Publications

2021

Transposon-Based Tagging in Silico using FastPCR software

Kalendar, R., Kospanova, D. & Schulman, A., 20 Jan 2021, Plant Transposable Elements. Cho, J. (ed.). 1 ed. Springer, Vol. 2250. (Methods in molecular biology).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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2020

A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context

Radhakrishnan, D., Shanmukhan, A. P., Kareem, A., Aiyaz, M., Varapparambathu, V., Toms, A., Kerstens, M., Valsakumar, D., Landge, A. N., Shaji, A., Mathew, M. K., Sawchuk, M. G., Scarpella, E., Krizek, B. A., Efroni, I., Mähönen, A. P., Willemsen, V., Scheres, B. & Prasad, K., Mar 2020, In : Development. 147, 6, 13 p., 185710.

Research output: Contribution to journalArticleScientificpeer-review

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Actin/microtubule crosstalk during platelet biogenesis in mice is critically regulated by Twinfilin1 and Cofilin1

Becker, I. C., Scheller, I., Wackerbarth, L. M., Beck, S., Heib, T., Aurbach, K., Manukjan, G., Gross, C., Spindler, M., Nagy, Z., Witke, W., Lappalainen, P., Bender, M., Schulze, H., Pleines, I. & Nieswandt, B., 26 May 2020, In : Blood advances. 4, 10, p. 2124-2134 11 p.

Research output: Contribution to journalArticleScientificpeer-review

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Age-associated changes in the immune system may influence the response to anti-PD1 therapy in metastatic melanoma patients

Kasanen, H., Hernberg, M., Mäkelä, S., Brück, O., Juteau, S., Kohtamäki, L., Ilander, M., Mustjoki, S. & Kreutzman, A., May 2020, In : Cancer Immunology, Immunotherapy. 69, 5, p. 717-730 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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Alternative NADH dehydrogenase extends lifespan and increases resistance to xenobiotics in Drosophila (vol 147, pg 2311, 2020)

Gospodaryov, D. V., Strilbytska, O. M., Semaniuk, U. V., Perkhulyn, N. V., Rovenko, B. M., Yurkevych, I. S., Barata, A. G., Dick, T. P., Lushchak, O. V. & Jacobs, H. T., Apr 2020, In : Biogerontology. 21, 2, p. 173-174 2 p.

Research output: Contribution to journalArticleScientificpeer-review

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A major locus controls a biologically active pheromone component in Heliconius melpomene

Byers, K. J. R. P., Darragh, K., Musgrove, J., Abondano Almeida, D., Fernanda Garza, S., Warren, I. A., Rastas, P. M., Kucka, M., Chan, Y. F., Merrill, R. M., Schulz, S., Owen McMillan, W. & Jiggins, C. D., Feb 2020, In : Evolution. 74, 2, p. 349-364 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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An inducible genome editing system for plants

Wang, X., Ye, L., Lyu, M., Ursache, R., Löytynoja, A. & Mähönen, A. P., Jul 2020, In : Nature plants. 6, 7, p. 766–772 24 p.

Research output: Contribution to journalArticleScientificpeer-review

An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel

Dunn, C., Akpinar, A. & Sharma, V., 1 Jul 2020, In : G3 - Genes genomes genetics. 10, 7, p. 2477-2485 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

Purhonen, J., Banerjee, R., McDonald, A. E., Fellman, V. & Kallijarvi, J., 4 Sep 2020, In : Nucleic Acids Research. 48, 15, 17 p., 87.

Research output: Contribution to journalArticleScientificpeer-review

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A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice

Purhonen, J., Grigorjev, V., Ekiert, R., Aho, N., Rajendran, J., Pietras, R., Truve, K., Wikström, M., Sharma, V., Osyczka, A., Fellman, V. & Kallijärvi, J., 16 Jan 2020, In : Nature Communications. 11, 1, 12 p., 322.

