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  • PL 56 (Viikinkaari 5)

    00014

    Finland

  • Viikinkaari 5, Biocenter 2

    00790 Helsinki

    Finland

19982019
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Publications 1998 2019

2015

Differential Isoform Expression and Selective Muscle Involvement in Muscular Dystrophies

Huovinen, S., Penttila, S., Somervuo, P., Keto, J., Auvinen, P., Vihola, A., Huovinen, S., Pelin, K., Raheem, O., Salenius, J., Suominen, T., Hackman, P. & Udd, B., Oct 2015, In : The American Journal of Pathology. 185, 10, p. 2833-2842 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Expression of BKV and JCV encoded microRNA in human cerebrospinal fluid, plasma and urine

Pietila, T., Nummi, M., Auvinen, P., Mannonen, L. & Auvinen, E., Apr 2015, In : Journal of Clinical Virology. 65, p. 1-5 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Flight-induced changes in gene expression in the Glanville fritillary butterfly

Kvist, J., Mattila, A. L. K., Somervuo, P., Ahola, V., Koskinen, P., Paulin, L., Salmela, L., Fountain, T., Rastas, P., Ruokolainen, A., Taipale, M., Holm, L., Auvinen, P., Lehtonen, R., Frilander, M. J. & Hanski, I., Oct 2015, In : Molecular Ecology. 24, 19, p. 4886-4900 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47

Andreevskaya, M., Johansson, P., Laine, P., Smolander, O-P., Sonck, M., Rahkila, R., Jääskeläinen, E., Paulin, L., Auvinen, P. & Björkroth, J., Jun 2015, In : Applied and Environmental Microbiology. 81, 11, p. 3800-3811 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Green areas around homes reduce atopic sensitization in children

Ruokolainen, L., von Hertzen, L., Fyhrquist, N., Laatikainen, T., Lehtomaki, J., Auvinen, P., Karvonen, A. M., Hyvarinen, A., Tillmann, V., Niemela, O., Knip, M., Haahtela, T., Pekkanen, J. & Hanski, I., Feb 2015, In : Allergy : European journal of allergy and clinical immunology. 70, 2, p. 195-202 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Gut Microbiota Are Related to Parkinson's Disease and Clinical Phenotype

Scheperjans, F., Aho, V., Pereira, P. A. B., Koskinen, K., Paulin, L., Pekkonen, E., Haapaniemi, E., Kaakkola, S., Eerola-Rautio, J., Pohja, M., Kinnunen, E., Murros, K. & Auvinen, P., Mar 2015, In : Movement Disorders. 30, 3, p. 350-358 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Hunt for the origin of allergy - comparing the Finnish and Russian Karelia.

Haahtela, T., Laatikainen, T., Alenius, H., Auvinen, P., Fyhrquist, N., Hanski, I., von Hertzen, L., Jousilahti, P., Kosunen, T. U., Markelova, O., Mäkelä, M. J., Pantelejev, V., Uhanov, M., Zilber, E. & Vartiainen, E., May 2015, In : Clinical and Experimental Allergy. 45, 5, p. 891-901 11 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

Open Access
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Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data

Koskinen, K., Auvinen, P., Björkroth, J. & Hultman, J., 1 Aug 2015, In : Journal of Computational Biology. 22, 8, p. 743-751 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Increased transcriptome sequencing efficiency with modified Mint-2 digestion-ligation protocol

Kammonen, J. I., Smolander, O-P., Sipilä, T., Overmyer, K., Auvinen, P. & Paulin, L., 15 May 2015, In : Analytical Biochemistry. 477, p. 38-40 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Linking Smoking, Coffee, Urate, and Parkinson's Disease - A Role for Gut Microbiota?

Scheperjans, F., Pekkonen, E., Kaakkola, S. & Auvinen, P., 2015, In : Journal of Parkinson's disease. 5, 2, p. 255-262 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Seasonal patterns of bacterial communities in the coastal brackish sediments of the Gulf of Finland, Baltic Sea

Vetterli, A., Hyytiäinen, K., Ahjos, M., Auvinen, P., Paulin, L., Hietanen, S. & Leskinen, E., 11 Sep 2015, In : Estuarine, Coastal and Shelf Science. 165, p. 86-96 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Temperature- and sex-related effects of serine protease alleles on larval development in the Glanville fritillary butterfly

Ahola, V., Koskinen, P., Wong, S. C., Kvist, J., Paulin, L., Auvinen, P., Saastamoinen, M., Frilander, M. J., Lehtonen, R. & Hanski, I., Dec 2015, In : Journal of Evolutionary Biology. 28, 12, p. 2224-2235 12 p.

