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2017

Enhanced heterologous protein productivity by genome reduction in Lactococcus lactis NZ9000

Zhu, D., Fu, Y., Liu, F., Xu, H., Saris, P. E. J. & Qiao, M., 3 Jan 2017, In : Microbial Cell Factories. 16, 13 p., 1.

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Expanding the feruloyl esterase gene family of Aspergillus niger by characterization of a feruloyl esterase, FaeC

Dilokpimol, A., Mäkelä, M. R., Mansouri, S., Belova, O., Waterstraat, M., Bunzel, M., de Vries, R. P. & Hilden, K. S., 25 Jul 2017, In : New Biotechnology. 37, p. 200-209 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef

Säde, E. J., Penttinen, K., Björkroth, K. J. & Hultman, J. J., Apr 2017, In : Food Microbiology. 62, p. 147–152 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Functional diversity in Dichomitus squalens monokaryons

Lopez, S. C., Theelen, B., Manserra, S., Issak, T. Y., Rytioja, J., Makelä, M. R. & de Vries, R. P., Jun 2017, In : IMA Fungus. 8, 1, p. 17-25 9 p.

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Genetic organization of anabaenopeptin and spumigin biosynthetic gene clusters in the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024

Lima, S. T., Alvarenga, D. O., Etchegaray, A., Fewer, D. P., Jokela, J. K., Varani, A. M., Sanz, M., Dörr, F. A., Pinto, E., Sivonen, A. K. & Fiore, P. M. D. F., 2017, In : ACS Chemical Biology. 12, 3, p. 769–778 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Genomiikka muuttaa eliökunnan luokittelua

Juslen, A. K., Muona, J. E. & Timonen, S. S., Dec 2017, In : Natura. 54, 4, p. 37-39 3 p.

Research output: Contribution to journalArticleProfessional

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Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use

Muurinen, J., Stedtfeld, R., Karkman, A., Parnanen, K., Tiedje, J. & Virta, M., 6 Jun 2017, In : Environmental Science & Technology. 51, 11, p. 5989-5999 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes

Mali, T., Kuuskeri, J., Shah, F. & Lundell, T. K., 27 Sep 2017, In : PLoS One. 12, 9, 21 p., e0185171.

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Jokapaikan arkeonit - globaalit vaikuttajat

Translated title of the contribution: Archaea everywhere - a global force Timonen, S. S. & Rinta-Kanto, J. M., 2017, In : Natura. 54, 3, p. 32-33 2 p.

Research output: Contribution to journalArticleProfessional

Kokeellisen evoluution laboratoriokurssi Viikissä

Cairns, J., Hiltunen, T. J. & Virolainen, T. L. E., Mar 2017, In : Inocula : mikrobiologikillan julkaisu.. 2017, 1, p. 6-7 2 p.

Research output: Contribution to journalArticleProfessional

Lipid biomarker signatures as tracers for harmful cyanobacterial blooms in the Baltic Sea

Bauersachs, T., Talbot, H. M., Sidgwick, F., Sivonen, K. & Schwark, L., 16 Oct 2017, In : PLoS One. 12, 10, 25 p., 0186360.

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Newly isolated Nodularia phage influences cyanobacterial community dynamics

Coloma, S. E., Dienstbier, A., Bamford, D. H., Sivonen, K., Roine, E. & Hiltunen, T., Jan 2017, In : Environmental Microbiology. 19, 1, p. 273-286 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Newtonian boreal forest ecology: The Scots pine ecosystem as an example

Hari, P., Aakala, T., Aalto, J., Back, J., Hollmen, J., Jogiste, K., Koupaei, K. K., Kahkonen, M. A., Korpela, M., Kulmala, L., Nikinmaa, E., Pumpanen, J., Salkinoja-Salonen, M., Schiestl-Aalto, P., Simojoki, A. & Havimo, M., 14 Jun 2017, In : PLoS One. 12, 6, 27 p., 0177927.

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Obatoclax Inhibits Alphavirus Membrane Fusion by Neutralizing the Acidic Environment of Endocytic Compartments

Varghese, F. S., Rausalu, K., Hakanen, M., Saul, S., Kuemmerer, B. M., Susi, P., Merits, A. & Ahola, T., Mar 2017, In : Antimicrobial Agents and Chemotherapy. 61, 3, 17 p., e02227-16.

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Partially Uncleaved Alphavirus Replicase Forms Spherule Structures in the Presence and Absence of RNA Template

Hellström, K., Kallio, K., Utt, A., Quirin, T., Jokitalo, E., Merits, A. & Ahola, T., Sep 2017, In : Journal of Virology. 91, 18, 13 p., e00787-17.

