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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

2011

Comparative study of transcriptional and physiological responses to salinity stress in two contrasting Populus alba L. genotypes

Beritognolo, I., Harfouche, A., Brilli, F., Prosperini, G., Gaudet, M., Brosche, M., Salani, F., Kuzminsky, E., Auvinen, P., Paulin, L. G., Kangasjärvi, J., Loreto, F., Valentini, R., Scarascia Mugnozza, G. & Sabatti, M., 2011, In : Tree Physiology. 31, 12, p. 1335-1355 21 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparison of Dorsocervical With Abdominal Subcutaneous Adipose Tissue in Patients With and Without Antiretroviral Therapy-Associated Lipodystrophy

Sevastianova, K., Sutinen, J., Greco, D., Sievers, M., Salmenkivi, K., Perttilä, J., Olkkonen, V. M., Wagsater, D., Lidell, M. E., Enerback, S., Eriksson, P., Walker, U. A., Auvinen, P., Ristola, M. & Yki-Järvinen, H., 2011, In : Diabetes Care. 60, p. 1894-1900 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Genome sequence of a food spoilage lactic acid bacterium, Leuconostoc gasicomitatum LMG 18811T, in association with specific spoilage reactions

Johansson, P., Paulin, L., Säde, E., Salovuori, N., Alatalo, E. R., Björkroth, K. J. & Auvinen, P., 2011, In : Applied and Environmental Microbiology. 77, 13, p. 4344-4351 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium

Laakso, K., Koskenniemi, K., Koponen, J., Kankainen, M., Surakka, A., Salusjarvi, T., Auvinen, P., Savijoki, K., Nyman, T. A., Kalkkinen, N., Tynkkynen, S. & Varmanen, P., 2011, In : Microbial Biotechnology. 4, 6, p. 746-766 21 p.

Research output: Contribution to journalArticleScientificpeer-review

Human papillomavirus 16 E5 modulates the expression of host microRNAs

Greco, D., Kivi, N. J., Qian, K., Leivonen, S-K. A., Auvinen, P. O. V. & Auvinen, E., 2011, In : PLoS One. 6, 7, p. e21646 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Metagenomiikka ja DNA –mikrosirut mikrobien määrittämisessä

Ritari, J. J., Koskinen, K. M., Paulin, L. G. & Auvinen, P. O. V., 2011, Uudet ympäristömittausmenetelmät – haasteita, mahdollisuuksia ja liiketoimintaa . p. 38-45

Research output: Chapter in Book/Report/Conference proceedingChapterProfessional

Microbial sampling and analyisis of the Outokumpu deep drill hole biosphere in 2007-2009.

Itävaara, M., Nyyssönen, M., Bomberg, M., Kapanen, A., Nousiainen, A., Ahonen, L., Hultman, J., Paulin, L., Auvinen, P. & Kukkonen, IT., 2011, Outokumpu deep drilling project 2003-2010. Kukkonen, I. T. (ed.). p. 199-206 8 p. (Geological survey of Finland. Special paper; vol. 2011, no. 51).

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

Molecular profiling of fungal communities in moisture damaged buildings before and after remediation - a comparison of culture-dependent and culture-independent methods

Pitkäranta, M. J., Meklin, T., Hyvarinen, A., Nevalainen, A., Paulin, L., Auvinen, P., Lignell, U. & Rintala, H., 2011, In : BMC Microbiology. 11, p. 235 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG

Koskenniemi, K., Laakso, K., Koponen, J., Kankainen, M., Greco, D., Auvinen, P., Savijoki, K., Nyman, T., Surakka, A., Salusjärvi, T., de Vos, W. M., Tynkkynen, S., Kalkkinen, N. & Varmanen, P. K., 2011, In : Molecular & Cellular Proteomics. 10, 2, 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Spatially differing bacterial communities in water columns of the northern Baltic Sea

Koskinen, K., Hultman, J., Paulin, L. G., Auvinen, P. & Kankaanpää, H., 2011, In : FEMS Microbiology Ecology. 75, 1, p. 99-110 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Vascular endothelial growth factor C acts as a neurotrophic factor for dopamine neurons in vitro and in vivo

Piltonen, M. H., Planken, A., Leskelä, O., Myöhänen, T. T., Hänninen, A-L., Auvinen, P., Alitalo, K., Anderssoo, J-O., Saarma, M. & Männistö, P., 14 Jul 2011, In : Neuroscience. 192, p. 550-563 14 p.

