Publications

Use this table to quickly navigate to the publication list of a specific year.

2024

Waszczak, C., Yarmolinsky, D., Leal-Gavarrón, M., Vahisalu, T., Sierla, M., Zamora, O., Carter, R., Puukko, T., Sipari, N., Lamminmäki, A., Durner, J., Ernst, D., Winkler, J. B., Paulin, L., Auvinen, P., Fleming, A., Andersson, M., Kollist, H. & Kangasjärvi, J. 2024. Synthesis and import of GDP-L-fucose into the Golgi affect plant-water relations. New Phytologist 241:747-763. 

Honkimaa, A., Laine, P., Suppula, J., Tynninen, O., Saarela, M., Laakso, SM., Hetemäki, I., Liimatainen, H., Auvinen, P. & Auvinen, E. Exploring JC polyomavirus sequences and human gene expression in brain tissue of patients with progressive multifocal leukoencephalopathy. The Journal of Infectious Diseases (in press). 

Auvinen, E., Honkimaa, A., Laine, P., Passerini, S., Moens, U., Pietropaolo, V., Saarela, M., Maunula, L., Mannonen, L., Tynninen, O., Haapasalo, H., Rauramaa, T., Auvinen, P & Liimatainen. H. Differentiation of highly pathogenic strains of human JC polyomavirus in neurological patients by next generation sequencing. Journal of Clinical Virology (in press). 

Brandt, E., Koivisto, A., Pereira, P., Mustanoja, E., Auvinen, P., Saari, T., Lehtola, J-M., Hannonen, S., Rusanen, M., Leinonen, V., Scheperjans, F. & Kärkkäinen, V. Gut microbiome changes in patients with idiopathic normal pressure hydrocephalus. Alzheimer's disease and Associated Disorders (in press). 

Sjövall., A., Mustanoja, E., Lyyski, A., Auvinen, P., Silvola, J., Aarnisalo, A., Pätäri-Sampo, A. & Laulajainen-Hongisto, A. Microbiome of the external auditory canal; Changes after long-term hearing aid use. Otology & Neurotology (in press). 

Scheperjans, F. & Auvinen, P. 2024. Parkinsonin taudista tuli systeemisairaus – Suolistobakteerit syyllisiä? Lääketieteen parantava voima. p270-272. Duodecim Kustannus Oy 

Michell, C., Collins, J., Laine, PK., Fekete, Z., Tapanainen, R., Wood, JMD., Goffart, S., Pohjoismäki, JLO. High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding. Peer Community Journal, Volume 4 (2024), article no. e26. doi : 10.24072/pcjournal.393. https://peercommunityjournal.org/articles/10.24072/pcjournal.393/

2023

Rosing-Asvid, A., Löytynoja, A., Momigliano, P., Hansen, R., Scharff-Olsen, C., Valtonen, M., Kammonen, J., Dietz, R., Rigét, F., Ferguson, S., Lydersen, C., Kovacs, K., Holland, D., Jernvall, J., Auvinen, P, & Tange Olsen, M. 2023. An evolutionarily distinct ringed seal in the Ilulissat Icefjord. Molecular Ecology 32:5932–5943.

Paasela, T., Lim, K-J., Pavicic, M., Harju, A., Venäläinen, M., Paulin, L., Auvinen, P., Kärkkäinen, K., & Teeri, TH. 2023. Transcriptome analysis reveals novel regulators of the Scots pine stilbene pathway. Plant and Cell Physiology 64:1204-1219.

Löytynoja, A., Rastas, P., Valtonen, M., Kammonen, J., Holm, L., Tange Olsen, M., Paulin, L., Jernvall, J. & Auvinen, P. 2023. Fragmented habitat compensates for the adverse effects of genetic bottleneck. Current Biology 33: 1009–1018.

Haahtela, T., Alenius, H., Auvinen, P., Fyhrquist, N., von Hertzen, L., Jousilahti, P., Karisola, P., Laatikainen, T. Lehtimäki, J., Paalanen, L., Ruokolainen, R., Saarinen, K., Valovirta, E., Vasankari, T., Vlasoff, T., Erhola, M., Bousquet, J., Vartiainen, E., Mäkelä, MJ., & the Karelia Allergy Study Group. 2023. A short history from Karelia study to biodiversity and public health interventions. Frontiers in Allergy Determinants. 14;4:1152927. 

Auvinen, P., Chang, W., Holm, L., James, M., Jääskeläinen, M., Khazaei, H., Laine, P., Paulin, L., Guedes Salgado, M. P., Stoddard, F., Tanskanen, J., Törönen, P. & Schulman, A. 2023. A faba bean pan-genome for advancing sustainable protein security. Legume perspectives. 24: 7-9. 

Sundell, T., Kammonen, JI., Mustanoja, E., Biard, V., Kunnasranta, M., Niemi, M., Nykänen, M., Nyman, T., Palo, JU., Valtonen, M., Paulin, L., Jernvall, J. & Auvinen, P. 2023. Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population. Conservation Genetics 24:155-165.

Honkimaa, A., Suppula, J., Tynninen, O., Saarela, M., Liimatainen, H., Laine, P., Auvinen, P. & Auvinen, E. JC polyomavirus modifies the expression of human microRNAs in PML brain. J Infect Dis. 2023 Oct 3;228(7):829-833. 

2022

Johansson, P., Säde, E., Hultman, J., Auvinen, P. & Björkroth, J. 2022. Pangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum. BMC Genomics 23:818.

Plavec, Z., Domanska, A., Liu, X., Laine, P., Paulin, L., Varjosalo, M., Auvinen, P., Wolf, SG., Anastasina, M. & Butcher, SJ. 2022. SARS-CoV-2 production, purification and inactivation. Viruses 14;1989.

Boertien, JM., Murtomäki, K., Pereira, PAB., van der Zee, S., Mertsalmi, TH., Levo, R., Nojonen, T., Mäkinen, E., Jaakkola, E., Laine, P., Paulin, L., Pekkonen, E., Kaasinen, V., Auvinen, P., Scheperjans, R. & van Laar. 2022. Fecal microbiome alterations in treatment-naïve de novo Parkinson’s disease. npj Parkinson's Disease 8:129.

Almeida, BLB., Barhudeen, MNM., Chauhan, M., Dash, S., Vinodh, K., Häkkinen, A., Lloyd-Price, J., Palma, CSD., Baptista, ISC., Gupta, A., Kesseli, J., Dufour, E., Smolander, OP., Nykter, M., Auvinen, P., Jacobs, H., Oliveira, S. & Ribeiro, A. 2022. The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Research 50:6801-6819.

Xie, A., Ensink, E., Li, P., Gordevičius, J., Marshall, LL., George, S., Pospisilik, AJ., Aho, VTE., Houser, MD., Pereira, PAB., Rudi, K., Paulin, L., Tansey, MG., Auvinen, P., Brundin, P., Brundin, L., Labrie, V. & Scheperjans, F. 2022. Bacterial butyrate in Parkinson’s disease is linked to epigenetic changes and depressive symptoms. Movement Disorders 37:1644-1653.

Pereira, PAB., Trivedi, DK., Silverman, J., Duru, IC., Paulin, L., Auvinen, P. & Scheperjans, F. 2022. Multiomics implicate gut microbiota in altered lipid and energy metabolism in Parkinsons disease. npj Parkinson's Disease 8:39.

Smolander, O-P., Blande, D., Ahola, V., Rastas, P., Tanskanen, J., Kammonen, JI., Oostra, V., Pellegrini, L., Ikonen. S., Dallas, T., DiLeo, MF., Duploy, A., Duru, IC., Halimaa, P., Kahilainen, A., Kuwar, SS., Kärenlampi, SO., Lafuente, E., Luo, S., Makkonen, J., Nair, A., de la Paz Celorio-Mancera, M., Pennanen, V., Ruokolainen, A., Sundell, T., Tervahauta, AI., Twort, V., van Bergen, E., Österman-Udd, J., Paulin, L., Frilander, MJ., Auvinen, P & Saastamoinen, M. 2022 Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating PacBio long reads and a high-density linkage map. GigaScience 11, giab097.

2021

Laine,P., Rowell, WJ., Paulin, L., Kujawa, S., Raterman, D., Mayhew, G., Wendt, J., Burgess, DL., Partonen, T., Paunio, T., Auvinen, P. & Ekholm, JM. 2021. Alu element in the RNA Binding Motif Protein, X-Linked 2 (RBMX2) gene found to be linked to bipolar disorder. PLoS ONE 16: e0261170.

van Kessel, SP., Auvinen, P., Scheperjans, F. & El Aidy, S. 2021. Gut bacterial-tyrosine decarboxylase associates with clinical variables in a longitudinal cohort study of Parkinsons disease. npj Parkinson's Disease 7:115.

Laine, P., Nihtilä, H., Mustanoja, E., Lyyski. A., Ylinen, A., Hurme, J., Paulin, L., Jokiranta, S., Auvinen, P & Meri, T. 2022. SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers. Journal of Medical Virology 94:1227-1231.

Shishido, TK., Wahlsten, M., Laine, P., Rikkinen, J., Lundell, T. & Auvinen, P. 2021. Microbial communities of Cladonia lichens and their biosynthetic gene clusters potentially encoding natural products. Microorganisms 9, 1347.

Nikinmaa, S., Moilanen, N., Sorsa, T., Rantala, J., Alapulli, H., Kotiranta, A., Auvinen, P., Kankuri, E., Meurman, JH. & Pätilä, T. 2021. Indocyanine green-assisted and LED-light-activated antibacterial photodynamic therapy reduces dental plaque. Dentistry Journal 9:52.

Duru, IC., Bucur. FI., Andreevskaya, M., Ylinen, A., Crauwels, P., Grigore-Gurgu, L., Nikparvar, B., Rode, TM., Laine, P., Paulin, L., Løvdal, T., Riedel, CU., Bar, N., Borda, D., Nicolau, AI. & Auvinen, P. 2021.The complete genome sequence of Listeria monocytogenes strain S2542 and expression of selected genes under high-pressure processing. BMC Research Notes 14:137.

Nikparvar, B., Andreevskaya, M., Duru, IC, Bucur, FI., Grigore-Gurgu, L., Borda, D., Nicolau, AI., Riedel, CU., Auvinen, P. & Bar, N. 2021. Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing. BMC Genomics 22:266.

Duru, IC., Bucur. FI., Andreevskaya, M., Nikparvar, B., Ylinen, Y., Grigore-Gurgu, L., Rode, TM., Crauwels, P., Laine, P., Paulin, L., Løvdal, T., Riedel, CU., Bar, N., Borda, D., Nicolau, AI. & Auvinen, P. 2021. High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes. BMC Genomics 22:117.

Lim, K-J., Paasela, T., Harju, A., Venäläinen, M., Paulin, L., Auvinen, P., Kärkkäinen, K. & Teeri, TH. 2021. A transcriptomic view to wounding response in young Scots pine stems. Scientific Reports 11:3778.

Aho, VT., Crawford Houser, M., Pereira, PAB., Chang, J., Rudi, K., Paulin, L., Hertzberg, V., Auvinen, P., Scheperjans, F. & Tansey, MG. 2021. Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson's disease. Molecular Neurodegeneration 16:6.

Duru, IC., Ylinen, A., Belanov, S., Pulido, AA., Paulin, L., & Auvinen, P. 2021. Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria. BMC Genomics 22:28.

Holmer, J., Aho, V., Eriksdotter, M., Paulin, L., Pietiäinen, M., Auvinen, P., Schultzberg, M., Pussinen, PJ. & Buhlin, K. 2021. Subgingival microbiota in a population with and without cognitive dysfunction. Journal of Oral Microbiology 13:1854552.

Sjövall, AO., Aho, VTE., Hyyrynen, T., Kinnari, TJ., Auvinen, P., Silvola, J., Aarnisalo, A. & Laulajainen-Hongisto, A., 2021. Microbiome of the healthy external auditory canal. Otology & Neurotology 42:e609-e614.

2020

Salava, A., Deptula, P., Lyyski, A., Laine, P., Paulin, L., Väkevä, L., Ranki, A., Auvinen, P. & Lauerma, A. 2020. Skin microbiome in cutaneous T cell lymphoma by 16S and whole genome shotgun sequencing. The Journal of Investigative Dermatology 140:2304-2308.

Nikinmaa S., Alapulli H., Auvinen P., Vaara M., Rantala J., Kankuri E., Sorsa T., Meurman J., Sorsa T. & Pätilä T. 2020. Dual-light photodynamic therapy administered daily provides a sustained antibacterial effect on biofilm and prevents Streptococcus mutans adaptation. PLoS ONE PLoS ONE 15:e0232775.

Heinzel, S., Aho, VTE., Suenkel, U., Thaler, A-K von., Schulte, C., Deuschle, C., Paulin, L., Hantunen, S., Brockmann, K.,. Eschweiler, GW., Maetzler, W., Berg, D., Auvinen, P. & Scheperjans, F. 2020. Gut microbiome signatures of risk and prodromal markers of Parkinson’s disease. Annals of Neurology 88:320-331.

Duru, IC., Andreevskaya, M., Laine, P., Rode, TM., Ylinen, A., Løvdal, T., Bar, N., Crauwels, P., Riedel, CU., Bucur, FI., Nicolau, AI & Auvinen, P. 2020. Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing. BMC genomics 21:455.

Deptula, P., Laine, P., Paulín, P., Auvinen, P., Roberts, R., Johnston, C. & Varmanen, P. 2020. Complete genomes and methylome analyses of Cutibacterium acnes DSM 16379 and Cutibacterium acnes DSM1897T. Microbiology Resource Announcements 9/e00705-20.

Savarese, M., Qureshi, T., Torella, A., Laine, P., Giugliano, T., Jonson, PH., Johari, M., Paulin, L., Piluso, G., Auvinen, P., Nigro, V., Udd, B., & Hackman, P. 2020. Identification and characterization of splicing defects by single-molecule real-time sequencing technology (PacBio). Journal of Neuromuscular Diseases 7:477-481.

Aho, VTE., Tolonen, T., Haverinen, J., Jaakkola, M., Paulin, L., Auvinen, P. & Laine, MM. 2020. Survey of microbes in industrial scale second generation bioethanol production for better process knowledge and operation. Applied Microbiology and Biotechnology 104:8049-8064.