Research output: Contribution to journalArticleScientificpeer-review

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Assembly of Peripheral Actomyosin Bundles in Epithelial Cells Is Dependent on the CaMKK2/AMPK Pathway

Rajakylä, E. K., Lehtimäki, J. I., Acheva, A., Schaible, N., Lappalainen, P., Krishnan, R. & Tojkander, S., 24 Mar 2020, In : Cell Reports. 30, 12, p. 4266-4280 19 p.

Research output: Contribution to journalArticleScientificpeer-review

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Back and to the Future: From Neurotoxin-Induced to Human Parkinson's Disease Models

Airavaara, M., Parkkinen, I., Konovalova, J., Albert, K., Chmielarz, P. & Domanskyi, A., 12 Feb 2020, In : Current Protocols in Neuroscience. 91, 1, 33 p., e88.

Research output: Contribution to journalArticleScientificpeer-review

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B cells rapidly target antigen and surface-derived MHCII into peripheral degradative compartments

Hernandez-Perez, S., Vainio, M., Kuokkanen, E., Sustar, V., Petrov, P., Forsten, S., Paavola, V., Rajala, J., Awoniyi, L. O., Sarapulov, A., Vihinen, H., Jokitalo, E., Bruckbauer, A. & Mattila, P. K., Mar 2020, In : Journal of Cell Science. 133, 5, 15 p., 235192.

Research output: Contribution to journalArticleScientificpeer-review

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Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon

Sinclair-Waters, M., Odegard, J., Korsvoll, S. A., Moen, T., Lien, S., Primmer, C. R. & Barson, N. J., 12 Feb 2020, In : Genetics Selection Evolution. 52, 1, 11 p., 9.

Research output: Contribution to journalArticleScientificpeer-review

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BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data

Serra, A., Saarimaki, L. A., Fratello, M., Marwah, V. S. & Greco, D., 1 May 2020, In : Bioinformatics. 36, 9, p. 2932-2933 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Buried in water, burdened by nature-Resilience carried the Iron Age people through Fimbulvinter

Oinonen, M., Alenius, T., Arppe, L., Bocherens, H., Etu-Sihvola, H., Helama, S., Huhtamaa, H., Lahtinen, M., Mannermaa, K., Onkamo, P., Palo, J., Sajantila, A., Salo, K., Sundell, T., Vanhanen, S. & Wessman, A., 21 Apr 2020, In : PLoS One. 15, 4, 27 p., 0231787.

Research output: Contribution to journalArticleScientificpeer-review

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Carbon Nanomaterials Promote M1/M2 Macrophage Activation

Kinaret, P. A. S., Scala, G., Federico, A., Sund, J. & Greco, D., May 2020, In : Small. 16, 21, 12 p., 1907609.

Research output: Contribution to journalArticleScientificpeer-review

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Cerebral dopamine neurotrophic factor-deficiency leads to degeneration of enteric neurons and altered brain dopamine neuronal function in mice

Lindahl, M., Chalazonitis, A., Palm, E., Pakarinen, E., Danilova, T., Pham, T. D., Setlik, W., Rao, M., Voikar, V., Huotari, J., Kopra, J., Andressoo, J-O., Piepponen, P. T., Airavaara, M., Panhelainen, A., Gershon, M. D. & Saarma, M., Feb 2020, In : Neurobiology of Disease. 134, 18 p., 104696.

Research output: Contribution to journalArticleScientificpeer-review

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Cerebral Dopamine Neurotrophic Factor Is Essential for Enteric Neuronal Development, Maintenance and Regulation of Gastrointestinal Transit

Chalazonitis, A., Li, Z., Pham, T. D., Chen, J., Rao, M., Lindholm, P., Saarma, M., Lindahl, M. & Gershon, M. D., Oct 2020, In : Journal of Comparative Neurology. 528, 14, p. 2420-2444 25 p.

Research output: Contribution to journalArticleScientificpeer-review

Characterization of JAK1 Pseudokinase Domain in Cytokine Signaling

Raivola, J., Haikarainen, T. & Silvennoinen, O., Jan 2020, In : Cancers. 12, 1, 20 p., 78.