Research output: Contribution to journalArticleScientificpeer-review

2010

An Association Analysis of Circadian Genes in Anxiety Disorders

Sipila, T., Kananen, L., Greco, D., Donner, J., Silander, K., Terwilliger, J. D., Auvinen, P., Peltonen, L., Lönnqvist, J., Pirkola, S., Partonen, T. & Hovatta, I., 2010, In : Biological Psychiatry. 67, 12, p. 1163-1170 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Bacterial diversity at different stages of the composting process

Partanen, P., Hultman, J., Paulin, L., Auvinen, P. & Romantschuk, M., 2010, In : BMC Microbiology. 10, 94, 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Bayesian integrated modeling of expression data: a case study on RhoG

Gupta, R., Greco, D., Auvinen, P. & Arjas, E., 2010, In : BMC Bioinformatics. 11, 295, p. - 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Determination of fungal succession during municipal solid waste composting using a cloning-based analysis

Hultman, J., Vasara, T., Partanen, P., Kurola, J., Kontro, M. H., Paulin, L., Auvinen, P. & Romantschuk, M., 2010, In : Journal of Applied Microbiology. 108, 2, p. 472-487 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Differential gene expression in senescing leaves of two silver birch genotypes in response to elevated CO2 and tropospheric ozone

Kontunen-Soppela, S., Riikonen, J., Ruhanen, H., Brosche, M., Somervuo, P., Peltonen, P., Kangasjärvi, J., Auvinen, P., Paulin, L., Keinanen, M., Oksanen, E. & Vapaavuori, E., 2010, In : Plant, Cell and Environment. 33, 6, p. 1016-1028 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Factors underpinning the responsiveness and higher levels of virus resistance realised in potato genotypes carrying virus-specific R genes

Vuorinen, A. L., Gammelgard, E., Auvinen, P., Somervuo, P., Dere, S. & Valkonen, J. P. T., 2010, In : Annals of Applied Biology. 157, 2, p. 229-241 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Gene expression analysis in SV-40 immortalized human corneal epithelial cells cultured with an air-liquid interface

Greco, D., Vellonen, K-S., Turner, H. C., Häkli, M., Tervo, T., Auvinen, P., Wolosin, J. M. & Urtti, A., 2010, In : Molecular Vision. 16, p. 2109-2120 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Gene Expression Profiling of U12-Type Spliceosome Mutant Drosophila Reveals Widespread Changes in Metabolic Pathways

Pessa, H. K. J., Greco, D., Kvist, J., Wahlström, G. M., Heino, T. I., Auvinen, P. & Frilander, M. J., 2010, In : PLoS One. 5, 10, p. e13215 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Genome Sequence of Lactobacillus crispatus ST1

Ojala, T., Kuparinen, V., Koskinen, P., Alatalo, R. M. E., Holm, L., Auvinen, P., Edelman, S., Westerlund-Wikström, B., Korhonen, T., Paulin, L. G. & Kankainen, M., 2010, In : Journal of Bacteriology. 192, 13, p. 3547-3548 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Identifying wood-inhabiting fungi with 454 sequencing: what is the probability that BLAST gives the correct species?

Ovaskainen, O., Nokso-Koivisto, J. P., Hottola, J., Rajala, T., Pennanen, T., Ali-Kovero, H., Miettinen, O., Oinonen, P., Auvinen, P., Paulin, L., Larsson, K-H. & Makipaa, R., 2010, In : Fungal Ecology. 3, 4, p. 274-283 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Metagonomiikka avaa uusia ovia mikrobiologiassa

Hultman, J. & Auvinen, P., 2010, In : Duodecim. 126, 11, p. 1278-1285 8 p.

Research output: Contribution to journalArticleScientific

Mikrosirutekniikka bakteeritaudinaiheuttajien tutkimuksessa ja diagnostiikassa

Aittamaa, M., Söderholm, H., Somervuo, P. J., Nykäsenoja, S., Auvinen, P., Selby, K., Derman, Y., Nuppunen, M., Myllys, V., Rantala, L. & Valkonen, J., 2010, Helsingin yliopisto, Maataloustieteiden laitos, Elintarvikehygienian ja ympäristöterveyden osasto ja Biotekniikan instituutti. 29 p.