Lecomte, A., Barateau, L., Pereira, P., Paulin, L., Auvinen, P., Scheperjans, F. & Dauvilliers Y., 2020. Gut microbiota composition is associated with Narcolepsy type 1. Neurology: Neuroimmunology & Neuroinflammation 7:e896.

Ruokolainen, L., Fyhrquist, N., Laatikainen, T., Auvinen, P., Fortino, V., Scala, G., Jousilahti, P-. Karisola, P., Karkman, A., Mäkelä, M., Lehtimäki, S., Ndika, J., Ottman, N., Paalanen, L., Paulin, L., Vartiainen, E., von Hertzen, L., Greco, D., Haahtela, T. & Alenius, H. 2020. Immune-microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence. Clinical and Experimental Allergy 50:1148-1158.

2019

Aho, VTE., Pereira, PAB., Voutilainen, S., Paulin, L., Pekkonen, E., Auvinen, P. & Scheperjans, F. 2019. Gut microbiota in Parkinson’s disease: Temporal stability and relations to disease progression. EBioMedicine 44:691-707. (PubMed)

Deptula P., Loivamaa, I.,Smolander, OP., Laine, PK., Roberts, RJ., Piironen, V.,Paulin, L., Savijoki, K.,Auvinen, P & Varmanen, P. 2019.Red-brown pigmentation ofAcidipropionibacterium jensenii is tied to haemolytic activity and a cyl-like gene cluster. Microorganisms  7, 512.

Dhandapani, PK., Lyyski, AM., Paulin, L., Khan, NA., Suomalainen, A., Auvinen, P., Dufour. E., Szibor, M. & Jacobs, HT. 2019. Phenotypic effects of dietary stress in combination with a respiratory-chain by-pass in mice. Physiological Reports e14159:1-13. (PubMed)

Misiewicz, Z., Iurato, S., Kulesskaya, N., Salminen, L., Rodrigues, L., Maccarrone, G., Martins, J., Czamara, D., Laine, M., Sokolowska, E., Trontti, K., Balcells, I., Rewerts, C., Novak, B., Volk, N., Park, DI., Jokitalo, E., Paulin, L., Auvinen, P., Voikar, V., Chen, A., Erhardt, A., Turck, CW. & Hovatta, I. Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior. PLoS Genetics 15:e1008358.

Mäkinen, M., Kuuskeri, J., Laine, P., Smolander, OP., Kovalchuk, A., Zeng, Z., Asiegbu, FO., Paulin, L., Auvinen, P. & Lundell, T. 2019. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics 28;20: 430. (PubMed)

Naskali, E., Dettmer, K., Oefner, PJ., Pereira, PAB, Krohn, K., Auvinen, P., Ranki, A & Kluger, N. 2019. Serotonin and tryptophan metabolites, autoantibodies and gut microbiome in APECED. Endocrine connections Jan 1;8:69-77. (PubMed)

Pentinmikko, N., Iqbal, S., Mana, M., Andersson, S., Cognetta, AB., Suciu, RM., Roper, J., Luopajärvi, K., Markelin, E., Gopalakrishnan, S., Smolander, OP., Naranjo, S., Saarinen, T., Juuti, A., Pietiläinen, K., Auvinen, P., Ristimäki, A., Gupta, N., Tammela, T., Jacks, T., Sabatini, DM., Cravatt, BF., Yilmaz, ÖH. & Katajisto, P. Age-induced expression of Notum in the stem cell niche attenuates regeneration of intestinal epithelium. Nature (in press).

Kammonen, JI., Smolander, OP., Paulin, L., Pereira, PAB., Laine, PK., Koskinen, P., Jernvall, J. & Auvinen, P. gapFinisher: a reliable gap filling pipeline for SSPACE-LongRead scaffolder output. PLoS One 14: e0216885.

Liimatainen, H., Auvinen, P. & Auvinen, E. 2018, Mikä mikrobi, mikä lääke? - Onko uusista sekvensointimenetelmistä apua mikrobiologisissa laboratoriotutkimuksissa? Duodecim (in press).

Rehbinder, EM., Winger, AJ., Landro, L., Asarnoj, A., Berents, TL., Carlsen, KH., Hedlin, G., Jonassen, CM., Nordlund, B., Sandvik, L., Skjerven, HO., Soderhall, C., Vettukattil, R., Carlsen, KCL.,Auvinen, P., Bains, KES., Carlsen, MH., Carlsen, OCL., Endre, KA., Granlund, PA., Granum, B., Gudmundsdottir, HK., Haugen, G., Hilde, K., Kreyberg, I., Magi, CAO., Nordhagen, LS., Nygaard, UC., Rudi, K., Saunders, CM., Skrindo, I., Sjoborg, K., Staff, AC., Tedner, SG., Vaernesbranden, MR. & Wiik, J. 2019. Dry skin and skin barrier in early infancy.British Journal of Dermatology 181: 218-219.

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2018

Aho, V. & Auvinen, P. 2018. Mikrobiomforskning och sjukdomsassociationer. Finska Läkaresällskapets Handlingar 178/2: 4-9. (PDF)

Andreevskaya, M., Jääskeläinen, E., Johansson, P., Rantala-Ylinen, A., Paulin, L., Björkroth J. & Auvinen, P. Food-spoilage-associated Leuconostoc, Lactococcus, and Lactobacillus species display different survival strategies in response to competition. Applied and Environmental Microbiology 84:e00554-18. (PubMed)

Deptula, P., Smolander, OP., Laine, P., Roberts, RJ., Edelmann, M., Peltola, P., Piironen, V., Paulin, L., Storgårds, E., Savijoki, K., Laitila, A., Auvinen, P. & Varmanen, P. 2018. Acidipropionibacterium virtanenii sp. nov., isolated from malted barley. International Journal of Systematic and Evolutionary Microbiology 68:3175-3183. (PubMed)

Duru, IC., Laine, P., Andreevskaya, M., Paulin, L., Kananen, S., Tynkkynen, S., Auvinen, P. & Smolander, OP. 2018. Metagenomic and metatranscriptomic analysis of the microbial community in swiss-type Maasdam cheese during ripening. International Journal of Food Microbiology 281:10-22. (PubMed)

Frohnmeyer, E., Deptula, P., Nyman, TA., Laine, PKS., Vihinen, H., Paulin, L., Auvinen, P., Jokitalo, E., Piironen, V., Varmanen, P. & Savijoki, K. 2018. Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains. Microbial Biotechnology 11:510-526. (PubMed)

Hasan, MS., Aho, V., Pereira, P., Paulin, L., Koivusalo, SB., Auvinen, P. & Eriksson, JG. 2018. Gut Microbiome in women at high-risk for Gestational Diabetes: A Cross-sectional Study of Mothers and Offspring 5 Years post-partum. Acta Obstetricia et Gynecologica Scandinavica 97:38-46. (PubMed)

Kelhälä, HL., Aho, V., Fyhrquist, N., Pereira, P., Kubin, M., Paulin, L., Palatsi, R., Auvinen, P., Tasanen, K. & Lauerma, A. 2018. Isotretinoin and lymecycline treatments modify the skin microbiota in acne. Experimental Dermatology, 27:30-36. (PubMed)

Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH & Fahima T. 2018. Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nature Communications 3;9: 3735. (PubMed)

Laine, M., Trontti, K., Misiewicz, Z., Sokolowska, E., Kulesskaya, N., Heikkinen, A., Saarnio, S., Balcells, I., Ameslon, P., Greco, D., Mattila, P., Ellonen, P., Paulin, L., Auvinen, P., Jokitalo, E. & Hovatta, I. 2018. Genetic control of myelin plasticity after chronic psychosocial stress. eNeuro 5: e0166-18.2018 1–16. (PubMed)

Ndika, J., Suojalehto, H., Täubel, M., Lehto, M., Karvala, K., Pallasaho, P., Sund, J., Auvinen, P., Järvi, K., Pekkanen, J., Kinaret, P., Greco, D., Hyvärinen, A. & Alenius, H. 2018. Nasal mucosa and blood cell transcriptome profiles do not reflect respiratory symptoms associated with moisture-damage. Indoor Air 28:721–731. (PubMed)

Rajendran, J., Purhonen, J., Tegelberg, S., Smolander, OP., Mörgelin, M., Rozman, J., Gailus-Durner, V., Fuchs, H., Hrabe de Angelis, M., Auvinen, P., Mervaala, E., Jacobs, HT. Szibor, M., Fellman, V. & Kallijärvi, J. 2018. Alternative oxidase-mediated respiration prevents lethal mitochondrial cardiomyopathy. EMBO Molecular Medicine e9456. (PubMed)

Sierla, M., Hõrak, H., Overmyer, K., Waszczak, C., Yarmolinsky, D., Maierhofer, T., Vainonen, JP., Denessiouk, K., Laanemets, K., Tõldsepp, K., Vahisalu, T., Gauthier, A., Puukko, T., Salojärvi, J., Paulin, L., Auvinen, P., Geiger, D., Hedrich, R., Kollist, H., & Kangasjärvi, J. 2018. The receptor-like pseudokinase GHR1 is required for stomatal closure. The Plant Cell 30:2813-2837. (PubMed)

Savarese, M., Jonson, PH., Huovinen, S., Paulin, L., Auvinen, P., Udd, B. & Hackman, P. 2018. The complexity of titin splicing pattern in human adult skeletal muscles. Skeletal Muscle, 8:11. (PubMed)

Savriama, Y., Valtonen, M., Kammonen, JI., Rastas, P., Smolander, OP., Lyyski, A., Häkkinen, TJ., Corfe, IJ., Gerber, S., Salazar-Ciudad, I., Paulin, L., Holm, L., Löytynoja, A., Auvinen, P. & Jernvall, J. 2018. Bracketing phenogenotypic limits of mammalian hybridization. Royal Society Open Science 5:180913. (PubMed)

Somervuo, P., Koskinen, P., Mei, P., Holm, L., Auvinen, P. & Paulin, L. 2018. BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing. BMC bioinformatics 19:257. (PubMed)

Virtanen, E., Seppälä, H., Helanterä, I., Laine, P., Lautenschlager, I., Paulin, L., Mannonen, L., Auvinen, P. & Auvinen, E. 2018. BK polyomavirus microRNA expression and sequence variation in polyomavirus-associated nephropathy. Journal of Clinical Virology, 102:70-76. (PubMed)

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2017

Auvinen E. & Auvinen P. 2017. Massiiviparalleelisekvensointi (NGS) mikrobiologian näkökulmasta – ja miten se liittyy Leo Tolstoihin. Moodi, 2017/4:27-31.

Auvinen P. 2017. Suolen mikrobiomi ja aivot vuorovaikutuksessa. Parkinson-postia, 3/17:20-23.

Deptula, P., Laine, PK., Roberts, RJ., Smolander, OP., Vihinen, H., Piironen, V., Paulin, L., Jokitalo, E., Savijoki, K., Auvinen, P. & Varmanen, P. De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. BMC Genomics, 18:790. (PubMed)

Kinaret, P., Marwah, V., Fortino, V., Ilves, M., Wolff, H., Ruokolainen, L., Auvinen, P., Savolainen, K., Alenius, H., & Greco, D. 2017. Network analysis reveals similar transcriptomic responses to intrinsic properties of carbon nanomaterials in vitro and in vivo. ACS Nano, 11(4):3786-3796. (PubMed)

Koivula, TT., Laakso, SM., Niemi, HJ., Kekäläinen, E., Laine, P., Paulin, L., Auvinen, P. & Arstila, TP. 2017. Clonal analysis of regulatory T cell defect in patients with autoimmune polyendocrine syndrome type 1 suggests intrathymic impairment. Scand J Immunol. 86:221-228. doi: 10.1111/sji.12586. (PubMed)

Mertsalmi, T., Aho, V., Pereira, P., Paulin, L., Pekkonen, E., Auvinen, P. & Scheperjans, F. 2017. More than constipation – Bowel symptoms in Parkinson’s disease and their connection to gut microbiota. European Journal of Neurology, 24:1375-1383. (PubMed)

Niemi, O., Laine, P., Koskinen, P., Pasanen, M., Pennanen, V., Harjunpää, H., Nykyri, J., Holm, L., Paulin, L., Auvinen, P., Palva, ET., & Pirhonen, M. 2017. Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1. Standards in Genomic Sciences, 12:87. (PubMed)

Ojala, T., Laine, PK., Ahlroos, T., Tanskanen, J., Pitkänen, S., Salusjärvi, T., Kankainen, M., Tynkkynen, S., Paulin, L. & Auvinen, P. Functional genomics provides insights into the role of Propionibacterium freudenreichii ssp. shermanii JS in cheese ripening. International Journal of Food Microbiology, 241:39-48. (PubMed)

Pereira, PAB., Aho, VTE., Arola, J., Boyd, S., Jokelainen, K., Paulin, L., Auvinen, P. & Färkkilä, MA. Bile microbiota in primary sclerosing cholangitis: impact on disease progression and development of biliary dysplasia. PLoS ONE, 2(8):e0182924. (PubMed)

Pereira, PAB., Aho, VTE., Paulin, L., Pekkonen, E., Auvinen, P. & Scheperjans, F. 2017. Oral and Nasal Microbiota in Parkinson's Disease. Parkinsonism & Related Disorders, 38:61-67. (PubMed)

Ruokolainen, L., Paalanen, L., Karkman, A., Laatikainen, T., von Hertzen, L., Vlasoff, T., Markelova, O., Masyuk, V., Auvinen, P., Paulin, L., Alenius, H., Fyhrquist, N., Hanski, I., Mäkelä, M., Zilber, E., Jousilahti, P., Vartiainen, E. & Haahtela, T. Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia. Clinical & Experimental Allergy, 47:665-674. (PubMed)

Salava, A., Aho, V., Lybeck, E., Pereira, P., Paulin, L., Nupponen, I, Ranki A., Auvinen, P., Andersson, S. & Lauerma, A. Loss of cutaneous microbial diversity during first 3 weeks of life in very low birth weight infants. Experimental Dermatology, 26(10):861-867. (PubMed)

Salava, A., Pereira, P., Aho, V., Väkevä, L., Paulin, L., Auvinen. P., Ranki, A. & Lauerma, A. Skin microbiome in small and large plaque parapsoriasis. Acta Dermato-Venerologica, 97:685-691. (PubMed)