Research output: Contribution to journalArticleScientificpeer-review

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Characterization of the clinical and immunological phenotype and management of 157 individuals with 56 distinct heterozygous NFKB1 mutations

Lorenzini, T., Fliegauf, M., Klammer, N., Frede, N., Proietti, M., Bulashevska, A., Camacho-Ordonez, N., Varjosalo, M., Kinnunen, M., de Vries, E., van der Meer, J. W. M., Ameratunga, R., Roifman, C. M., Schejter, Y. D., Kobbe, R., Hautala, T., Atschekzei, F., Schmidt, R. E., Schröder, C., Stepensky, P. & 54 others, Shadur, B., Pedroza, L. A., van der Flier, M., Martínez-Gallo, M., Gonzalez-Granado, L. I., Allende, L. M., Shcherbina, A., Kuzmenko, N., Zakharova, V., Neves, J. F., Svec, P., Fischer, U., Ip, W., Bartsch, O., Barış, S., Klein, C., Geha, R., Chou, J., Alosaimi, M., Weintraub, L., Boztug, K., Hirschmugl, T., Dos Santos Vilela, M. M., Holzinger, D., Seidl, M., Lougaris, V., Plebani, A., Alsina, L., Piquer-Gibert, M., Deyà-Martínez, A., Slade, C. A., Aghamohammadi, A., Abolhassani, H., Hammarström, L., Kuismin, O., Helminen, M., Allen, H. L., Thaventhiran, J. E., Freeman, A. F., Cook, M., Bakhtiar, S., Christiansen, M., Cunningham-Rundles, C., Patel, N. C., Rae, W., Niehues, T., Brauer, N., Syrjänen, J., Seppänen, M. R. J., Burns, S. O., Tuijnenburg, P., Kuijpers, T. W., Warnatz, K. & Grimbacher, B., 9 Apr 2020, In : Journal of Allergy and Clinical Immunology.

Research output: Contribution to journalArticleScientificpeer-review

Chronic 2-Fold Elevation of Endogenous GDNF Levels Is Safe and Enhances Motor and Dopaminergic Function in Aged Mice

Turconi, G., Kopra, J., Võikar, V., Kulesskaya, N., Vilenius, C., Piepponen, T. P. & Andressoo, J-O., 12 Jun 2020, In : Molecular therapy-Methods & clinical development. 17, p. 831-842 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

Verta, J-P., Debes, P., Piavchenko, N., Ruokolainen, A., Ovaskainen, O. S., Moustakas-Verho, J., Tillanen, S. I., Parre, N., Aykanat, T., Erkinaro, J. & Primmer, C., 30 Sep 2020, In : PLoS Genetics. e1009055.

Research output: Contribution to journalArticleScientificpeer-review

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Climate mediates continental scale patterns of stream microbial functional diversity

Picazo, F., Vilmi, A., Aalto, J., Soininen, J., Casamayor, E. O., Liu, Y., Wu, Q., Ren, L., Zhou, J., Shen, J. & Wang, J., 13 Jun 2020, In : Microbiome. 8, 1, 14 p., 92.

Research output: Contribution to journalArticleScientificpeer-review

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Cobalt nanoparticles trigger ferroptosis-like cell death (oxytosis) in neuronal cells: Potential implications for neurodegenerative disease

Gupta, G., Gliga, A., Hedberg, J., Serra, A., Greco, D., Odnevall Wallinder, I. & Fadeel, B., Apr 2020, In : FASEB Journal. 34, 4, p. 5262-5281 20 p.

Research output: Contribution to journalArticleScientificpeer-review

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Coibamide A Targets Sec61 to Prevent Biogenesis of Secretory and Membrane Proteins

Tranter, D., Paatero, A. O., Kawaguchi, S., Kazemi, S., Serrill, J. D., Kellosalo, J., Vogel, W. K., Richter, U., Mattos, D. R., Wan, X., Thornburg, C. C., Oishi, S., McPhail, K. L., Ishmael, J. E. & Paavilainen, V. O., 21 Aug 2020, In : ACS Chemical Biology. 15, 8, p. 2125-2136 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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Comparative Cr, As and CCA induced Cytostaticity in mice kidney: A contribution to assess CCA toxicity

Matos, R. C., Oliveira, H., Fonseca, H. M. A. C., Morais, S., Sharma, B., Santos, C. & Pereira, M. D. L., Jan 2020, In : Environmental Toxicology and Pharmacology. 73, 7 p., 103297.