Research output: Book/ReportCommissioned reportProfessional

2009

A Naive Bayes classifier for protein function prediction

Kohonen, J., Talikota, S., Corander, J., Auvinen, P. & Arjas, E., 2009, In : In Silico Biology. 9, 1-2, p. 23-34 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays

Ritari, J., Paulin, L., Hultman, J. & Auvinen, P., 2009, In : BMC research notes. 2, 249, [7] s

Research output: Contribution to journalArticleScientificpeer-review

Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human-mucus binding protein

Kankainen, M., Paulin, L., Tynkkynen, S., von Ossowski, I., Reunanen, J., Partanen, P., Satokari, R., Vesterlund, S., Hendrickx, A. P. A., Lebeer, S., Keersmaecker, S. C. J. D., Vanderleyden, J., Hämäläinen, T., Laukkanen, S., Salovuori, N., Ritari, J., Alatalo, E., Korpela, R., Mattila-Sandholm, T., Lassig, A. & 10 othersHatakka, K., Kinnunen, K. T., Karjalainen, H., Saxelin, M., Laakso, K., Surakka, A., Palva, A., Salusjärvi, T., Auvinen, P. & Vos de, W. M., 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 40, p. 17193-17198 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparative genomic hybridization analysis of two predominant Nordic group I (proteolytic) Clostridium botulinum type B clusters

Lindström, M., Hinderink, K., Somervuo, P., Kiviniemi, K., Nevas, M., Chen, Y., Auvinen, P., Carter, A. T., Mason, D. R., Peck, M. W. & Korkeala, H., 2009, In : Applied and Environmental Microbiology. 75, 9, p. 2643-2651 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures

Greco, D., Volpicelli, F., Di Lieto, A., Leo, D., Perrone Capano, C., Auvinen, P. & di Porzio, U., 2009, In : PLoS One. 4, 3, p. e4977 1 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Identification of flowering genes in strawberry, a perennial SD plant

Mouhu, K., Hytönen, T., Folta, K., Rantanen, M., Paulin, L., Auvinen, P. & Elomaa, P., 2009, In : BMC Plant Biology. 9, p. art. 122 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Mikrobiyhteisöjen tutkiminen metagenomiikan avulla

Hultman, J. & Auvinen, P., 2009, In : Natura. 46, 4, p. 14-18 5 p.

Research output: Contribution to journalArticleScientific

2008

Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture

Pitkäranta, M., Meklin, T., Hyvärinen, A., Paulin, L., Auvinen, P., Nevalainen, A. & Rintala, H., 2008, In : Applied and Environmental Microbiology. 74, 1, p. 233-244 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Bakteeritaudinaiheuttajien tarkennettu tunnistus mikrosirudiagnostiikalla

Translated title of the contribution: Detection of bacterial pathogens using microarraysAittamaa, M., Auvinen, P., Hindernik, K., Kiviniemi, K., Korkeala, H., Leppäranta, O., Lindström, M., Mattila, M., Myllys, V., Nykäsenoja, S., Pirhonen, M., Rantala, L., Somervuo, P. J., Söderholm, H. & Valkonen, J., 2008, Maataloustieteen päivät 2008. Hopponen, A. (ed.). Helsinki: Suomen maataloustieteellinen seura, 6 p. (Suomen maataloustieteellisen seuran tiedotteita; vol. 23).

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

Bayesian hierarchical model for estimating gene expression intensity using multiple scanned microarrays

Gupta, R., Arjas, E., Kulathinal, S., Thomas, A. & Auvinen, P., 2008, In : EURASIP Journal on Bioinformatics and Systems Biology. 2008, p. 231950 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Distinguishing bacterial pathogens of potato using a genome-wide microarray approach

Aittamaa, M., Somervuo, P., Pirhonen, M., Mattinen, L., Nissinen, R., Auvinen, P., Valkonen, J. P. T. & Valkonen, J., 2008, In : Molecular Plant Pathology. 9, 5, p. 705-717 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Gene expression in human NAFLD

Greco, D., Kotronen, A., Westerbacka, J., Puig, O., Arkkila, P., Kiviluoto, T., Laitinen, S., Kolak, M., Fisher, R. M., Hamsten, A., Auvinen, P. & Yki-Järvinen, H., 2008, In : American Journal of Physiology: Gastrointestinal and Liver Physiology. 294, 5, p. G1281-G1287

Research output: Contribution to journalArticleScientificpeer-review

Genes involved in cell adhesion, cell motility and mitogenic signaling are altered due to HPV 16 E5 protein expression

Kivi, N., Greco, D., Auvinen, P. & Auvinen, E., 2008, In : Oncogene. 27, 18, p. 2532-2541 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Microarray analysis of a Chlamydia pneumoniae: infected human epithelial cell line by use of gene ontology hierarchy