Salojärvi, J., Smolander, OP., Nieminen, K., Rajaraman, S., Mohammadi, O., Safdari, P., Lamminmäki, A., Immanen, J., Lan, T., Tanskanen, J., Rastas, P., Amiryousefi, A., Jayaprakash, B., Kammonen, J., Hagqvist, R., Eswaran, G., Ahonen, VH., Alonso Serra, J., Asiegbu, FO., de Dios Barajas-Lopez, J., Blande, D., Blokhina, O., Blomster, T., Broholm, S., Brosché, M., Cui, F., Dardick, C., Ehonen, S., Elomaa, P., Escamez, S., Fagerstedt, KV., Fujii, H., Gauthier, A., Gollan, PJ., Halimaa, P., Heino, P., Himanen, K., Hollender, C., Kangasjärvi, S., Kauppinen, L., Kelleher, CT., Kontunen-Soppela, S., Koskinen, JP., Kovalchuk, A., Kärenlampi, S., Kärkönen, A., Lim, K-J., Leppälä, J., Macpherson, L., Mikola, J., Mouhu, K., Mähönen, AP-. Niinemets, U., Oksanen, E., Overmyer, K., Palva, ET., Pazouki, L., Pennanen, V., Puhakainen, T., Poczai, P., Possen, B. J.H.M., Punkkinen, M., Rahikainen, M., Rousi, M., Ruonala, R., van der Schoot, C., Shapiguzov, A., Sierla, M., Sipilä, TP., Sutela, S., Teeri, TH., Tervahauta, AI., Vaattovaara, A., Vahala, J., Vetchinnikova, L., Welling, A., Wrzaczek, M., Xu, E., Paulin, L., Schulman, AH., Lascoux, M., Albert, VA., Auvinen, P., Helariutta, Y. & Kangasjärvi, J. 2017. Adaptive landscape and population genomics of silver birch. Nature Genetics, 49(6):904-912. (PubMed)

Seppälä, H., Helanterä, I., Laine, P., Lautenschlager, I., Paulin, L., Jahnukainen, T., Auvinen, P. & Auvinen, E. Archetype JC polyomavirus prevails in a rare case of JC polyomavirus nephropathy and in stable renal transplant recipients with JC polyomavirus viruria. Journal of Infectious Diseases, 216:981-989. (PubMed)

Seppälä, H., Virtanen, E., Saarela, M., Laine, P., Paulin, L., Mannonen, L., Auvinen, P. & Auvinen, E. 2017. Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy. Journal of Infectious Diseases, 215:889-895.

Seppälä, H., Virtanen, E., Saarela, M., Laine, P., Paulin, L., Mannonen, L., Auvinen, P., & Auvinen, E. 2017. Etenevää multifokaalista leukoenkefalopatiaa sairastavan potilaan aivoissa kolme JC-viruskantaa. Duodecim, 133:507.

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2016

Andreevskaya, M., Hultman, J., Johansson, P. Laine, P., Paulin, L., Auvinen, P. & Björkroth, J. 2016. Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages. Standards in Genomic Sciences, 11: 40. (PubMed)

Andreevskaya, M., Johansson, P. Jääskeläinen, E., Rämö, T., Ritari, J., Paulin, L., Björkroth, J. & Auvinen, P. 2016 Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase. BMC Genomics, 17:539. (PubMed)

Auvinen, P. 2016. The brain to gut axis. Brain, Behavior, and Immunity, 57:8-9.

Auvinen, P. & Scheperjans, F. 2016. Parkinsonin tauti ja mikrobiomi. Lääkärilehti, 71:2102-2103.

Fyhrquist, N., Salava, A., Auvinen, P., & Lauerma A. 2016. Skin Biomes. Current allergy and asthma reports, 16:40.

Hyötyläinen, T., Jerby, J., Petäjä, E., Mattila, I., Jäntti, S., Auvinen, P., Gastaldelli, A., Yki-Järvinen, H., Ruppin, E. & Oresic, M. 2016. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nature communications, 7: 8994. (PubMed)

Immanen, J., Nieminen, K., Smolander, OP., Kojima, M., Serra, JA., Koskinen, P., Zhang, J., Elo, A., Mähönen, AP., Street, N., Bhalerao, RP., Paulin, L., Auvinen, P., Sakakibara, H. & Helariutta, Y. 2016. Cytokinin and auxin display distinct but interconnected distribution and signaling profiles to stimulate cambial activity. Current Biology, 26: 1990-1997. (PubMed)

Kuuskeri, J., Häkkinen, M., Laine, P., Smolander, OP., Tamene, F., Miettinen, S., Nousiainen, P., Kemell, M., Auvinen, P. & Lundell, T. 2016. Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata - growth on spruce wood and decay effect on lignocellulose. Biotechnology for Biofuels, 9:192. (PubMed)

Lim, K-J., Paasela, T., Harju, A., Venäläinen, M., Paulin, L., Auvinen, P., Kärkkäinen, K., & Teeri, TH. Developmental changes in Scots pine transcriptome during heartwood formation. Plant Physiology, 172:1403-1417. (PubMed)

Penttinen, P., Greco, D., Muntyan, V., Terefework, Z., De Lajudie, P., Roumiantseva, M., Becker, A., Auvinen, P. & Lindström, K. 2016. Divergent genes in potential inoculant Sinorhizobium strains are related to DNA replication, recombination and repair. Journal of Basic Microbiology, 56: 1-6. (PubMed)

Rouhiainen, A., Zhao, X., Vanttola, P., Qian, K., Kulesskiy, E., Kuja-Panula, J., Gransalke, K., Grönholm, M., Unni, E., Meistrich, M., Tian, L., Auvinen, P. & Rauvala, H. 2016. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. Scientific Reports, 6:32960. (PubMed)

Rämö, O., Kumar, D., Gucciardo, E., Joensuu, M., Saarekas, M., Vihinen, H., Belevich, I., Smolander, OP., Qian, K., Auvinen, P. & Jokitalo E. 2016. NOGO-A/RTN4A and NOGO-B/RTN4B are simultaneously expressed in epithelial, fibroblast and neuronal cells and maintain ER morphology. Scientific Reports, 6:35969. (PubMed)

Salava, A., Aho, V., Pereira, P.A.B., Koskinen, K., Paulin, L., Auvinen, P. & Lauerma, A. 2016. Skin microbiome in melanomas and melanocytic nevi. European Journal of Dermatology, 26: 49-55. (PubMed)

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2015

Aho, V.T.E., Pereira, P.A.B., Haahtela, T., Pawankar, R., Auvinen, P. & Koskinen, K. 2015. The microbiome of the human lower airways: a next generation sequencing perspective. World Allergy Organization Journal, 8: 23. (PubMed)

Ahola, V., Koskinen, P., Wong, S.C., Kvist, J., Paulin, L., Auvinen, P., Saastamoinen, M., Frilander, M.J., Lehtonen, R. & Hanski, I. 2015. Temperature and sex related effects of serine protease alleles on larval development in the Glanville fritillary butterfly. Journal of Evolutionary Biology, 28: 2224-2235. (PubMed)

Andreevskaya, M., Johansson, P., Laine, P., Smolander, O.P., Sonck, M., Rahkila, R., Jääskeläinen, E., Paulin, L., Auvinen, P. & Björkroth, J. 2015. Genome sequence and transcriptome analysis of meat-spoilage-associated lactic acid bacterium Lactococcus piscium MKFS47. Applied and Environmental Microbiology, 81: 3800-3811. (PubMed)

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. 2015. Hunt for the origin of allergy - comparing the Finnish and Russian Karelia. Clinical & Experimental Allergy, 45: 891-901. (PubMed)

Huovinen, S., Penttilä, S., Somervuo, P., Keto, J., Auvinen, P., Vihola, A., Huovinen, S., Pelin, K., Raheem, O., Salenius, J., Suominen, T., Hackman, P. & Udd, B. 2015. Differential isoform expression and selective muscle involvement in muscular dystrophies. The American Journal of Pathology, 185: 2833-2842. (PubMed)

Kammonen, J.I., Smolander, OP., Sipilä, T., Overmyer, K., Auvinen, P. & Paulin, L. 2015. Increased transcriptome sequencing efficiency with modified Mint-2 digestion-ligation protocol. Analytical Biochemistry, 477: 38-40. (PubMed)

Kant, R., Taponen, S., Koort, J., Paulin, L., Åvall-Jääskeläinen, S. & Palva, A. 2015. Genome sequences of four Staphylococcus aureus strains isolated from bovine mastitis. Genome Announcement, 3: e00334-15. (PubMed)

Koskinen, K., Auvinen, P., Björkroth, KJ. & Hultman, J. 2015. Inconsistent denoising and clustering algorithms for amplicon sequence data. Journal of Computational Biology, 22: 743-751. (PubMed)

Koskinen, P., Deptula, P., Smolander, O.-P., Tamene, F., Kammonen, J., Savijoki, K., Paulin, L., Piironen, V., Auvinen, P. & Varmanen, P. 2015. Complete genome of Propionibacterium freudenreichii DSM 20271. Standards in Genomic Sciences, 10: 87. (PubMed)

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. 2015. Flight-induced changes in gene expression in the Glanville fritillary butterfly. Molecular Ecology, 24: 4886-4900. (PubMed)

Nyholm, O., Halkilahti, J., Wiklund, G., Okeke, U., Paulin, L., Auvinen, P., Haukka, K. & Siitonen, A. 2015. Comparative genomics and characterization of hybrid Shigatoxigenic and enterotoxigenic Escherichia coli (STEC/ETEC) strains. PLOS ONE, 10: e0135936. (PubMed)

Pietilä, T., Nummi, M., Auvinen, P., Mannonen, L. & Auvinen, E. 2015. Expression of BKV and JCV encoded microRNA in human cerebrospinal fluid, plasma and urine. Journal of Clinical Virology, 65: 1-5. (PubMed)

Rahkila, R., Johansson, P., Säde, E., Paulin, L., Auvinen, P. & Björkroth, J. 2015. Multilocus sequence typing of Leuconostoc gelidum subsp. gasicomitatum, a psychrotrophic lactic acid bacterium causing spoilage of packaged perishable foods. Applied and Environmental Microbiology, 81: 2474-2480. (PubMed)

Ruokolainen, L., Von Hertzen, L., Fyhrquist, N., Laatikainen, T., Lehtomäki, J., Auvinen, P., Karvonen, A., Hyvärinen, A., Tillmann, V., Niemelä, O., Knip, M., Haahtela, T. M. K., Pekkanen, J. & Hanski, I. 2015. Green areas around homes reduce atopic sensitization in children. Allergy, 70: 195-202. (PubMed)

Scheperjans, F., Aho, V., Pereira, PAB., Koskinen, K., Paulin, L., Pekkonen, E., Haapaniemi, E., Kaakkola, S., Eerola-Rautio, J., Pohja, M., Kinnunen, E., Murros, K. & Auvinen, P. 2015. Microbiota are Related to Parkinsons Disease and Clinical Phenotype. Movement Disorders, 30: 350-358. (PubMed)

Scheperjans, F., Aho, V., Pereira, PAB., Koskinen, K., Paulin, L., Pekkonen, E., Haapaniemi, E., Kaakkola, S., Eerola-Rautio, J., Pohja, M., Kinnunen, E., Murros, K. & Auvinen, P. 2015. Suoliston mikrobiston muutokset yhteydessä Parkinsonin tautiin. Duodecim, 131:276.

Scheperjans, F., Pekkonen, E., Kaakkola, S. & Auvinen, P. 2015. Linking smoking, coffee, urate and Parkinson's disease - a role for gut microbiota? Journal of Parkinsons Disease, 15: 255-262. (PubMed)

Vetterli, A., Hyytiäinen, K., Ahjos, M., Auvinen, P., Paulin, L., Hietanen, S. & Leskinen, E. 2015. Seasonal patterns of bacterial communities in the coastal brackish sediments of the Gulf of Finland, Baltic Sea. Estuarine, Coastal and Shelf Science, 165: 86-96. (ScienceDirect)

Österman, J., Mousavi, S.A., Koskinen, P., Paulin, L. & Lindström, K. 2015. Genomic features separating ten strains of Neorhizobium galegae with different symbiotic phenotypes. BMC Genomics, 16: 348. (PubMed)

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2014

Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Välimäki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, EA., Ferguson, LC., Luo, S., Cao, Z., de Jong, MA., Duplouy, A., Smolander, OP., Vogel, H., McCoy, RC., Qian, K., Chong, WS., Zhang, Q., Ahmad, F., Haukka, JK., Joshi, A., Salojärvi, J., Wheat, CW., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkänen, E., Ylinen, J., Waterhouse, RM., Turunen, M., Vähärautio, A., Ojanen, SP., Schulman, AH., Taipale, M., Lawson, D., Ukkonen, E., Mäkinen, V., Goldsmith, MR., Holm, L., Auvinen, P., Frilander, MJ., & Hanski., I. 2014. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature communications 5: 4737. (PubMed)

Bomberg, M., Nyyssönen, M., Nousiainen, A., Hultman, J., Paulin, L., Auvinen, P. & Itävaara, M. 2014. Evaluation of molecular techniques in characterization of deep terrestrial biosphere. Open Journal of Ecology 4: 468-487. (Scientific Research)

Fortino, V., Smolander, OP., Auvinen, P., Tagliaferri, R. & Greco, D. 2014. Transcriptome dynamics-based operon prediction in prokaryotes. BMC Bioinformatics 15: 145. (PubMed)

Furuta. KM., Yadav, SR., Lehesranta, S., Belevich, I., Miyashima, S., Heo, J., Vatén, 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. Arabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation. Science 345: 933-937. (PubMed)

Fyhrquist, N., Ruokolainen, L., Suomalainen, A., Lehtimäki, S., Veckman, V., Vendelin, J., Karisola, P., Lehto, M., Savinko, T., Jarva, H., Kosunen, TU., Corander, J., Auvinen, P., Paulin., L., von Hertzen, L., Laatikainen, T., Mäkelä, M., Haahtela, T., Greco, D., Hanski, I., & Alenius, H. 2014. Acinetobacter species in the skin microbiota protect against allergic sensitization and inflammation. Journal of Allergy and Clinical Immunology 134: 1301-1309. (PubMed)