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Phylogenomic Analysis of the Microviridin Biosynthetic Pathway Coupled with Targeted Chemo-Enzymatic Synthesis Yields Potent Protease Inhibitors

Ahmed, M. N., Reyna-Gonzalez, E., Schmid, B., Wiebach, V., Süssmuth, R. D., Dittmann, E. & Fewer, D. P., Jun 2017, In : ACS Chemical Biology. 12, 6, p. 1538-1546 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Plant and insect genetic variation mediate the impact of arbuscular mycorrhizal fungi on a natural plant-herbivore interaction

RASMUSSEN, P., Amin, T., Bennett, A., Karlsson Green, K., Timonen, S., van Nouhuys, S. & Tack, A. J. M., Aug 2017, In : Ecological Entomology. 42, 6, p. 793-802 10 p.

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Polyprotein processing as a determinant for in vitro activity of Semliki Forest virus replicase

Pietilä, M. K., Albulescu, I. C., van Hemert, M. J. & Ahola, T. T., 2017, In : Viruses. 9, 10, 18 p., 292.

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Production of High Amounts of Hepatotoxin Nodularin and New Protease Inhibitors Pseudospumigins by the Brazilian Benthic Nostoc sp CENA543

Jokela, J., Heinilä, L. M. P., Shishido, T. K., Wahlsten, M., Fewer, D. P., Fiore, M. F., Wang, H., Haapaniemi, E., Permi, P. & Sivonen, K., 9 Oct 2017, In : Frontiers in Microbiology. 8, 14 p., 1963.

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Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

Somervuo, P., Yu, D. W., Xu, C. C. Y., Ji, Y., Hultman, J., Wirta, H. & Ovaskainen, O., Apr 2017, In : Methods in Ecology and Evolution. 8, 4, p. 398-407 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Rearranged Biosynthetic Gene Cluster and Synthesis of Hassallidin E in Planktothrix serta PCC 8927

Pancrace, C., Jokela, J., Sassoon, N., Ganneau, C., Desnos-Ollivier, M., Wahlsten, M., Humisto, A., Calteau, A., Bay, S., Fewer, D. P., Sivonen, K. & Gugger, M., Jul 2017, In : ACS Chemical Biology. 12, 7, p. 1796-1804 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Simultaneous Production of Anabaenopeptins and Namalides by the Cyanobacterium Nostoc sp. CENA543

Shishido Joutsen, T. K., Jokela, J. K., Fewer, D. P., Wahlsten, M. P-V., Fiore, M. F. & Sivonen, A. K., 27 Sep 2017, In : ACS Chemical Biology. 12, 11, p. 2746-2755 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Staining and microscopy of mycorrhizal fungal colonization in preserved ericoid plant roots

Kiheri, H., Heinonsalo, J. & Timonen, S., Dec 2017, In : Journal of Berry Research. 7, 4, p. 231-237 7 p.

Research output: Contribution to journalArticleScientificpeer-review

The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi

Peng, M., Dilokpirnol, A., Mäkelä, M. R., Hilden, K., Bervoets, S., Riley, R., Grigoriev, I. V., Hainaut, M., Henrissat, B., de Vries, R. P. & Granchi, Z., 20 Mar 2017, In : Journal of Biotechnology. 246, p. 1-3 3 p.

Research output: Contribution to journalArticleScientificpeer-review

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The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses

Rytioja, J., Hilden, K., Di Falco, M., Zhou, M., Aguilar-Pontes, M. V., Sietiö, O-M., Tsang, A., de Vries, R. & Mäkelä, M. R., 2017, In : Environmental Microbiology. 19, 3, p. 1237-1250 14 p.

Research output: Contribution to journalArticleScientificpeer-review

The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms

Muziasari, W. I., Pitkänen, L. K., Sorum, H., Stedtfeld, R. D., Tiedje, J. M. & Virta, M., 6 Jan 2017, In : Frontiers in Microbiology. 7, 10 p., 2137.

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2016

Ability of minus strands and modified plus strands to act as templates in Semliki Forest virus RNA replication.

Hellström, K. J., Kallio, K. A., Meriläinen, H-M., Jokitalo, E. S. & Ahola, T. T., 2016, In : Journal of General Virology. 87, 6, p. 1395-1407 13 p.