Alvesalo, J., Greco, D., Leinonen, M., Raitila, T., Vuorela, P. & Auvinen, P., 2008, In : Journal of Infectious Diseases. 197, 1, p. 156-162 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Microarray profiling of host-extract-induced genes and characterization of the type VI secretion cluster in the potato pathogen Pectobacterium atrosepticum

Mattinen, L., Somervuo, P., Nykyri, J., Nissinen, R., Kouvonen, P., Corthals, G., Auvinen, P., Aittamaa, M., Valkonen, J. & Pirhonen, M., 2008, In : Microbiology. 154, 8, p. 2387-2396 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Optimal designs for microarray experiments with biological and technical replicates

Gupta, R., Somervuo, P., Kulathinal, S. & Auvinen, P., 2008, Recent Advances in Linear Models and Related Areas. Heidelberg: Physica-Verlag Heidelberg, p. 389-400 12 p.

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

Physiology, pathology and relatedness of human tissues from gene expression meta-analysis

Greco, D., Somervuo, P., Di Lieto, A., Raitila, T., Nitsch, L., Castren, E. & Auvinen, P., 2008, In : PLoS One. 3, 4, p. e1880 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Plant, animal and food pathogens analyzed using genome-wide microarrays: towards improved diagnostics and control of bacterial pathogens

Aittamaa, M., Auvinen, P., Hinderink, K., Kiviniemi, K., Korkeala, H., Leppäranta, O., Lindström, M., Mattinen, L., Myllys, V., Nevas, M., Nykäsenoja, S., Pirhonen, M., Rantala, L., Somervuo, P. & Valkonen, J. P. T., 2008, COST Action 853: Agricultural biomarkers for array technology. Frey, J. E. & Pasquer, F. (eds.). Wädenswil, Switzerland: Agroscope Changins-Wädenswil, p. 47-51 5 p.

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

Pre-filtering improves reliability of Affymetrix GeneChips results when used to analyze gene expression in complex tissues

Greco, D., Leo, D., Di Porzio, U., Perrone Capano, C. & Auvinen, P., 2008, In : Molecular and Cellular Probes. 22, 2, p. 115-121 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Probe-based negative selection for underrepresented phylotypes in large environmental clone libraries

Hultman, J., Pitkäranta, M., Romantschuk, M., Auvinen, P. & Paulin, L., 2008, In : Journal of Microbiological Methods. 75, 3, p. 457-463 7 p.

Research output: Contribution to journalArticleScientificpeer-review

SINORHIZOBIUM ARBORIS GENES ARE DIFFERENTIALLY EXPRESSED UNDER SALT STRESS

Penttinen, P., Terefework, Z., Paulin, L., Auvinen, P., Greco, D. & Lindström, K., 2008, Unknown host publication. Dakora, FD., Chimphango, SBM., Valentine, AJ., Elmerich, C. & Newton, WE. (eds.). p. 371-371 1 p. (CURRENT PLANT SCIENCE AND BIOTECHNOLOGY IN AGRICULTURE).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Universal ligation-detection-reaction microarray applied for compost microbes

Hultman, J., Ritari, J., Romantschuk, M., Paulin, L. & Auvinen, P., 2008, In : BMC Microbiology. 8, 237, 36, p. + 4 liitel 1 p.

Research output: Contribution to journalArticleScientificpeer-review

2007

Bakteeritaudinaiheuttajien tarkennettu tunnistus mikrosirudiagnostiikalla: loppuraportti

Translated title of the contribution: Detection of bacterial pathogens using microarray-based diagnosticsAittamaa, M., Auvinen, P., Hinderink, K., Kiviniemi, K., Korkeala, H., Leppäranta, O., Lindström, M., Mattila, M., Myllys, V., Nykäsenoja, S., Rantala, L., Somervuo, P., Söderholm, H. & Valkonen, J., 2007, Helsinki, Finland: Helsingin yliopisto, soveltavan biologian laitos, kasvipatologian laboratorio. 30 p.

Research output: Book/ReportCommissioned reportProfessional

Microarray image segmentation using additional dye - An experimental study

Gupta, R., Ruosaari, S., Kulathinal, S., Hollmen, J. & Auvinen, P., 2007, In : Molecular and Cellular Probes. 21, p. 321-328 8 p.

Research output: Contribution to journalArticleScientificpeer-review