Kahala, M., Ahola, V., Mäkimattila, E., Paulin, L. & Joutsjoki, V. 2014. The use of macroarray as a simple tool to follow the metabolic profile of Lactobacillus plantarum during fermentation. Advances in Microbiology 4: 996-1016. (Scientific Research)

Kant, R., Rintahaka, J., Yu, X., Sigvart-Mattila, P., Paulin, L., Mecklin, J.-P., Saarela, M., Palva, A. & von Ossowski, I. 2014. A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus. PLOS ONE 9: e102762. (PubMed)

Mousavi, S.A., Österman, J., de Lajudie, P., Nesme, X., Lavire, C., Vial, L., Paulin, L., Wahlberg, N. & Lindström, K. 2014. Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov. Systematic and Applied Microbiology 37: 208-215. (PubMed)

Nyyssönen, M., Hultman, J., Ahonen, L., Kukkonen, I., Paulin, L., Laine, P., Itävaara, M., & Auvinen, P. 2014. Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield. The ISME Journal 8: 126-138. (PubMed)

Ojala, T., Kankainen, M., Castro, J., Cerca, N., Edelman, S., Westerlund-Wikström, B., Paulin, L., Holm, L. & Auvinen, P. 2014. Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis. BMC Genomics 15:1070. (PubMed)

Salavirta, H., Oksanen, I., Kuuskeri, J., Mäkelä, M.R., Laine, P., Paulin, L. & Lundell, T. 2014. Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events. PLOS ONE 9: e97141. (PubMed)

Savijoki, K., Iivanainen, A., Siljamäki, P., Laine, P., Paulin, L., Karonen, T., Pyörälä, S., Kankainen, M., Nyman, T., Salomäki, T., Koskinen, P., Holm, L., Simojoki, H., Taponen, S., Sukura, A., Kalkkinen, N., Auvinen, P. & Varmanen, P. 2014. Genomics and proteomics provide new insight into the commensal and pathogenic lifestyles of bovine and human-associated Staphylococcus epidermidis strains. Journal of Proteome Research 13: 3748-3762. (PubMed)

Siljamäki. P., Varmanen, P., Kankainen, M., Pyörälä, P., Karonen, T., Iivanainen, A., Auvinen, P., Paulin, L., Laine, PK., Taponen, S., Simojoki, H., Sukura, A., Nyman, TA. & Savijoki, K. 2014. Comparative proteome profiling of bovine and human Staphylococcus epidermidis strains for screening specifically expressed virulence and adaptation proteins. Proteomics 14: 1890-1894. (PubMed)

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., Ahola, V. & Hanski, I. 2014. Transcriptome analysis reveals signature of adaptation to landscape fragmentation. PLOS ONE 9: e101467. (PubMed)

Sun, H., Terhonen, E., Koskinen, K., Paulin, L., Kasanen, R. & Asiegbu, F.O. 2014. Bacterial diversity and community structure along different peat soils in boreal forest. Applied Soil Ecology 74: 37-45. (ScienceDirect)

Torvinen, E., Suomalainen, S., Paulin, L. & Kusnetsov, J. 2014. Mycobacteria in Finnish cooling tower waters. APMIS. 122:353-8. (PubMed)

Wacklin, P., Tuimala, J., Nikkilä, J.,Tims, S., Mäkivuokko, H., Alakulppi, N., Laine, P., Rajilic-Stojanovic, M., Paulin, L., de Vos, W.M. & Mättö, J. 2014. Faecal microbiota composition in adults is associated with the FUT2 gene determining the secretor status. PLOS ONE 9: e94863. (PubMed)

Österman, J., Marsh, J., Laine, P., Zeng, Z., Alatalo, E., Sullivan, J.T., Young, J.P.W., Thomas-Oates, J., Paulin, L. & Lindström, K. 2014. Genome sequencing of two Neorhizobium galegae strains revealed a noeT gene responsible for the unusual acetylation of the nodulation factor. BMC Genomics 15: 500. (PubMed)

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2013

Douillard, F.P, Kant, R., Ritari, J., Paulin, L., Palva, A. & de Vos, W.M. 2013. Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin. Microbial Biotechnology 6: 576-578. (PubMed)

Douillard, F.P., Ribbera, A., Järvinen, H.M., Kant, R., Pietilä, T.E., Randazzo, C., Paulin, L., Laine, P.K., Caggia, C., von Ossowski, I., Reunanen, J., Satokari, R., Salminen, S., Palva, A. & de Vos, W.M. 2013. Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Applied and Environmental Microbiology 79:1923-1933. (PubMed)

Douillard, F.P., Ribbera, A., Kant, R., Pietilä, T.E., Järvinen, H.M., Messing, M., Randazzo, C.L., Paulin, L., Laine, P., Ritari, J., Caggia, C., Lähteinen, T., Brouns, S.J.J., Satokari, R., von Ossowski, I., Reunanen, J., Palva, A. & de Vos, W.M. 2013. Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG PLOS Genetics 8: e1003683. (PubMed)

Garlant, L., Koskinen, P., Rouhiainen, L., Laine, P., Paulin, L., Auvinen, P., Holm, L. & Pirhonen, M. 2013. 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. Diversity 5: 824-842. (MDPI)

Havula, E., Teesalu, M., Hyötyläinen, T., Seppälä, H., Hasygar, K., Auvinen, P., Orešič, M., Sandmann, T. & Hietakangas, V. 2013. Mondo/ChREBP-Mlx-regulated transcriptional network is essential for dietary sugar tolerance in Drosophila. PLOS Genetics 9: e1003438. (PubMed)

Jääskeläinen, E., Johansson, P., Kostiainen, O., Nieminen, T., Schmidt, G., Somervuo, P., Mohsina, M., Vanninen, P., Auvinen, P., & Björkroth, J. 2013. Significance of heme-based respiration in meat spoilage caused by Leuconostoc gasicomitatum. Applied and Environmental Microbiology 79:1078-1085. (PubMed)

Kõiv, V., Andresen, L., Broberg, M., Frolova, J., Somervuo, P., Auvinen, P., Pirhonen, M., Tenson, T. & Mäe, A. 2013. Lack of RsmA-mediated control results in constant hypervirulence, cell elongation, and hyperflagellation in Pectobacterium wasabiae. PLOS ONE 8: e54248. (PubMed)

Lyra, C., Sinkko, H., Rantanen, M., Paulin, L. & Kotilainen, A. 2013. Sediment bacterial communities reflect the history of a sea basin. PLOS ONE, 8:e54326. (PubMed)

Nykyri, J., Mattinen, L., Niemi, O., Adhikari, S., Kõiv, V., Somervuo, P., Fang, X., Auvinen, P., Mäe, A., Palva, E.T. & Pirhonen, M. 2013. Role and Regulation of the Flp/Tad Pilus in the Virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193. PLOS ONE 8: e73718. (PubMed)

Ovaskainen, O., Schigel, D., Ali-Kovero, H., Auvinen, P., Paulin, L., Nordén, B., & Nordén, J. 2013. Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi. The ISME Journal 7: 1696-1709. (PubMed)

Pesquet, E., Zhang, B., Puhakainen, T., Barbier, O., Gerber, L., Escamez, S., Gorzsás, A., Courtois-Moreau, C., Alatalo, E., Paulin, L., Kangasjärvi, J., Sundberg, B., Goffner, D. & Tuominen, H. 2013. Non-cell autonomous lignification of tracheary elements. The Plant Cell 25: 1314-1328. (PubMed)

Qian, K., Pietilä, T., Rönty, M., Michon, F., Frilander, M.J., Ritari, J., Tarkkanen, J., Paulin, L., Auvinen, P., & Auvinen, E. 2013. Identification and validation of human papillomavirus encoded microRNAs. PLOS ONE, 8: e70202. (PubMed)

Rastas, P., Paulin, L., Hanski, I., Lehtonen, L. & Auvinen, P. 2013. Lep-MAP: fast and accurate linkage map construction for large SNP datasets. Bioinformatics 29:3128-3134. (PubMed)

Sinkko, H., Lukkari, K., Sihvonen, L.M., Sivonen, K., Leivuori, M., Rantanen, M., Paulin, L. & Lyra, C. 2013. Bacteria contribute to sediment nutrient release and reflect progressed eutrophication-driven hypoxia in an organic-rich continental sea. PLOS ONE 8:e67061. (PubMed)

Sun, H., Terhonen, E., Koskinen, K., Paulin, L., Kasanen, R. & Asiegbu, F. 2013. The impacts of treatment with biocontrol fungus Phlebiopsis gigantea on bacterial diversity in Norway spruce stumps. Biological Control 64:238-246. (ScienceDirect)

Söderholm, H., Jaakkola, K., Somervuo, P., Laine, P., Auvinen, P., Paulin, L., Lindström, M. & Korkeala, H. 2013. Comparison of Clostridium botulinum genomes shows the absence of cold shock protein coding genes in type E neurotoxin producing strains. The Botulinum Journal 2:189--207. (Inderscience)

Terhonen, E., Sun, H., Buée, M., Kasanen, R., Paulin, L. & Asiegbu, F.O. 2013. Effects of the use of biocontrol agent (Phlebiopsis gigantea) on fungal communities on the surface of Picea abies stumps. Forest Ecology and Management 310: 428-433. (ScienceDirect)

Tiraboschi, E., Guirado, R., Greco, D., Auvinen, P., Maya-Vetencourt, J.F., Maffei, L. & Castren, E. 2013. Gene expression patterns underlying the reinstatement of plasticity in the adult visual system. Neural Plasticity, article ID: 605079. (PubMed)

Tuohimaa, P., Wang, J.H., Khan, S., Kuuslahti, M., Qian, K., Manninen, T., Auvinen, P., Vihinen, M., & Lou, Y-R. Gene expression profiles in human and mouse primary cells provide new insights into the differential actions of vitamin D metabolites. PLOS ONE 8: e75338. (PubMed)

Tuulasvaara, A., Baussand, J., Laine, P., Paulin, L., Salminen, J., Auvinen, P., Gorochov, G. & Arstila, T.P. 2013. High sequence diversity and structural conservation in the human T-cell receptor β junctional region during thymic development. European Journal of Immunology 43:2185-2193. (PubMed)

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2012

Hanski, I., von Hertzen, L., Fyhrquist, N., Koskinen, K., Torppa, K., Laatikainen, T., Karisola, P., Auvinen, P., Paulin, L., Mäkelä, MJ., Vartiainen, E., Kosunen, TU., Alenius, H. & Haahtela, T. 2012. Environmental biodiversity, human microbiota and allergy are interrelated. Proceedings of the National Academy of Sciences U.S.A. 109:8334-8339. (PubMed)

Kivi, N., Rönty, M., Tarkkanen, J., Auvinen, P. & Auvinen, E. 2012. Cell culture model predicts human disease: Altered expression of junction proteins and matrix metalloproteinases in cervical dysplasia. BMC Clinical Pathology 12:9. (PubMed)

Kondadi, P., Rossi, M., Twelkmeyer, B., Schur, M., Li, J., Schott, T., Paulin, L., Auvinen, P., Hänninen, M-L., Schweda,E. & Wakarchuk, W. 2012. Identification and characterization of a lipopolysaccharide α2,3-sialyltransferase from the human pathogen Helicobacter bizzozeronii. Journal of Bacteriology 194:2540-2550. (PubMed)

Koskinen, J.P., Laine, P., Niemi, O., Nykyri, J., Harjunpää, H., Auvinen, P., Paulin, L., Pirhonen, M., Palva, T. & Holm, L. 2012. Genome sequence of Pectobacterium sp. strain SCC3193. Journal of Bacteriology 194:6004. (PubMed)

Laitila, J., Hanif, M., Paetau, A., Hujanen, S., Keto, J., Somervuo, P., Huovinen, S., Udd, B., Wallgren-Pettersson, C. Auvinen, P., Hackman, P. & Pelin, K. 2012. Expression of multiple nebulin isoforms in human skeletal muscle and brain. Muscle and Nerve 46:730-737. (PubMed)

Maya-Vetencourt, JF., Tiraboschi, E., Greco, D., Restani, L., Cerri, C., Auvinen, P., Maffei, L. & Castrén, E. 2012. Experience-dependent expression of NPAS4 regulates plasticity in adult visual cortex. The Journal of Physiology 590:4777-4787. (PubMed)

Niemi, R.M., Ollinkangas, T., Paulin, L., Svec, P., Vandamme, P., Karkman, A., Kosina, M. & Lindström, K. 2012. Enterococcus rivorum sp. nov., from water of pristine brooks. International Journal of Systematic and Evolutionary Microbiology 62: 2169-73. (PubMed)

Nieminen, T.T., Koskinen, K., Laine, P., Hultman, J., Paulin, L., Paloranta, A., Säde, E., Johansson, P., Björkroth, J. & Auvinen, P. 2012. Metagenomic analysis of microbial communities in marinated and unmarinated broiler stored under modified atmosphere. International Journal of Food Microbiology 157:142-149. (PubMed)

Nieminen, T.T., Välitalo, H., Säde, E., Paloranta, A., Koskinen, K. & Björkroth, J. 2012. The effect of marination on lactic acid bacteria communities in raw broiler fillet strips. Frontiers in Microbiology 3: 376. (PubMed)

Palgi, M., Greco, D., Lindström, R., Auvinen, P. & Heino, TI. 2012. Gene expression analysis of Drosophila Manf mutants reveals perturbations in membrane traffic and major metabolic changes. BMC Genomics 13:134. (PubMed)

Procaccini, C., De Rosa, V., Galgani, M., Carbone, F., Greco, D., Qian, K., Auvinen, P., Calì,G., Stallone, G., Formisano, L., La Cava, A., & Matarese, G. 2012. Leptin-induced mTOR activation defines a specific molecular and transcriptional signature controlling CD4+ effector T cell responses. The Journal of Immunology 189:2941-2953. (Pubmed)

Qian, K., Auvinen, E., Greco, G. & Auvinen, P. 2012. miRSeqNovel: An R based workflow for analyzing miRNA sequencing data. Molecular and Cellular Probes 26:208-211. (PubMed)