Research output: Contribution to journalArticleScientificpeer-review

Comparison Between O and OH Intermediates of Cytochrome c Oxidase Studied by FTIR Spectroscopy

Gorbikova, E. & Kalendar, R., 5 May 2020, In : Frontiers in Chemistry. 8, 6 p., 387.

Research output: Contribution to journalArticleScientificpeer-review

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Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Kjaerner-Semb, E., Edvardsen, R. B., Ayllon, F., Vogelsang, P., Furmanek, T., Rubin, C. J., Veselov, A. E., Nilsen, T. O., McCormick, S. D., Primmer, C. R. & Wargelius, A., 13 Sep 2020, In : Evolutionary Applications. 16 p.

Research output: Contribution to journalArticleScientificpeer-review

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Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897T

Deptula, P., Laine, P., Auvinen, P., Paulin, L., Roberts, R. J., Johnston, C. D. & Varmanen, P., 16 Jul 2020, In : Microbiology Resource Announcements. 9, 29, 3 p., e00705-20.

Research output: Contribution to journalArticleScientificpeer-review

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Conservation and Management of Salmon in the Age of Genomics

Waples, R. S., Naish, K. A. & Primmer, C. R., 2020, ANNUAL REVIEW OF ANIMAL BIOSCIENCES. Lewin, HA. & Roberts, RM. (eds.). Annual Reviews, Vol. 8. p. 117-143 27 p. (Annual Review of Animal Biosciences; vol. 8).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Cuscuta, the Merchant of Proteins

Paterlini, A. & Helariutta, Y., 6 Apr 2020, In : Molecular Plant. 13, 4, p. 533-535 3 p.

Research output: Contribution to journalEditorialScientificpeer-review

Cytosine methylation patterns suggest a role of methylation in plastic and adaptive responses to temperature in European grayling (Thymallus thymallus) populations

Savilammi, T., Papakostas, S., Leder, E. H., Vollestad, L. A., Debes, P. V. & Primmer, C. R., 30 Jul 2020, In : Epigenetics. 18 p.

Research output: Contribution to journalArticleScientificpeer-review

DALI and the persistence of protein shape

Holm, L., Jan 2020, In : Protein Science. 29, 1, p. 128-140 13 p.

Research output: Contribution to journalArticleScientificpeer-review

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Deficiency of the ER-stress-regulator MANF triggers progressive outer hair cell death and hearing loss

Herranen, A., Ikäheimo, K., Lankinen, T., Pakarinen, E., Fritzsch, B., Saarma, M., Lindahl, M. & Pirvola, U., 6 Feb 2020, In : Cell Death and Disease. 11, 2, 12 p., 100.

Research output: Contribution to journalArticleScientificpeer-review

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Dereplication of Natural Products with Antimicrobial and Anticancer Activity from Brazilian Cyanobacteria

Shishido, T. K., Popin, R. V., Jokela, J., Wahlsten, M., Fiore, M. F., Fewer, D. P., Herfindal, L. & Sivonen, K., Jan 2020, In : Toxins. 12, 1, 17 p., 12.

Research output: Contribution to journalArticleScientificpeer-review

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Design, Synthesis and Characterization of a PEGylated Stanozolol for Potential Therapeutic Applications

Vergallo, C., Torrieri, G., Provenzani, R., Miettinen, S., Moslova, K., Varjosalo, M., Cristiano, M. C., Fresta, M., Celia, C., Santos, H. A., Cilurzo, F. & Di Marzio, L., 5 Jan 2020, In : International Journal of Pharmaceutics. 573, 11 p., 118826.