Research output: Contribution to journalArticleScientificpeer-review

The microbiome of the human lower airways: a next generation sequencing perspective

Aho, V. T. E., Bento Pereira, P. A., Haahtela, T., Pawankar, R., Auvinen, P. & Koskinen, K., 16 Jun 2015, In : World Allergy Organization journal. 8, 23, 13 p.

Research output: Contribution to journalArticleScientificpeer-review

2014

Acinetobacter species in the skin microbiota protect against allergic sensitization and inflammation

Fyhrquist, N., Ruokolainen, L., Suomalainen, A., Lehtimaki, S., Veckman, V., Vendelin, J., Karisola, P., Lehto, M., Savinko, T., Jarva, H., Kosunen, T. U., Corander, J., Auvinen, P., Paulin, L., von Hertzen, L., Laatikainen, T., Mäkelä, M., Haahtela, T., Greco, D., Hanski, I. & 1 othersAlenius, H., Dec 2014, In : Journal of Allergy and Clinical Immunology. 134, 6, p. 1301-1320 20 p.

Research output: Contribution to journalArticleScientificpeer-review

Arabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation

Furuta, K. M., Yadav, S. R., Lehesranta, S., Belevich, I., Miyashima, S., Heo, J., Vaten, A., Lindgren, O., De Rybel, B., Van Isterdael, G., Somervuo, P., Lichtenberger, R., Rocha, R., Thitamadee, S., Tähtiharju, S., Auvinen, P., Beeckman, T., Jokitalo, E. & Helariutta, Y., 2014, In : Science. 345, 6199, p. 933-937 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis

Ojala, T., Kankainen, M., Castro, J., Cerca, N., Edelman, S., Westerlund-Wikstroem, B., Paulin, L., Holm, L. & Auvinen, P., 5 Dec 2014, In : BMC Genomics. 15, 21 p., 1070.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Evaluation of Molecular Techniques in Characterization of Deep Terrestrial Biosphere

Bomberg, M., Nyyssönen, M., Nousiainen, A., Hultman, J. J., Paulin, L. G., Auvinen, P. O. V. & Itävaara, M., 2014, In : Open Journal of Ecology. p. 468-487

Research output: Contribution to journalArticleScientificpeer-review

Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains

Savijoki, K., Iivanainen, A., Siljamaki, P., Laine, P. K., Paulin, L., Karonen (os. Miettinen), T., Pyörälä, S., Kankainen, M., Nyman, T. A., Salomaki, T., Koskinen, P., Holm, L., Simojoki, H., Taponen, S., Sukura, A., Kalkkinen, N., Auvinen, P. & Varmanen, P., Aug 2014, In : Journal of Proteome Research. 13, 8, p. 3748-3762 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

Nyyssonen, M., Hultman, J., Ahonen, L., Kukkonen, I., Paulin, L., Laine, P., Itävaara, M. & Auvinen, P., 2014, In : ISME Journal. 8, 1, p. 126-138 13 p.

Research output: Contribution to journalArticleScientificpeer-review

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Valimaki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E. A., Ferguson, L. C., Luo, S., Cao, Z., de Jong, M. A., Duplouy, A., Smolander, O-P., Vogel, H., McCoy, R. C. & 27 othersQian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J. K., Joshi, A., Salojarvi, J., Wheat, C. W., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkanen, E., Ylinen, J., Waterhouse, R. M., Turunen, M., Vaharautio, A., Ojanen, S. P., Schulman, A. H., Taipale, M., Lawson, D., Ukkonen, E., Makinen, V., Goldsmith, M. R., Holm, L., Auvinen, P., Frilander, M. J. & Hanski, I., Sep 2014, In : Nature Communications. 5, 9 p., 4737.

Research output: Contribution to journalArticleScientificpeer-review

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

Somervuo, P., Kvist, J., Ikonen, S., Auvinen, P., Paulin, L., Koskinen, P., Holm, L., Taipale, M., Duplouy, A., Ruokolainen, A., Saarnio, S., Siren, J., Kohonen, J., Corander, J., Frilander, M. J., Ahola, V. & Hanski, I., 2 Jul 2014, In : PLoS One. 9, 7, 12 p., 101467.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Transcriptome dynamics-based operon prediction in prokaryotes

Fortino, V., Smolander, O-P., Auvinen, P., Tagliaferri, R. & Greco, D., 16 May 2014, In : BMC Bioinformatics. 15, 14 p., 145.

Research output: Contribution to journalArticleScientificpeer-review

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2013

Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi

Ovaskainen, O., Schigel, D., Ali-Kovero, H., Auvinen, P., Paulin, L., Norden, B. & Norden, J., Sep 2013, In : ISME Journal. 7, 9, p. 1696-1709 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparison of Clostridium botulinum genomes shows the absence of cold shock protein coding genes in type E neurotoxin producing strains

Söderholm, H., Jaakkola, K., Somervuo, P., Laine, P., Auvinen, P., Paulin, L., Lindström, M. & Korkeala, H., 2013, In : Botulinum Journal. 2, 3-4, p. 189-207 19 p.