Qian, K., Di Lieto, A., Corander, J., Auvinen, P. & Greco, D. 2012. Re-analysis of bipolar disorder and schizophrenia gene expression complements the Kraepelinian dichotomy. Advances in Experimental Medicine and Biology, 736:563-577. (PubMed)

Rasila, TS, Vihinen, M., Paulin, L., Haapa-Paananen, S. & Savilahti, H. 2012. Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues. PLoS ONE 7: e37922. (PubMed)

Rintala, H., Pitkäranta, M. & Täubel, M. 2012. Microbial communities associated with house dust. Advances in Applied Microbiology 78: 75-120. (PubMed)

Ritari, J., Hultman, J., Fingerroos, R., Tarkkanen, J., Pullat, J., Paulin, L., Kivi, N., Auvinen, P. & Auvinen, E. 2012. Detection of human papillomaviruses by polymerase chain reaction and ligation detection reaction on universal microarray. PLoS ONE 7: e34211. (PubMed)

Ritari,J., Koskinen, K., Hultman, J., Kurola, KM., Kymäläinen, M., Romantschuk, M., Paulin L. & Auvinen, P. 2012. Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation. BMC Microbiology 12: 121. (PubMed)

Sencilo, A., Paulin, L., Kellner, S., Helm, M. & Roine, E. 2012. Related haloarchaeal pleomorphic viruses contain different genome types. Nucleic Acids Research 40: 5523-34. (PubMed)

Tollenaere, C., Susi, H., Nokso-Koivisto, J., Koskinen, P., Tack, A, Auvinen, P., Paulin, L., Frilander, MJ, Lehtonen, R. & Laine, A-L. 2012. SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed-genotype infection. PLOS ONE 7: e52492. (PubMed)

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2011

Beritognolo, I., Harfouche, A., Brilli, F., Prosperini, G., Gaudet, M., Brosché, M., Salani, F., Kuzminsky, E., Auvinen, P., Paulin, L., Kangasjärvi, J., Loreto, F., Valentini, R., Scarascia-Mugnozza, G., & Sabatti, M. 2011. Comparative study of transcriptional and physiological responses to salinity stress in two contrasting Populus alba L. genotypes. Tree physiology 12: 1335-1355. (PubMed)

Greco, D., Kivi, N., Qian, K., Auvinen, P. & Auvinen, E. 2011. Human Papillomavirus 16 E5 modulates the expression of host microRNAs. PLoS ONE 6(7): e21646. (PubMed)

Guo, L., Brügger, K., Liu, C., Shah, SA., Zheng, H., Zhu, Y., Wang, S., Lillestøl, RK., Chen, L., Frank, J., Prangishvili, D., Paulin, L., She, Q., Huang, L. & Garrett, RA. 2011. Genome analyses of icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies. Journal of Bacteriology 193: 1672-1680. (PubMed)

Itävaara, M., Nyyssönen, M., Bomberg, M., Kapanen, A., Nousiainen, A., Ahonen, L., Hultman, J., Paulin, L., Auvinen, P. & Kukkonen, IT. 2011. Microbial sampling and analysis of the Outokumpu deep drill hole biosphere in 2007-2009. In Geological survey of Finland, Special paper 51’Outokumpu deep drilling project 2003-2010’. Kukkonen (ed), Geological survey of Finland, ISBN 978-952-217-151-1, ISBN 978-952-217-151-8, ISSN 0782-8535, pages, 199-206. (PDF [255 pages])

Johansson, P., Paulin, L., Vihavainen, E., Salovuori, N., Alatalo, ER., Björkroth, J. & Auvinen, P. 2011. Genome sequence of a food spoilage lactic acid bacterium Leuconostoc gasicomitatum LMG 18811T in association with specific spoilage reactions. Applied and Environmental Microbiology, 77: 4344-4351. (PubMed)

Kant R., Paulin L., Alatalo E., de Vos, W.M. & Palva, A. 2011. Genome sequence of Lactobacillus amylovorus GRL1112. Journal of Bacteriology 193: 789-790. (PubMed)

Kant R., Paulin L., Alatalo E., de Vos, W.M. & Palva, A. 2011. Genome sequence of Lactobacillus amylovorus GRL1118, isolated from the pig ileum. Journal of Bacteriology, 193: 3147-3148.(PubMed)

Koskenniemi, K., Laakso, K., Koponen, J., Kankainen, M., Greco, D., Auvinen, P., Savijoki, K., Nyman, TA., Surakka, A., Salusjärvi, T., de Vos., WM, Tynkkynen, S., Kalkkinen, N. & Varmanen, P. 2011. Proteomic and transcriptomic characterization of bile stress response in Lactobacillus rhamnosus GG. Molecular & Cellular Proteomics, 10: M110.002741. (PubMed)

Koskinen, K., Hultman, J., Paulin, L., Auvinen, P. & Kankaanpää, H. 2011. Spatially differing bacterial communities in water columns of the northern Baltic Sea. FEMS microbiology ecology 75: 99-110. (PubMed)

Laakso, K., Koskenniemi, K., Koponen, J., Kankainen, M., Surakka, A., Salusjärvi, T., Auvinen, P., Savijoki, K., Nyman, T.A., Kalkkinen, N., Tynkkynen, S. & Varmanen, P. 2011. Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium. Microbial Biotechnology, 4: 746-766. (PubMed)

Nieminen, T.T., Vihavainen, E. Paloranta, A., Lehto, J., Paulin, L. Auvinen, P. & Björkroth, KJ., 2011. Characterization of bacterial communities in modified-atmosphere packed meat with terminal restriction fragment length polymorphism. International Journal of Food Microbiology 144: 360-366. (PubMed)

Piltonen, M., Planken, A., Leskelä, O., Hänninen, A.-L., Leppänen, V.-M., Auvinen, P., Alitalo, K., Andressoo, J.-O., Saarma, M. & Männistö, PT. 2011. Vascular endothelial growth factor C (VEGF-C) acts as a neurotrophic factor for dopamine neurons in vitro and in vivo. Neuroscience, 192: 550-563. (PubMed)

Pitkäranta, M.J., Meklin, T., Hyvärinen, A., Nevalainen, A., Paulin, L., Auvinen, P., Lignell, U. & Rintala, H. 2011. Molecular profiling of fungal communities in moisture- damaged buildings before and after remediation – a comparison of culture-dependent and culture-independent methods. BMC Microbiology, 11: 235. (PubMed)

Pitkäranta, M.J. & Richardson, M. 2011. Aureobasidium. In: Molecular Detection of Human Fungal Pathogens. Liu, D. (ed.). Chapter 6. CRC Press, Taylor & Francis Group. (Routledge)

Qian, K., Di Lieto, A., Corander, J., Auvinen, P. & Greco, D. 2011. Reanalysis of bipolar disorder and schizophrenia gene expression complements the Kraepelinian dichotomy. Advances in Experimental Medicine and Biology 736: 563-577. (PubMed)

Sevastianova, K., Sutinen, J., Greco, D., Sievers, M., Salmenkivi, K., Perttilä, J., Häkkinen, A-M., Wågsäter, D., Lidell, M., Enerbäck, S., Eriksson. P., Walker. U., Auvinen, P., Ristola, M. & Yki-Järvinen, H. 2011. Comparison of dorsocervical to abdominal subcutaneus adipose tissue in patients with and without combination antiretroviral therapy-associated lipodystrophy. Diabetes. 60:1894-1900 (PubMed)

Sinkko, H., Lukkari, K., Jama, A.S., Sihvonen, L.M., Sivonen, K., Leivuori, M., Rantanen, M., Paulin, L. & Lyra, C. 2011. Phosphorus chemistry and bacterial community composition interact in brackish sediments receiving agricultural discharges. PLoS ONE 6: e21555. (PubMed)

Sun, H., Paulin, L., Alatalo, E. & Asiegbu, F.O. 2011. Response of living tissues of Pinus sylvestris to the saprotrophic biocontrol fungus Phlebiopsis gigantea. Tree Physiology, 31: 438-451. (PubMed)

Tamminen, M., Karkman, A., Corander, J., Paulin, L. & Virta, M. 2011. Differences in bacterial community composition in Baltic Sea sediment in response to fish farming. Aquaculture 313: 15-23. (ScienceDirect)

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2010

Aittamaa, M., Somervuo, P., Laakso, I., Auvinen, P. & Valkonen J.P.T. 2010. Microarray-based comparison of genetic differences between strains of Streptomyces turgidiscabies with focus on pathogenecity island. Molecular Plant Pathology 11:733-746. (PubMed)

Greco, D., Vellonen K.-S., Turner, C.H., Häkli, M., Tervo, T. Wolosin, J.M., Auvinen, P. & Urtti, A. 2010. Gene expression analysis in a SV-40 immortalized human corneal epithelial cells cultured with an air-liquid interface. Molecular Vision, 16: 2109-2120. (PubMed)

Gupta, R., Greco, D., Auvinen, P. & Arjas, E. 2010. Bayesian integrated modeling for correcting signal saturation, normalization and finding differentially expressed genes: A case study on RhoG. BMC Bioinformatics 11: 295. (PubMed)

Hultman, J. & Auvinen, P. 2010. Metagenomiikka avaa uusia ovia mikrobiologiassa. Duodecim, 126: 1278-1285. (PubMed)

Hultman, J., Vasara, T., Partanen, P., Paulin, L., Kontro, M.H., Auvinen, P. & Romantschuk, M. 2010. Determination of fungal succession during municipal waste composting using a cloning-based analysis. Journal of Applied Microbiology 108: 472-487. (PubMed)

Kontunen-Soppela, S., Riikonen, J., Ruhanen, H., Brosché, M., Somervuo, P., Peltonen, P., Kangasjärvi, J., Auvinen, P., Paulin, L., Keinänen M,. Oksanen, E., Vapaavuori, E. 2010. Differential gene expression in senescing leaves of two silver birch genotypes in responce to elevated CO2 and tropospheric ozone. Plant, Cell and Environment 33: 1016-1028. (PubMed)

Mäkivuokko, H., Tiihonen, K., Tynkkynen, S., Paulin, L. & Rautonen, N. 2010. The effect of age and nonsteroidal anti-inflammatory drugs on human intestinal microbiota composition. British Journal of Nutrition 103: 227-234. (PubMed)

Ojala, T., Kuparinen,V., Koskinen, J.P., Alatalo, E., Holm, L., Auvinen, P., Edelman, S., Westerlund-Wikström, B., Korhonen, T.K., Paulin, L. & Kankainen, M. 2010. Genome sequence of Lactobacillus crispatus ST1. Journal of Bacteriology 192: 3547-3548. (PubMed)

Ovaskainen, O., Nokso-Koivisto, J., Hottola, J., Rajala, T., Pennanen, T., Ali-Kovero, H., Miettinen, O., Oinonen, P., Auvinen, P., Paulin, L., Larsson, K.H. & Mäkipää, R. 2010. What is the probability that the best BLAST hit represents the correct species - identifying wood-inhabiting fungi from environmental samples with pyrosequencing Fungal Ecology 3: 274-283. (ScienceDirect)

Partanen, P., Hultman, J., Paulin, L., Auvinen, P. & Romantschuk, M. 2010. Bacterial diversity at different stages of the composting process. BMC Microbiology 10: 94. (PubMed)

Pessa, H.K.J., Greco, D., Kvist, J., Wahlström, G., Heino, T.I., Auvinen, P. & Frilander, M.J. 2010. Gene expression profiling of U12-type spliceosome mutant Drosophila reveals widespread changes in metabolic pathways. PLoS ONE 5: e13215). (PubMed)

Roine, E., Kukkaro, P., Paulin, L., Laurinavicius, S., Domanska, A., Somerharju, P. & Bamford D.H. 2010. New, closely related haloarchaeal viral elements with different nucleic Acid types. Journal of Virology 84:3682-3689. (PubMed)

Sipilä, T., Kananen, L., Greco, D., Donner, J., Silander, K., Terwilliger, J.D., Auvinen, P., Peltonen, L., Lönnqvist, J., Pirkola, T., Partonen, T., & Hovatta, I. 2010. An association analysis of circadian genes in anxiety disorders. Biological Psychiatry. 67: 1163-1170. (PubMed)

Sipilä, T., Väisänen, P., Paulin, L. & Yrjälä, K. 2010. Sphingobium sp. HV3 degrades both herbicides and polyaromatic hydrocarbons using ortho- and meta-pathways with differential expression shown by RT-PCR. Biodegradation 21(5):771-84. (PubMed)

Vuorinen, A.L., Gammelgård, E., Auvinen, P., Somervuo, P., Dere, S. & Valkonen, J.P.T. 2010. Factors underpinning the responsiveness and higher levels of virus resistance realized in potato genotypes carrying virus-specific R genes. Annals of Applied Biology 157: 229-241. (Wiley Online)

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2009

Berg, K.A., Lyra, C., Sivonen, K., Paulin, L., Suomalainen, S., Tuomi, P. & Rapala, J. 2009. High diversity of cultivable heterotrophic bacteria in association with mass occurrences of cyanobacteria., ISME Journal 3: 314-325. (PubMed)

Greco, D., Volpicelli, F., Di Lieto, A., Leo, D., Perrone-Capano, C., Auvinen, P. & di Porzio, U., 2009. Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures. PLoS ONE, 4: e4977. (PubMed)

Hultman, J. & Auvinen, P. Mikrobiyhteisöjen tutkiminen metagenomiikan avulla. Natura, 04/2009: 14-18. (Natura ordering page [including currently free issues])

Hytönen, M.K., Grall, A., Hédan, B., Dréano, S., Seguin, S.J., Delattre, D., Thomas, A., Galibert, F., Paulin, L., Lohi, H., Sainio, K. & André, C. 2009. Ancestral T-box mutation is present in many, but not all, short-tailed dog breeds. Journal of Heredity 100: 236-240. (PubMed)

Jokela-Määttä, M., Vartio, A., Paulin, L. & Donner, K. 2009. Individual variation in rod absorbance spectra correlated with opsin gene polymorphism in sand goby (Pomatoschistus minutus). Journal of Experimental Biology, 212: 3403-3414. (PubMed)