Research output: Contribution to journalArticleScientificpeer-review

Determinants of genetic variation across eco-evolutionary scales in pinnipeds

Peart, C. R., Tusso, S., Pophaly, S. D., Botero-Castro, F., Wu, C-C., Aurioles-Gamboa, D., Baird, A. B., Bickham, J. W., Forcada, J., Galimberti, F., Gemmell, N. J., Hoffman, J., Kovacs, K. M., Kunnasranta, M., Lydersen, C., Nyman, T., de Oliveira, L. R., Orr, A. J., Sanvito, S., Valtonen, M. & 2 others, Shafer, A. B. A. & Wolf, J. B. W., Aug 2020, In : Nature Ecology & Evolution. 4, 8, p. 1095-+ 20 p.

Research output: Contribution to journalArticleScientificpeer-review

Deubiquitinase USP29 promotes gastric cancer cell migration by cooperating with phosphatase SCP1 to stabilize Snail protein

Qian, W., Li, Q., Wu, X., Li, W., Li, Q., Zhang, J., Li, M., Zhang, D., Zhao, H., Zou, X., Jia, H., Zhang, L., Yang, X-D. & Hou, Z., 24 Sep 2020, In : Oncogene. 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Developmental expression patterns of six6: a gene linked with spawning ecotypes in Atlantic salmon

Moustakas-Verho, J., Kurko, J., House, A., Erkinaro, J., Debes, P. & Primmer, C., 30 Sep 2020, In : Gene expression patterns. 38, 7 p.

Research output: Contribution to journalArticleScientificpeer-review

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Dual-light photodynamic therapy administered daily provides a sustained antibacterial effect on biofilm and prevents Streptococcus mutans adaptation

Nikinmaa, S., Alapulli, H., Auvinen, P., Vaara, M., Rantala, J., Kankuri, E., Sorsa, T., Meurman, J. & Pätilä, T., 6 May 2020, In : PLoS One. 15, 5, 16 p., 0232775.

Research output: Contribution to journalArticleScientificpeer-review

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Eco-evolutionary control of pathogens

Laessig, M. & Mustonen, V., 18 Aug 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 33, p. 19694-19704 11 p.

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Effects on Dopaminergic Neurons Are Secondary in COX-Deficient Locomotor Dysfunction in Drosophila

Yalgin, C., Rovenko, B., Andjelkovic, A., Neefjes, M., Oymak, B., Dufour, E., Hietakangas, V. & Jacobs, H. T., 21 Aug 2020, In : iScience. 23, 8, 75 p., 101362.

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Electrical synapses interconnecting axons revealed in the optic nerve head – a novel model of gap junctions’ involvement in optic nerve function

Smedowski, A., Akhtar, S., Liu, X., Pietrucha-Dutczak, M., Podracka, L., Toropainen, E., Alkanaan, A., Ruponen, M., Urtti, A., Varjosalo, M., Kaarniranta, K. & Lewin-Kowalik, J., Jun 2020, In : Acta Ophthalmologica. 98, 4, p. 408-417 10 p.

Research output: Contribution to journalArticleScientificpeer-review

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ELIMAKI Locus Is Required for Vertical Proprioceptive Response in Birch Trees

Alonso Serra, J. A., Shi, X., Peaucelle, A., Rastas, P., Bourdon, M., Immanen, J., Takahashi, J., Koivula, H., Eswaran, G., Muranen, S. J., Help-Rinta-Rahko, H., Smolander, O-P., Su, C., Safronov, O., Gerber, L., Salojärvi, J., Hagqvist, R., Mähönen, A. P., Helariutta, Y. & Nieminen, K., 24 Feb 2020, In : Current Biology. 30, 4, p. 589-599 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Embryonic development of skull bones in the Sahara horned viper (Cerastes cerastes), with new insights into structures related to the basicranium and braincase roof

Khannoon, E. R., Ollonen, J. & Di-Poi, N., Jul 2020, In : Journal of Anatomy. 237, 1, p. 1-19 19 p.

Research output: Contribution to journalArticleScientificpeer-review