van Wezel, G. P., Wilkinson, B., Willey, J. M., Wohlleben, W., Wright, G. D., Ziemert, N., Zhang, C., Zotchev, S. B., Breitling, R., Takano, E. & Gloeckner, F. O., Sep 2015, In : Nature Chemical Biology. 11, 9, p. 625-631 7 p.

Research output: Contribution to journalArticleScientificpeer-review