Kankainen, M., Paulin, L., Tynkkynen, S., von Ossowski, I., Reunanen, J., Partanen, P., Satokari, R., Vesterlund, S., Hendrickx, A.P.A., Lebeer, S., De Keersmaeker, S.C.J., Vanderleyden, J., Hämäläinen, T., Laukkanen, S., Salovuori, N., Ritari, J., Alatalo, E., Korpela, R., Mattila-Sandholm, T., Lassig, A., Hatakka, K., Kinnunen, K.T., Karjalainen, H., Saxelin, M., Laakso, K., Surakka, A., Palva, A., Salusjärvi, T., Auvinen, P. & de Vos, W.M. 2009. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili contains a human mucus-binding protein. Proceedings of the National Academy of Sciences U.S.A. 106: 17193-17198. (PubMed)

Kohonen, J., Talikota, S., Corander, J., Auvinen, P. & Arjas, E. 2009. A Naive Bayes classifier for protein function prediction. In Silico Biology 9: 23-34. (PubMed)

Krogius-Kurikka, L., Kassinen, A.H., Paulin, L., Corander, J., Mäkivuokko, H., Tuimala, J. & Palva, A. 2009. Sequence analysis of G+C fraction libraries of human fecal bacterial DNA reveals a high number of Actinobacteria. BMC Microbiology 9: 68. (PubMed)

Krogius-Kurikka, L., Lyra, A., Malinen,E., Aarnikunnas, J., Tuimala, J., Paulin, L., Mäkivuokko, H., Kajander, K. & Palva, A. 2009. Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC Gastroenterology 9: 95. (PubMed)

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. Comparative genomic hybridization analysis of Nordic Group I (proteolytic) Clostridium botulinum type B clusters. Applied and Environmental Microbiology 75: 2643-2651. (PubMed)

Mouhu, K., Hytönen, T., Folta, K., Rantanen, M., Paulin, L., Auvinen, P. & Elomaa, P. 2009. Identification of flowering pathways in strawberry a perennial SD plant. BMC Plant Biology 9: 122. (PubMed)

Pietilä, M.K., Roine, E., Paulin, L., Kalkkinen, N., & Bamford, D.H. 2009. Isolation and characterization of HRPV-1, the first described ssDNA virus infecting archaea. Molecular Microbiology 72: 307-319. (PubMed)

Ritari, J., Paulin, L., Hultman, J. & Auvinen, P. 2009. Application of a hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays. BMC Research Notes 2: 249 (PubMed)

Täubel, M., Rintala, H., Pitkäranta, M., Paulin, L., Laitinen, S., Pekkanen, J. & Hyvärinen, A. 2009. The occupant as a source of house dust bacteria. Journal of Allergy and Clinical Immunology 4: 834-840. (PubMed)

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2008

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. Plant, animal and food pathogens analyzed using genome-wide microarrays: towards improved diagnostics and control of bacterial pathogens. In: Agricultural biomarkers for array technology (COST action 853). Frey, J.E. & Pasquer, F. (Eds.). pp. 47-51. ISBN 978-3-033-01770-2. (COST EU)

Aittamaa, M., Somervuo, P., Pirhonen, M., Mattinen, L., Nissinen, R., Auvinen, P. & Valkonen, J.P.T. 2008. Distinguishing bacterial pathogens of potato using a genome-wide -microarray approach. Molecular Plant Pathology 9: 705-717. (PubMed)

Alvesalo, J., Greco, D., Leinonen, M., Vuorela, P. & Auvinen, P. 2008. Microarray analysis of Chlamydia pneumoniae infected human epithelial cell line using gene ontology hierarchy. Journal of Infectious Diseases 197: 156-162. (PubMed)

Greco, D., Kotronen, A., Westerbacka, J., Puig, O., Arkkila, P., Kiviluoto, T., Laitinen, S., Kolak, M., Fisher, R., Hamsten, A., Auvinen, P. & Yki-Järvinen, H. 2008. Gene expression in human NAFLD. American Journal of Physiology: Gastrointestinal and Liver Physiology 294: G1281-G1287. (PubMed)

Greco, D., Leo, D., Capano, C.P., di Porzio, U. & Auvinen, P. 2008: Pre-filtering improves reliability of Affymetrix GeneChips results when used to analyze gene expression in complex tissues. Molecular and Cellular Probes 22: 115-121. (PubMed)

Greco, D., Somervuo, P., Di Lieto, A., Raitila, T., Nitsch, L., Castren, E. & Auvinen, P. 2008. Physiology, pathology and relatedness of human tissues from gene expression meta-analysis. PLoS ONE 3: e1880. (PubMed)

Gupta, R., Arjas, E., Kulathinal, S., Thomas, A., & Auvinen, P. 2008. Bayesian hierarchical model for estimating gene expression intensity using multiple scanned microarrays. EURASIP Journal on Bioinformatics and Systems Biology Article ID 231950. doi:10.1155/2008/231950. (PubMed)

Gupta, R., Somervuo, P., Kulathinal, S. & Auvinen, P. 2008. Optimal Designs for Microarray Experiments with Biological and Technical Replicates. In: Recent advances in linear models and related areas. Shalabh & Heumann, C. (Eds.), pp. 389-400. Springer-Verlag, ISBN:978-3-7908-2063-8. (SpringerLink preview)

Hultman, J., Pitkäranta, M., Romantschuk, M., Auvinen, P. & Paulin, L. 2008. Probe-based negative selection for underrepresented phylotypes in large environmental clone libraries. Journal of Microbiological Methods 75: 457-463. (PubMed)

Hultman, J., Ritari, J., Romantschuk, M., Paulin, L. & Auvinen, P. 2008. Universal Ligation-Detection-Reaction microarray applied for compost microbes. BMC Microbiology 8: 237. (PubMed)

Kivi, N., Greco, D., Auvinen, P. & Auvinen, E. 2008. Genes involved in cell adhesion, cell motility and mitogenic signaling are altered due to HPV 16 E5 protein expression. Oncogene 27: 2532-2541. (PubMed)

Mattinen, L., Somervuo, P., Nykyri, J., Nissinen, R., Kouvonen, P., Cortjals, G., Auvinen, P., Aittamaa, M., Valkonen, J.P.T. & Pirhonen, M. 2008. Microarrays profiling and characterization of host-extract induced genes and type VI secretion cluster of potato pathogen Pectobacterium atrosepticum. Microbiology 154: 2387-2396. (PubMed)

Metlin, A.E., Paulin, L., Suomalainen, S., Neuvonen, E., Rybakov, S.S. & Huovilainen, A. 2008. Characterization of Russian rabies virus vaccine strain RV-97. Virus Research 132: 242-247. (PubMed)

Pitkäranta, M., Meklin, T., Hyvärinen, A., Paulin, L., Auvinen, P., Nevalainen, A. & Rintala, H. 2008. Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR and culture. Applied and Environmental Microbiology 74: 233-244. (PubMed)

Rintala, H., Pitkäranta, M., Toivola, M., Paulin, L. & Nevalainen, A. 2008. Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiology 8: 5. (PubMed)

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2007

Conti, A ., Fabbrini, F ., D'Agostino, P ., Negri, R ., Greco, D., Genesio, R ., D'Armiento, M., Olla, C., Paladini, D ., Zannini, M . & Nitsch, L . 2007. Altered expression of mitochondrial and extracellular matrix genes in the heart of human fetuses with chromosome 21 trisomy. BMC Genomics 8: 268. (PubMed)

Greco, D., Somervuo, P., Raitila, T. & Auvinen, P. 2007. Unique expression fingerprints of human tissues. In: CSC Report on Computational Science in Finland 2006-2007. Sillanpää, Fagerholm, Kotila, Ahokas, Forsström, Järvinen, Saren, Tarus & Talvitie (Eds.), pp. 98-100. ISBN 978-952-5520-27-9(print), ISBN 978-952-5520-28-6 (PDF). (CSC publications)

Gupta, R., Ruosaari, S., Kulathinal, S., Hollmén,J., & Auvinen, P. 2007 . Microarray image segmentation using additional dye- an experimental study . Molecular and Cellular Probes 21: 321-328. (PubMed)

Kassinen, A., Krogius-Kurikka, L., Mäkivuokko, H., Paulin, L., Rinttilä, T., Corander, J., Malinen, E., Apajalahti, J. & Palva, A. 2007. The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133: 24-33. (PubMed)

Koutaniemi, S., Warinowski, T., Kärkönen, A., Alatalo, E., Fossdal, C.G., Saranpää, P., Laakso, T., Fagerstedt, K.V., Simola, L.K., Paulin, L., Rudd, S. & Teeri, T.H. 2007. Expression profiling of the lignin biosynthetic pathway in Norway spruce using EST sequencing and real-time RT-PCR. Plant Molecular Biology 65: 311-28. (PubMed)

Kärenlampi, R., Rautelin, H., Schönberg-Norio, D., Paulin, L. & Hänninen, M.-L. 2007. Longitudinal study of Finnish human Campylobacter jejuni and C. coli isolates from humans, using multilocus sequence typing, including comparison with epidemiological data and isolates from poultry and cattle. Applied and Environmental Microbiology 73: 148-155. (PubMed)

Mijatovic, J., Airavaara, M., Planken, A., Auvinen, P., Raasmaja, A., Piepponen, T.P., Constantini, F., Ahtee, L. & Saarma, M. 2007. Constitutive Ret activity in knock-in neoplasia type B mice induces profound elevation of brain dopamine concentration via enhanced synthesis and increases number of TH-positive cells in substancia nigra. Journal of Neuroscience 27: 4799-4809. (PubMed)

Pitkänen, T., Paakkari, P., Miettinen, I.T., Heinonen-Tanski, H., Paulin, L. & Hänninen, M.-L. 2007. Comparison of media for enumeration of coliform bacteria and Escherichia coli in non-disinfected water. Journal of Microbiological Methods 68: 522-529. (PubMed)

Vihavainen, E., Lundström, H.-S., Susiluoto, T., Koort, J., Paulin, L., Auvinen, P., & Björkroth, K.J. 2007 . The role of broiler carcasses and processing plant air in contamination of MAP broiler products with psychrotrphic LAB. Applied and Environmental Microbiology 73: 1136-1145. (PubMed)

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2006

Gupta, R., Auvinen, P., Thomas, A. & Arjas, E. A. 2006 . Bayesian hierarchical model for correcting signal saturation in microarrays using pixel intensities. Statistical Applications in Genetics and Molecular Biology 5: Article 20. (PubMed)

Poranen, M.M., Ravantti, J.J., Grahn, A.M., Gupta, R., Auvinen, P. & Bamford, D.H. 2006 . Global changes in cellular gene expression during viral infection. Journal of Virology 80: 8081-8088. (PubMed)

Torvinen, E., Meklin, T., Torkko, P., Suomalainen, S., Reiman, M., Katila, M.-L., Paulin, L. & Nevalainen, A. 2006. Mycobacteria and fungi in moisture-damaged building materials. Applied and Environmental Microbiology 72: 6822-4. (PubMed)

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2005

Alakuijala, A., Palgi, M., Wegelius, K., Schmidt, M., Enz, R., Paulin, L., Saarma, M. & Pasternack, M. 2005. GABA receptor Rho subunit expression in the developing rat brain. Developmental Brain Research 154: 15-23. (PubMed)

Ala-Poikela, M., Svensson, E., Rojas, A., Horko, T., Paulin, L., Valkonen, J.P.T. & Kvarnheden, A. 2005. Genetic diversity and mixed infections of begomoviruses infecting tomato, pepper and cucurbit crops in Nicaragua. Plant Pathology 54: 448-459. (Wiley Online)

Brosché, M., Vinocur,B., Alatalo, E.R., Lamminmäki, A., Teichmann, T., Ottow, E.A., Djilianov, D., Afif, D., Triboulot-Bogeat, M.B., Altman, A., Polle, A., Dreyer, E., Rudd, S., Paulin, L., Auvinen, P. & Kangasjärvi J . 2005 . Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biology 6: R101. (PubMed)

Juuti, J.T., Jokela, S., Tarkka, M., Paulin, L. & Lahdensalo, J. 2005. Two phylogenetically highly distinct beta-tubulin genes of the basidiomycete Suillus bovinus. Current Genetics 47: 253-263. (PubMed)

Laitinen, R.A.E., Immanen, J., Auvinen, P., Rudd, S., Alatalo, E., Paulin, L., Ainasoja, M., Kotilainen, M., Koskela, S., Teeri, T.H., & Elomaa, P. 2005. Analysis of floral transcriptosome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae). Genome Research 15: 475-486. (PubMed)

Pitkäranta, M., Rintala, H., Hänninen, M. & Paulin, L. 2005. Characterization of fungal flora from moisture damaged building material by rDNA sequencing and culture. In: Bioaerosols, Fungi, Bacteria, Mycotoxins and Human Health. Eckardt, J. (ed.). Boyd Publishing, Albany, NY, USA. pp. 375-383. (PDF [494 pages])

Rapala, J, Berg, K.A., Lyra, C., Niemi, R.M., Manz, W., Suomalainen, S., Paulin, L . & Lahti, K. 2005. Paucibacter toxinivorans gen. nov., sp. nov., a bacterium degrading cyclic cyanobacterial hepatotoxins, microcystins and nodularin,. International Journal of Systematic and Evolutionary Microbiology 55: 1563-1568. (PubMed)

Sarén, A.-M ., Ravantti, J.J., Benson, S.D., Burnett, R.M., Paulin, L., Bamford, D.H. & Bamford, J.K.H. 2005. A Snapshot of Viral Evolution from Genome Analysis of the Tectiviridae Family. Journal of Molecular Biology 350: 427-440. (PubMed)

Tortoli, E., Rindi, L., Goh, K.S., Katila, M.-L., Mariottini, A., Mattei, R., Mazzarelli, G., Suomalainen S., Torkko, P. & Rastogi, N. 2005. Mycobacterium florentinum sp. nov ., isolated from humans. International Journal of Systematic and Evolutionary Microbiology 55: 1101-1106. (PubMed)

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2004

Airavaara, M., Planken, A., Gäddnäs, H., Piepponen, T.P., Saarma, M. & Ahtee, L. 2004. Increased extracellular dopamine concentrations and FosB/DeltaFosB expression in striatal brain areas of heterozygous GDNF knockout mice. European Journal of Neuroscience 20: 2336-2344. (PubMed)