Research output: Contribution to journalArticleScientificpeer-review

A liquid chromatography-mass spectrometric method for the detection of cyclic β-amino fatty acid lipopeptides

Urajova, P., Hajek, J., Wahlsten, M., Jokela, J., Galica, T., Fewer, D. P., Kust, A., Zapomelova-Kozlikova, E., Delawska, K., Sivonen, K., Kopecky, J. & Hrouzek, P., 18 Mar 2016, In : Journal of Chromatography. A. 1438, p. 76-83 8 p.

Research output: Contribution to journalArticleScientificpeer-review

An siRNA screen for ATG protein depletion reveals the extent of the unconventional functions of the autophagy proteome in virus replication

Mauthe, M., Langereis, M., Jung, J., Zhou, X., Jones, A., Omta, W., Tooze, S. A., Stork, B., Riis Paludan, S., Ahola, T., Egan, D., Behrends, C., Mokry, M., de Haan, C., van Kuppeveld, F. & Reggiori, F., 2016, In : Journal of Cell Biology. 214, 5, p. 619-635 17 p.

Research output: Contribution to journalArticleScientificpeer-review

Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments

Muziasari, W. I., Parnanen, K., Johnson, T. A., Lyra, C., Karkman, A. V., Stedtfeld, R. D., Tamminen, M., Tiedje, J. M. & Virta, M., Apr 2016, In : FEMS Microbiology Ecology. 92, 4, 7 p., fiw052.

Research output: Contribution to journalArticleScientificpeer-review

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A Unique Tryptophan C-Prenyltransferase from the Kawaguchipeptin Biosynthetic Pathway

Parajuli, A., Kwak, D. H., Dalponte, L., Leikoski, N., Galica, T., Umeobika, U., Trembleau, L., Bent, A., Sivonen, K., Wahlsten, M., Wang, H., Rizzi, E., De Bellis, G., Naismith, J., Jaspars, M., Liu, X., Houssen, W. & Fewer, D. P., 7 Mar 2016, In : Angewandte Chemie (International Edition). 55, 11, p. 3596-3599 4 p.

Research output: Contribution to journalArticleScientificpeer-review

Carotenoid Biosynthesis in Calothrix sp 336/3: Composition of Carotenoids on Full Medium, During Diazotrophic Growth and After Long-Term H-2 Photoproduction

Kosourov, S., Murukesan, G., Jokela, J. & Allahverdiyeva, Y., Nov 2016, In : Plant and Cell Physiology. 57, 11, p. 2269-2282 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Challenges in the Measurement of Antibiotics and in Evaluating Their Impacts in Agroecosystems: A Critical Review

Aga, D. S., Lenczewski, M., Snow, D., Muurinen, J., Sallach, J. B. & Wallace, J. S., 2016, In : Journal of Environmental Quality. 45, 2, p. 407-419 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Chikungunya virus infectivity, RNA replication and non-structural polyprotein processing depend on the nsP2 protease's active site cysteine residue

Rausalu, K., Utt, A., Quirin, T., Varghese, F. S., Zusinaite, E., Das, P. K., Ahola, T. & Merits, A., 15 Nov 2016, In : Scientific Reports. 6, 17 p., 37124.

Research output: Contribution to journalArticleScientificpeer-review

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Design and Validation of Novel Chikungunya Virus Protease Inhibitors

Das, P. K., Puusepp, L., Varghese, F. S., Utt, A., Ahola, T., Kananovich, D. G., Lopp, M., Merits, A. & Karelson, M., Dec 2016, In : Antimicrobial Agents and Chemotherapy. 60, 12, p. 7382-7395 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Discovery of berberine, abamectin and ivermectin as antivirals against chikungunya and other alphaviruses

Varghese, F. S., Kaukinen, P., Glasker, S., Bespalov, M., Hanski, L., Wennerberg, K., Kummerer, B. M. & Ahola, T., Feb 2016, In : Antiviral Research. 126, p. 117-124 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2

Miettinen, O., Riley, R., Barry, K., Cullen, D., de Vries, R. P., Hainaut, M., Hatakka, A., Henrissat, B., Hildén, K., Kuo, R., LaButti, K., Lipzen, A., Mäkelä, M. R., Sandor, L., Spatafora, J. W., Grigoriev, I. V. & Hibbett, D. S., 2016, In : Genome Announcements. 4, 5, 2 p., e00976-16.

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Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics

Pärnänen, K., Karkman, A., Tamminen, M., Lyra, C., Hultman, J., Paulin, L. & Virta, M., 2016, In : Scientific Reports. 6, p. 35790 9 p., 35790.

Research output: Contribution to journalArticleScientificpeer-review

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"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.

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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.

Research output: Contribution to journalArticleScientificpeer-review

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