Research output: Contribution to journalArticleScientificpeer-review

Gene Expression Patterns Underlying the Reinstatement of Plasticity in the Adult Visual System

Tiraboschi, E., Guirado, R., Greco, D., Auvinen, P., Fernando Maya-Vetencourt, J., Maffei, L. & Castren, E., 2013, In : Neural Plasticity. 2013, 8 p., 605079.

Research output: Contribution to journalArticleScientificpeer-review

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Gene Expression Profiles in Human and Mouse Primary Cells Provide New Insights into the Differential Actions of Vitamin D-3 Metabolites

Tuohimaa, P., Wang, J-H., Khan, S., Kuuslahti, M., Qian, K., Manninen, T., Auvinen, P., Vihinen, M. & Lou, Y-R., 8 Oct 2013, In : PLoS One. 8, 10, 14 p., e75338.

Research output: Contribution to journalArticleScientificpeer-review

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Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase Clusters

Garlant, L., Koskinen, P., Rouhiainen, L. A. O., Laine, P., Paulin, L., Auvinen, P., Holm, L. & Pirhonen, M., 2013, In : Diversity. 5, 4, p. 824-842 19 p.

Research output: Contribution to journalArticleScientificpeer-review

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High-sequence diversity and structural conservation in the human T-cell receptor beta junctional region during thymic development

Tuulasvaara, A., Baussand, J., Laine, P., Paulin, L., Salminen, J., Auvinen, P., Gorochov, G. & Arstila, T. P., Aug 2013, In : European Journal of Immunology. 43, 8, p. 2185-2193 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Identification and Validation of Human Papillomavirus Encoded microRNAs

Qian, K., Pietila, T., Rönty, M. J., Michon, F., Frilander, M. J., Ritari, J., Tarkkanen, J., Paulin, L., Auvinen, P. & Auvinen, E., 30 Jul 2013, In : PLoS One. 8, 7, p. Article Number: e70202 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Lack of RsmA-Mediated Control Results in Constant Hypervirulence, Cell 655 Elongation, and Hyperflagellation in Pectobacterium wasabiae

Kõiv, V., Andresen, L., Broberg, E. M., Frolova, J., Somervuo, P. J., Auvinen, P., Pirhonen, M., Tenson, T. & Mäe, A., 2013, In : PLoS One. 8, 1, 12 p., 54248.

Research output: Contribution to journalArticleScientificpeer-review

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Lep-MAP: fast and accurate linkage map construction for large SNP datasets

Rastas, P., Paulin, L., Hanski, I., Lehtonen, R. J. & Auvinen, P., 2013, In : Bioinformatics. 29, 24, p. 3128-3134 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Mondo/ChREBP-Mlx-Regulated Transcriptional Network Is Essential for Dietary Sugar Tolerance in Drosophila

Havula, E., Teesalu, M., Hyötyläinen, T., Seppälä, H., Hasygar, K., Auvinen, P., Oresic, M., Sandmann, T. & Hietakangas, V., 2013, In : PLoS Genetics. 9, 4, 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Role and Regulation of the Flp/Tad Pilus in the Virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193

Nykyri, J., Mattinen, L., Niemi, O. A., Adhikari, S., Kõiv, V., Somervuo, P., Fang, X., Auvinen, P., Mäe, A., Palva, E. T. & Pirhonen, M., 2013, In : PLoS One. 8, 9, 11 p., e73718.

Research output: Contribution to journalArticleScientificpeer-review

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Significance of heme-based respiration in meat spoilage caused by Leuconostoc gasicomitatum

Jääskeläinen, E., Johansson, P., Kostiainen, O., Nieminen, T., Schmidt, G., Somervuo, P., Mohsina, M., Vanninen, P., Auvinen, P. & Björkroth, J., 2013, In : Applied and Environmental Microbiology. 79, 4, p. 1078-1085 8 p.

Research output: Contribution to journalArticleScientificpeer-review

2012

Cell culture model predicts human disease: Altered expression of junction proteins and matrix metalloproteinases in cervical dysplasia.