Auvinen, E., Alonso, A. Auvinen, P. 2004. Human papillomavirus 16 E5 protein colocalizes with the antiapoptotic Bcl-2 protein. Archives of Virology 149: 1745-1759. (PubMed)

Degefu, Y., Lohtander, K. & Paulin, L . 2004. Expression patterns and phylogenetic analysis of two xylanase genes (htxyl 1 and htxyl 2) from Helminthosporium turcicum, the cause of northern leaf blight of maize. Biochimie 86: 83-90. (PubMed)

Juuti, J.T., Jokela, S., Paulin, L ., Timonen, S. & Sen, R. 2004. Glutamine synthetase of Suillus bovinus: the gene, transcription and enzyme activity in the Scots pine mycorrihizosphere developed in forest humus. New Phytologist 164: 389-399. (Wiley Online)

Järvinen, A.K., Hautaniemi, S., Edgren, H., Auvinen, P., Saarela, S., Kallioniemi, O. & Monni, O. 2004. Are data from different gene expression microarray platforms comparable? Genomics 83: 1164-1168. (PubMed)

Poussu, E., Vihinen, M., Paulin, L. & Savilahti, H. 2004. Probing the alpha-complementing domain of E. coli beta-galactosidase using an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition. Proteins 54: 681-692. (PubMed)

Rautiala, S., Torvinen, E., Torkko, P., Suomalainen, S., Nevalainen, A., Kalliokoski, P. & Katila, M.-L. 2004. Potentially pathogenic, slow-growing mycobacteria released into workplace air during the remediation of buildings. Journal of Occupational and Environmental Hygiene 1: 1-6. (PubMed)

Rintala, H., Hyvärinen, A., Paulin, L. & Nevalainen, A. 2004. Detection of Streptomyces in house dust - Comparison of culture and PCR methods. Indoor Air 14: 112-119. (PubMed)

Torvinen, E., Suomalainen, S., Paulin, L., Katila, M.-L. & Martikainen, P.J. 2004. Mycobacteria in water and loose deposits of drinking water distribution systems in Finland. Applied and Environmental Microbiology 70: 1973-1981. (PubMed)

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2003

Grönberg, H., Paulin, L. & Sen, R. 2003. Molecular probe development for tree root associated Rhizoctonia spp. and Suillus bovinus and their detection by Southern dot blot and liquid hybridiztion-fragment lenght polymorphism. Mycology Research 107: 428-438. (PubMed)

Jokela, M., Vartio, A., Paulin, L., Fyhrqvist-Vanni, N. & Donner, K. 2003. Polymorphism of the rod visual pigment between allopatric populations of the sand goby (Pomatoschistus minutus): A microspectrophotometric study. Journal of Experimental Biology 206: 2611-2617. (PubMed)

Olonen, A., Kalkkinen, N. & Paulin, L . 2003. A new type of cysteine proteinase inhibitor - the salarin gene from Atlantic salmon (Salmo salar L.) and arctic charr (Salvelinus alpinus). Biochimie 85: 677-681. (PubMed)

van Berkum, P., Terefework, Z., Paulin, L., Suomalainen, S., Lindström, K. & Eardly, B.D. 2003. Discordant phylogenies within the rrn loci of Rhizobia. Journal of Bacteriology 185: 2988-2998. (PubMed)

Vilen, H., Aalto, J.-M., Kassinen, A., Paulin, L. & Savilahti, H. 2003. A direct transposon insertion tool for modification and functional analysis of viral genomes. Journal of Virology 77: 123-134. (PubMed)

Ålander-Damsten, Y.K., Brander, E.E. & Paulin, L. 2003. M. smegmatis, a cause for feline panniculitis also in a cold climate. Journal of Feline Medical Surgery 5: 19-26. (PubMed)

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2002

Perola, O., Nousiainen, T., Suomalainen, S., Aukee, S., Kärkkäinen, U.-M., Kauppinen, J, Ojanen, T. & Katila, M.-L. 2002. Recurrent Sphingomonas paucimobilis -bacteraemia associated with a multi-bacterial water-borne epidemic among neutropenic patients. Journal of Hospital Infection 50: 196-201. (PubMed)

Tiirola, M., Wang, H., Paulin, L. & Kulomaa, M.S. 2002. Evidence for natural horizontal transfer of the pcpB gene in the evolution of polychlorophenol-degrading Spingomonads. Applied and Environmental Microbiology 68: 4495-4501. (PubMed)

Torkko, P., Suomalainen, S., Iivanainen, E., Tortoli, E., Suutari, M., Seppänen, J., Paulin, L. & Katila, M.-L. 2002. Mycobacterium palustre sp. nov. , a potentially pathogenic, slow-growing mycobacterium isolated from clinical and veterinary specimens and from Finnish stream water. International Journal of Systematic and Evolutionary Microbiology 52: 1519-1525. (PubMed)

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2001

Degefu, Y., Paulin, L., & Lübeck, P.S. 2001. Cloning, sequencing and expression of a xylanase gene from the maize pathogen Helminthosporium turcicum, European Journal of Plant Pathology 107: 457-465. (SpringerLink)

Kujala, P., Ikäheimonen, A., Ehsani, N., Vihinen, H., Auvinen, P. & Kääriäinen, L. 2001. Biogenesis of Semliki Forest virus replication complex. Journal of Virology 75: 3873-3884. (PubMed)

Lyra, C., Suomalainen, S., Gugger, M., Vezie, C., Sundman P., Paulin, L . & Sivonen K. 2001. Molecular characterization of planktic cyanobacteria Anabaena, Aphanizomenon, Microcystis and Planktothrix genera. International Journal of Systematic and Evolutionary Microbiology 51: 513-526. (PubMed)

Magden, J., Takeda, N., Li, T., Auvinen, P., Ahola, T., Miyamura, T., Merits, A. & Kääriäinen, L. 2001. Virus-specific mRNA capping enzyme encoded by hepatitis E virus. Journal of Virology 75: 6249-55. (PubMed)

Merits, A., Vasiljeva, L., Ahola,T., Kääriäinen, L. & Auvinen, P. 2001. Proteolytic processing of Semliki Forest virus-specific non-structural-polyprotein by nsP2 protease. Journal of General Virology 82: 765-773. (PubMed)

Nieminen, P., Arte, S., Tanner, D., Paulin, L., Alaluusua, S., Thesleff, I. & Pirinen, S. 2001. Identification of a nonsense mutation in the PAX9 gene in molar oligodontia. European Journal of Human Genetics 9: 743-746. (PubMed)

Savolainen, K., Paulin, L., Westerlund-Wikström, B., Foster, T.J., Korhonen, T.K. & Kuusela, P. 2001. Expression of pls, a gene closely associated with the mecA gene of methicillin-resistant Staphylococcus aureus, prevents bacterial adhesion in vitro. Infection and Immunity 69: 3013-3020. (PubMed)

Suomalainen, S., Koukila-Kähkölä, P., Brander, E., Katila, M.-L., Paulin, L. & Mattson, K. 2001. Pulmonary infection caused by an unusual, slowly growing nontuberculous Mycobacterium. Journal of Clinical Microbiology 39: 2668-2671. (PubMed)

Suominen, L., Roos, C., Lortet, G., Paulin, L. & Lindström, K. 2001.Identification and structure of the Rhizobium galegae common nodulation genes: evidence for horizontal gene transfer. Molecular Biology and Evolution 18: 907-916. (PubMed)

Torkko, P., Suomalainen, S., Iivanainen, E., Suutari, M., Paulin, L ., Rudbäck, E., Tortoli, E., Vincent, V., Mattila, R. & Katila, M.-L. 2001. Characterization of Mycobacterium bohemicum isolated from human, veterinary and environmental sources. Journal of Clinical Microbiology 39: 207-211. (PubMed)

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2000

Ahola, T., Kujala, P., Tuittila, M., Blom, T., Laakkonen, P., Hinkkanen, A. & Auvinen, P. 2000. The effects of palmitoylation of replicase protein nsP1 on alphavirus infection. Journal of Virology 74: 6725-6733. (PubMed)

Hendolin, P.H., Paulin, L., Koukila-Kähkölä, P., Anttila, V.-J., Malmberg, H., Richardson, M. & Ylikoski, J. 2000. Panfungal PCR and multiplex liquid hybridization for detection of fungi in tissue specimens. Journal of Clinical Microbiology 38: 4186‑4192. (PubMed)

Hendolin P.H., Paulin, L. & Ylikoski, J. 2000. Clinically applicable multiplex PCR for four middle ear pathogens. Journal of Clinical Microbiology 38: 125-132. (PubMed)

Koukila-Kähkölä, P., Paulin, L., Brander, E., Jantzen, E., Eho-Remes, M. & Katila, M.L. 2000. Characterisation of a new isolate of Mycobacterium shimoidei from Finland. Journal of Medical Microbiology 49: 937-940. (PubMed)

Lehtimäki, J., Lyra, C., Suomalainen, S., Sundman, P., Rouhiainen, L., Paulin, L., Salkinoja-Salonen, M. & Sivonen, K. 2000. Characterization of Nodularia strains, cyanobacteria from brackish waters, by genotypic and phenotypic methods. International Journal of Systematic and Evolutionary Microbiology 50: 1043-1053. (PubMed)

Rouhiainen, L., Paulin, L., Suomalainen, S., Hyytiäinen, H., Buikema, W., Haselkorn, R. & Sivonen, K. 2000. Genes encoding synthetases of cyclic depsipeptides, anabaenopeptilides, in Anabaena strain 90. Molecular Microbiology 37: 156-167. (PubMed)

Torkko P., Suomalainen S., Iivanainen E., Suutari M., Tortoli E., Paulin, L. & Katila M.-L. 2000. Mycobacterium xenopi and related organisms isolated from stream waters in Finland and description of Mycobacterium botniense sp. nov. International Journal of Systematic and Evolutionary Microbiology 50: 283-289. (PubMed)

Vartiainen, M., Ojala, P.J., Auvinen, P., Peränen, J. & Lappalainen, P. 2000. Mouse A6/twinfilin is an actin monomer-binding protein that localizes to the regions of rapid actin dynamics. Molecular and Cellular Biology 20: 1772-1783. (PubMed)

Vasiljeva, L., Merits, A., Auvinen, P. & Kääriäinen, L. 2000. Identification of a novel function of the alphavirus capping apparatus: RNA 5’–triphosphatase activity of Nsp2. Journal of Biological Chemistry 275: 17281-17287. (PubMed)

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1999

Ahola, T., Lampio, A., Auvinen, P. & Kääriäinen, L. 1999. Semliki Forest virus mRNA capping enzyme requires association with anionic membrane phospholipids for activity. EMBO Journal 18: 3164-3172. (PubMed)

Gribbon, B.M., Pearce, S.R., Kalendar, R., Schulman, A.H., Paulin, L., Jack, P., Kumar, A. & Flavell, A.J. 1999. Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Molecular and General Genetics 261: 883-891. (PubMed)

Haapa, S., Suomalainen, S., Eerikäinen, S., Airaksinen, M., Paulin, L. & Savilahti, H. 1999. An efficient DNA sequencing strategy based on the bacteriophage mu in vitro DNA transposition reaction. Genome Research 9: 308-315. (PubMed)

Kujala, P., Ahola, T., Ehsani, N., Auvinen, P., Vihinen, H. & Kääriäinen, L. 1999. Intracellular distribution of Rubella virus nonstructural protein P150. Journal of Virology 73: 7805-7811. (PubMed)

Kreuze, J.F., Suomalainen, S., Paulin, L. & Valkonen, J.P. 1999. Phylogenetic analysis of 16S rRNA genes and PCR analysis of the nec1 gene from Streptomyces spp. causing common scab, pitted scab and netted scab in Finland. Phytopathology 89: 462-469. (PubMed)

Merits, A., Kettunen, R., Mäkinen, K., Lampio, A., Auvinen, P., Kääriäinen, L. & Ahola, T. 1999. Virus-specific capping of tobacco mosaic virus RNA: Methylation of GTP prior to formation of covalent complex p126-m7GMP. FEBS letters 455: 45-48. (PubMed)

Mikkola, M.L., Pispa, J., Pekkanen, M., Paulin, L., Nieminen, P., Kere, J. & Thesleff, I. 1999. Ectodysplasin, a protein required for epithelial morphogenesis, is a novel TNF homologue and promotes cell-matrix adhesion. Mechanisms in Develpoment 88: 133-146. (PubMed)

Männistö, R.H., Kivelä, H.M., Paulin, L., Bamford, D.H. & Bamford, J.K. 1999. The complete genome sequence of PM2, the first lipid-containing bacterial virus to be isolated. Virology 262: 355-363. (PubMed)

Nick, G., de Lajudie, P., Eardly, B.D., Suomalainen, S., Paulin, L., Zhang, X., Gillis, M., & Lindström, K. 1999. Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya. International Journal of Systematic Bacteriology 49: 1359-1368. (PubMed)

Suominen, L., Paulin, L., Saano, A., Sarén, A.M., Tas, E. & Lindström, K. 1999. Identification of nodulation promoter (nod-box) regions of Rhizobium galegae. FEMS Microbiology Letters 177: 217-223. (PubMed)

Vuorio, A.F., Paulin, L., Saltevo, J. & Kontula, K. 1999. Single-nucleotide polymorphisms may cause erroneous results in primer-introduced restriction analyses: a case of molecular misdiagnosis of homozygous vs heterozygous familial hypercholesterolemia. Molecular and Cellular Probes 13: 421-424. (PubMed)

Zhang, X.-X., Guo, X.-W., Terefework, Z., Paulin, L., Cao, Y.-Z., Hu, F.R., Lindström, K. & Li, F.-D. 1999. Genetic diversity among Rhizobial isolates from field-grown Astragalus sinicus of southern China. Systematic and Applied Microbiology 22: 312-320. (ScienceDirect)

Zhang, X., Nick, G., Kaijalainen, S., Terefework, Z., Paulin, L., Tighe, S.W., Graham, P.H. & Lindström, K. 1999. Phylogeny and diversity of Bradyrhizobium strains isolated from the root nodules of peanut (Arachis hypogaea) in Sichuan, China. Systematic and Applied Microbiology 22: 378-386. (PubMed)

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1998

Laakkonen, P., Auvinen, P., Kujala, P. & Kääriäinen, L. 1998. Alphavirus replicase protein NSP1 induces filopodia and rearrangement of actin filaments. Journal of Virology 72: 10265-10269. (PubMed)

Rajamäki, M., Merits, A., Rabenstein, F., Andrejeva, J., Paulin, L., Kekarainen, T., Kreuze, J.F., Forster, R.L. & Valkonen, J.P. 1998. Biological, serological and molecular differences among isolates of potato A potyvirus. Phytopathology 88: 311-321. (PubMed)

Terefework, Z., Nick, G., Suomalainen, S., Paulin, L. & Lindström, K. 1998. Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria. International Journal of Systematic Bacteriology 48: 349-356. (PubMed)

Torkko, P., Suutari, M., Suomalainen, S., Paulin, L., Larsson, L. & Katila, M.-L. 1998. Separation among the species of Mycobacterium terrae complex by lipid analyses: comparison with biochemical tests and 16S rRNA sequencing. Journal of Clinical Microbiology 36: 499-505. (PubMed)

Virtaneva, K., Paulin, L., Krahe, R., de la Chapelle, A. & Lehesjoki, A.-E. 1998. The minisatellite expansion mutation in EPM1: resolution of an initial discrepancy. Mutations in brief no. 186. Online. Human Mutation 12: 218. (PubMed)

Wartiovaara, K., Hytönen, M., Vuori, M., Paulin, L., Rinne, J. & Sariola, H. 1998. Mutation analysis of the glial cell line -derived neurotrophic factor gene in Parkinson’s disease. Experimental Neurology 152: 307-309. (PubMed)

Yrjälä, K., Suomalainen, S., Suhonen, E., Kilpi, S., Paulin, L. & Romantschuk, M. 1998. Characterization and reclassification of an aromatic- and chloroaromatic degrading Pseudomonas sp. strain HV3 as Spingomonas sp. HV3. International Journal of Systematic Bacteriology 48: 1057-1062. (PubMed)

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1997

Jacq, C., Alt-Mörbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Blöcker H., Blugeon C., Boskovic J., Brandt P., Bruckner M., Buitrago M.J., Coster F., Delaveau T. ,del Rey F., Dujon B., Eide L.G., Garcia‑Cantalejo J.M., Goffeau A., Gomez‑Peris A., Granotier C., Hanemann, V., Hankeln T., Hoheisel J.D., Jäger W., Jimenez A, Jonniaux J.‑L., Krämer C., Kuster H., Laamanen, P., Legros Y., Louis E., Möller‑Rieker S., Monnet A., Moro M., Muller‑Auer S., Nussbaumer B., Paricio N., Paulin, L ., Perea J., Perez‑Alonso M., Perez‑Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Sarén , A.M., Chäfer, M., Scharfe, M., Schmidt, E.R., Schneider, C., Scholler, P.,Schwarz, S., Soler‑Mira, A., Urrestarazu, L.A., Verhasselt, P. Vissers, S., Voet, M., Volckaert, G., Wagner, G., Wambutt, R., Wedler, E., Wedler, H., Wölfl, S., Harris, D.E., Bowman, S., Brown, D., Churcher, C.M., Connor, R., Dedman, K., Gentles, S., Hamlin, N., Hunt, S., Jones, L., McDonald, S., Murphy, L., Niblett, D., Odell, C., Oliver, K., Rajandream, M.A., Richards, C., Shore, L., Walsh, S.V., Barrell, B.G., Dietrich, F.S., Mulligan, J., Allen, E., Araujo, R., Aviles, E., Berno, A., Carpenter, J., Chen, E., Cherry, J.M.,Chung, E., Duncan, M., Hunicke‑Smith, S., Hyman, R., Komp, C., Lashkari, D., Lew, H., Lin, D., Mosedale, D., Nakahara, K., Namath, A., Oefner, P., Oh, C., Petel, F.X., Roberts, D., Schramm, S., Schroeder, M., Shogren, T., Shroff, N., Winant, A., Yelton, M., Botstein, D., Davis, R.W., Johnston, M., Hillier, L., Riles, L. and other members of the Genome Sequencing Center, Albermann, K., Hani, J., Heumann, K., Kleine, K., Mewes, H.W., Zollner, A. & Zaccaria, P. 1997. The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature 387 (Suppl. ): 75-78. (PubMed)

Kylmä, T., Paulin, L., Hurwitz, M.Y., Hurwitz, R.L. & Kommonen B. 1997. Cloning and analysis of the cDNA encoding the rod G-protein transduction alpha , beta1 and gamma1 subunits from the canine retina. Gene 193: 1-4. (PubMed)

Kylmä, T., Paulin, L., Hurwitz, M.Y., Hurwitz, R.L. & Kommonen, B. 1997. Cloning of the cDNA encoding rod cGMP-phosphodiesterase alpha and gamma subunits from the retinal degenerate Labrador retriever dog. Research in Veterinary Science 62: 293-296. (PubMed)

Kylmä, T. , Roos, C., Paulin, L. & Kommonen, B. 1997. The introns of the canine rod opsin gene show higher sequence homology to the human than to the rodent introns. DNA Sequence 8: 99-104. (PubMed)

Lübeck, P.S., Paulin, L. Degefu, Y., Lübeck, M., Alekhina, I., Bulat.S.A. & Collinge, D.B. 1997. PCR cloning, DNA sequencing and phylogenetic analysis of a xylanase gene from the phytopathogenic fungus Ascophyta pisi Lib. Physiological and Molecular Plant Pathology 51: 377-389. (ScienceDirect)

Miettinen, H.E., Gylling, H., Miettinen, T.A., Viikari, J., Paulin, L. & Kontula, K. 1997. Apolipoprotein A-IFin. Dominantly inherited hypoalphalipoproteinemia due to a single base substitution in the apolipoprotein A-I gene. Arteriosclerosis, Thrombosis and Vascular Biology 17: 83-90. (PubMed)

Sarén, A.M. , Laamanen, P., Lejarcegui, J.B. & Paulin, L. 1997. The sequence of a 36.7 kb segment on the left arm of chromosome IV from Saccharomyces cerevisiae reveals 20 non-overlapping open reading frames(ORFs) including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 new ORFs. Yeast 13: 65-71. (PubMed)

Vuorio, A., Paulin, L., Turtola, H. & Kontula, K. 1997. Deletions of the low density lipoprotein receptor gene underlying familial hypercholesterolaemia: screening by polymerase chain reaction using pooled DNA and blood samples. Molecular and Cellular Probes 11: 65-70. (PubMed)

Wartiovaara, K., Paavola, P., Suvanto, P., Paulin, L., Saarma. M., Peltonen, L. & Sariola, H. 1997. Exclusion of the p75 neurotrophin receptor gene as a candidate gene for Meckel syndrome. Clinical Dysmorphology 6: 1-5. (PubMed)

Yrjälä, K., Paulin, L. & Romantschuk, M. 1997. Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid. FEMS Microbiology Letters 154: 403-408. (PubMed)

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1996

Kommonen, B., Kylmä, T., Cohen, R.J., Penn, J.S., Paulin, L ., Hurwitz, M. & Hurwitz, R.L. 1996. Elevation of cGMP with normal expression and activity of rod cGMP-PDE in photoreceptor degenerate labrador retrievers. Ophthalmic Research 28: 19-28. (PubMed)

Murphy, C., Saffrich, R., Grummt, M., Gournier, H., Rybin, V., Rubino, M., Auvinen, P., Lütcke, A., Parton, R.G., & Zerial, M. 1996. Endosome dynamics regulated by a Rho protein. Nature 384: 427-432. (PubMed)

Peränen, J., Auvinen, P., Virta, H., Wepf, R. & Simons, K. 1996. Rab8 promotes polarized membrane transport through reorganization of actin and microtubules in fibroblasts. Journal of Cell Biology 135: 153-167. (PubMed)

Roine, E., Nunn, D.N., Paulin, L. & Romantschuk, M. 1996. Characterization of pilP, a gene required for pilus expression in Pseudomonas syringae pathovar phaseolicola. Journal of Bacteriology 178: 410-417. (PubMed)

Vihinen, T., Määttä, A., Jaakkola, P., Auvinen, P. & Jalkanen, M. 1996. Functional characterization of mouse syndecan-1 promoter. Journal of Biological Chemistry 271: 12532-12541. (PubMed)

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1995

Eaton, S., Auvinen, P., Luo, L., Jan, Y.N. & Simons, K. 1995. CDC42 and Rac1 control different actin-dependent processes in the Drosophila wing disc epithelium. Journal of Cell Biology 131: 151-164. (PubMed)

Immonen, T., Ye, S., Ra, R., Qiao, M., Paulin, L . & Saris, P.E.J. 1995. The codon usage of the nisZ operon in Lactococcus lactis N8 suggests a non-lactococcal origin of the conjugative nisin-sucrose transposon. DNA Sequence 5:203-218. (PubMed)

Koukila-Kähkölä, P., Springer, B., Böttger, E.C., Paulin, L., Janzen, E. & Katila, M.-L. 1995. Mycobacterium branderi sp. nov., a new potential human pathogen. International Journal of Systematic Bacteriology 45: 549-553. (PubMed)

Ridell, J., Siitonen, A., Paulin, L., Lindroos, O., Korkeala, H. & Albert, M.J. 1995. Characterization of Hafnia alvei with biochemical tests, random amplified polymorphic DNA PCR, and partial sequencing of 16S rRNA gene. Journal of Clinical Microbiology 33:2372-2376. (PubMed)

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Supervised master's theses

 Mirka Similä 2001, Perunan bakteeripatogeenien diagnosoiminen DNA-mikrosiruilla. (jointly with Jari Valkonen, Minna Pirhonen, Riitta Nissinen, Panu Somervuo) University of Helsinki.

 Miia Viikari (Pitkäranta) 2002, Homesienilajiston määritys kosteusvaurioisen rakennuksen materiaalinäytteestä molekyylibiologisin menetelmin. University of Helsinki.

 Dario Greco 2006, Computational analysis of gene expression using Affymetrix. Compromising between biological significance and analytical robustness. University of Helsinki.

 Tuomas Raitila 2007, Differential Gene Expression in Human Brain and Testis Tissues. University of Jyväskylä.

 Sanna Laaksonen 2007, DNA-mikrosirujen kehittäminen kompostinäytteiden analysointiin. (jointly with Martin Romantschuk) University of Helsinki.

 Sari Hujanen 2008, Lihasspesifisten ekspressio- ja SNP mikrosirujen toiminnan testaaminen. (jointly with Peter Hackman) University of Helsinki.

 Kui Qian 2009, Gene expression meta-analysis of prefrontal cortex disorder. (jointly with Dario Greco) University of Helsinki.

 Joni Keto 2011, Lihasgeenien isoformiekspression tutkiminen alaraajan lihaksissa mikrosirupohjaisella menetelmällä. (jointly with Peter Hackman and Panu Somervuo) University of Helsinki.

 Velma Aho 2014, Comparison of bioinformatic workflows for the analysis of fungal amplicon sequence data. (jointly with Kaisa Koskinen) University of Helsinki.

 Tuuli Pietilä 2015, Ihmisen papilloomaviruksen mikro-RNA:iden validointi. (jointly with Eeva Auvinen) University of Helsinki.

 Muhammad S. Hasan 2016, Gut Microbiome in Gestational Diabetes: A Cross-sectional Study of Mothers and Children. University of Helsinki.

 Ilhan Cem Duru 2017, Genomic and transcriptomic analysis of Lactobacillus rhamnosusLC705, (jointly with Olli-Pekka Smolander). University of Helsinki.

 Kaisu Henttonen Antibiotic Resistance Genes in Human Gut Microbiota (jointly with Pedro Pereira) 2020, University of Helsinki.

 Alan Avila Pulido Transcriptomic analysis of the response of the lactic acid bacteria Lactococcus piscium for the identification of possible adaptive genes during thermal shock in cold and warm temperatures. (jointly with Anne Ylinen) 2020, University of Helsinki.

 Supervised doctoral theses

 Roosa Laitinen 2006, The Gerbera cDNA microarray: a tool for large-scale identification of genes involved in flower development (jointly with Dr. Paula Elomaa and Dr. Teemu Teeri).

 Jenni Hultman 2009, Microbial diversity in the municipal composting process and development of detection methods. (jointly with Dr. Martin Romantschuk).

 Rashi Gupta 2009, Methods to improve gene signal: Application to cDNA microarrays (jointly with Dr. Elja Arjas).

 Dario Greco 2009, Gene expression: From microarrays to functional genomics.

 Elina Säde (nee Vihavainen) 2011, Leuconostoc spoilage of refrigerated, packaged foods. (jointly with Dr. Johanna Björkroth).

 Anu Planken 2012, Role of GDNF and its cross-talk with other growth factors in the dopaminergic system. (jointly with Dr. Mart Saarma and Dr. Jaan-Olle Andressoo).

 Miia Pitkäranta 2012, Molecular profiling of indoor microbial communities in moisture damaged and non-damaged buildings (jointly with Dr. Helena Rintala and with Dr. Martin Romantschuk).

 Jarmo Ritari 2012, Microbial identification by detection of ligation probes on DNA microarray.

 Kui Qian 2013, Bioinformatic analysis of HPV associated host microRNA functions and identification of viral microRNA (jointly with Dr. Dario Greco).

 Kaisa Koskinen 2013, Characterization of diverse microbial communities and application of novel detection techniques (jointly with Dr. Martin Romantschuk).

 Teija Ojala 2016, Lactobacillus crispatus and Propionibacterium freudenreichii: A genomic and transcriptomic view. (jointly with Dr. Liisa Holm).

 Margarita Andreevskaya 2017, Ecological fitness and interspecies interactions of food-spoilage-associated lactic acid bacteria: Insights from genome analysis and transcriptome profiles. (jointly with Dr. Johanna Björkroth).

 Pedro Alexandre Bento Pereira 2017, The human microbiome in Parkinson’s disease and primary sclerosing cholangitis.

Velma Aho 2019, Differential abundance analysis of human microbiota in Parkinsons’s disease.

Ilhan Cem Duru 2021, Transcriptomic analysis of food-related microorganisms: Cheese microbiota, food spoilage lactic acid bacteria, and foodborne pathogens (jointly with Olli-Pekka Smolander).