Kivi, N. J., Rönty, M. J., Tarkkanen, J., Auvinen, P. & Auvinen, E., 2012, In : BMC Clinical Pathology. 12, 9, 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics

Nieminen, T. T., Koskinen, K., Laine, P., Hultman, J., Säde, E., Paulin, L., Paloranta, A., Johansson, P., Björkroth, J. & Auvinen, P., 2012, In : International Journal of Food Microbiology. 157, 2, p. 142-149 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Detection of Human Papillomaviruses by Polymerase Chain Reaction and Ligation Reaction on Universal Microarray

Ritari, J., Hultman, J., Fingerroos, R., Tarkkanen, J., Pullat, J., Paulin, L., Kivi, N., Auvinen, P. & Auvinen, E., 2012, In : PLoS One. 7, 3, p. Article Number: e34211 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Environmental biodiversity, human microbiota, and allergy are interrelated

Hanski, I., von Hertzen, L., Fyhrquist, N., Koskinen, K., Torppa, K., Laatikainen, T., Karisola, P., Auvinen, P., Paulin, L., Mäkelä, M., Vartiainen, E., Kosunen, T. U., Alenius, H. & Haahtela, T., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 21, p. 8334-8339 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Experience-dependent expression of NPAS4 regulates plasticity in adult visual cortex

Maya-Vetencourt, J. F., Tiraboschi, E., Greco, D., Restani, L., Cerri, C., Auvinen, P., Maffei, L. & Castrén, E., Oct 2012, In : Journal of Physiology. 590, 19, p. 4777-4787 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Expression of multiple nebulin isoforms in human skeletal muscle and brain

Laitila, J., Hanif, M., Paetau, A., Hujanen, S., Keto, J., Somervuo, P. J., Huovinen, S., Udd, B., Wallgren-Pettersson, C., Auvinen, P., Hackman, P. & Pelin, K., 2012, In : Muscle & Nerve. 46, 5, p. 730-737 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Gene expression analysis of Drosophilaa Manf mutants reveals perturbations in membrane traffic and major metabolic changes

Palgi, M., Greco, D., Lindström, R., Auvinen, P. & Heino, T. I., 11 Apr 2012, In : BMC Genomics. 13, 134, p. - 20 p.

Research output: Contribution to journalArticleScientificpeer-review

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Genome Sequence of Pectobacterium sp. Strain SCC3193

Koskinen, J. P., Laine, P., Niemi, O., Nykyri, J., Harjunpää, H., Auvinen, P., Paulin, L., Pirhonen, M., Palva, T. & Holm, L., Nov 2012, In : Journal of Bacteriology. 194, 21, p. 6004 1 p.

Research output: Contribution to journalArticleScientificpeer-review

Identification and characterization of a lipopolysaccharide α,2,3-sialyltransferase from the human pathogen Helicobacter bizzozeronii

Kondadi, P. K., Rossi, M., Twelkmeyer, B., Schur, M. J., Li, J., Schott, T., Paulin, L., Auvinen, P., Hänninen, M-L., Schweda, E. K. H. & Wakarchuk, W., 2012, In : Journal of Bacteriology. 194, 10, p. 2540-2550 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Leptin-Induced mTOR Activation Defines a Specific Molecular and Transcriptional Signature Controlling CD4(+) Effector T Cell Responses

Procaccini, C., De Rosa, V., Galgani, M., Carbone, F., Cassano, S., Greco, D., Qian, K., Auvinen, P., Cali, G., Stallone, G., Formisano, L., La Cava, A. & Matarese, G., 15 Sep 2012, In : Journal of Immunology. 189, 6, p. 2941-2953 13 p.

Research output: Contribution to journalArticleScientificpeer-review

miRSeqNovel: An R based workflow for analyzing miRNA sequencing data

Qian, K., Auvinen, E., Greco, D. & Auvinen, P., 1 Oct 2012, In : Molecular and Cellular Probes. 26, 5, p. 208-211 4 p.

Research output: Contribution to journalArticleScientificpeer-review

Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation

Ritari, J., Koskinen, K., Hultman, J., Kurola, J. M., Kymäläinen, M., Romantschuk, M., Paulin, L. & Auvinen, P., 2012, In : BMC Microbiology. 12, 14 p., 121.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Re-analysis of Bipolar Disorder and Schizophrenia Gene Expression Complements the Kraepelinian Dichotomy

Qian, K., Di Lieto, A., Corander, J., Auvinen, P. & Greco, D., 2012, Advances in Systems Biology. Goryanin, I. I. & Goryachev, A. B. (eds.). New York: Springer, Vol. 736. p. 563-577 15 p. (Advances in Experimental Medicine and Biology; vol. 736, no. 5).

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

SNP Design from 454 Sequencing of Podosphaera plantaginis Transcriptome Reveals a Genetically Diverse Pathogen Metapopulation with High Levels of Mixed-Genotype Infection

Tollenaere, C. M. J., Susi, H., Nokso-Koivisto, J. P., Koskinen, P., Tack, A. J. M., Auvinen, P., Paulin, L., Frilander, M., Lehtonen, R. J. & Laine, A-L., 2012, In : PLoS One. 7, 12, p. e52492 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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