Department of Biochemistry and Developmental Biology

  • Finland

Publications 1980 2019

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2016

Phospholipid analysis in sera of horses with allergic dermatitis and in matched healthy controls

Hallamaa, R. & Batchu, K., 2 Mar 2016, In : Lipids in Health and Disease. 15, 9 p., 45.

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Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules

Tikka, S., Monogioudi, E., Gotsopoulos, A., Soliymani, R., Pezzini, F., Scifo, E., Uusi-Rauva, K., Tyynelä, J., Baumann, M. H., Jalanko, A., Simonati, A. & Lalowski, M. M., 22 Mar 2016, In : NeuroMolecular Medicine. 18, 1, p. 109-133

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SePIA: RNA and small RNA sequence processing, integration, and analysis

Icay, K., Chen, P., Cervera Taboada, A., Rantanen, V., Lehtonen, R. & Hautaniemi, S., 20 May 2016, In : BioData mining. 9, 18 p., 20.

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Sex chromosome recombination failure, apoptosis, and fertility in male mice

Faisal, I. & Kauppi, L., 1 Jun 2016, In : Chromosoma. 125, 2, SI, p. 227-235 9 p.

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Switching head group selectivity in mammalian sphingolipid biosynthesis by active-site engineering of sphingomyelin synthases

Kol, M., Panatala, R., Nordmann, M., Swart, L., van Suijlekom, L., Cabukusta, B., Hilderink, A., Grabietz, T., Mina, J. G. M., Somerharju, P., Korneev, S., Tafesse, F. G. & Holthuis, J. C. M., Jul 2016, In : Journal of Lipid Research. 57, 7, p. 1273-1285 13 p.

Research output: Contribution to journalArticleScientificpeer-review

The PNPLA-family phospholipases involved in glycerophospholipid homeostasis of HeLa cells

Hermansson, M., Hanninen, S., Hokynar, K. & Somerharju, P., Sep 2016, In : Biochimica and Biophysica Acta. Molecular and Cell Biology of Lipids. 1861, 9, p. 1058-1065 8 p.

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The two sides of Tat

Barboric, M. & Fujinaga, K., 19 Jan 2016, In : eLife. 5, 3 p., 12686.

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Trim37-deficient mice recapitulate several features of the multi-organ disorder Mulibrey nanism

Kettunen, K. M., Karikoski, R., Hamalainen, R. H., Toivonen, T. T., Antonenkov, V. D., Kulesskaya, N., Voikar, V., Holtta-Vuori, M., Ikonen, E., Sainio, K., Jalanko, A., Karlberg, S., Karlberg, N., Lipsanen-Nyman, M., Toppari, J., Jauhiainen, M., Hiltunen, J. K., Jalanko, H. & Lehesjoki, A-E., 15 May 2016, In : Biology open. 5, 5, p. 584-595 12 p.

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2015

Accurate genetic diagnosis of Finnish pulmonary arterial hypertension patients using oligonucleotide-selective sequencing

Vattulainen, S., Aho, J., Salmenperä, P., Bruce, S., Tallila, J., Gentile, M., Sankelo, M., Laitinen, T., Koskenvuo, J. W., Alastalo, T-P. & Myllykangas, S., 2015, In : Molecular Genetics & Genomic Medicine. 3, 4, p. 354-362 9 p.

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APOE and AGT in the Finnish p.Arg133Cys CADASIL population

Siitonen, M., Mykkanen, K., Pescini, F., Rovio, S., Kaariainen, H., Baumann, M., Poyhonen, M. & Viitanen, M., 1 Dec 2015, In : Acta Neurologica Scandinavica. 132, 6, p. 430-434 5 p.

Research output: Contribution to journalArticleScientific

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

Alkodsi, A., Louhimo, R. & Hautaniemi, S., Mar 2015, In : Briefings in Bioinformatics. 16, 2, p. 242-254 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Congenital Aural Atresia Associated With Agenesis of Internal Carotid Artery in a Girl With a FOXI3 Deletion

Tassano, E., Jagannathan, V., Drogemuller, C., Leoni, M., Hytonen, M. K., Severino, M., Gimelli, S., Cuoco, C., Di Rocco, M., Sainio, K., Groves, A. K., Leeb, T. & Gimelli, G., Mar 2015, In : American Journal of Medical Genetics. Part A. 167A, 3, p. 537-544 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model

Marjonen, H., Sierra, A., Nyman, A., Rogojin, V., Grohn, O., Linden, A-M., Hautaniemi, S. & Kaminen-Ahola, N., 13 May 2015, In : PLoS One. 10, 5, 20 p., 0124931.

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Functional characterization of enzymes catalyzing ceramide phosphoethanolamine biosynthesis in mice

Bickert, A., Ginkel, C., Kol, M., vom Dorp, K., Jastrow, H., Degen, J., Jacobs, R. L., Vance, D. E., Winterhager, E., Jiang, X-C., Doermann, P., Somerharju, P., Holthuis, J. C. M. & Willecke, K., Apr 2015, In : Journal of Lipid Research. 56, 4, p. 821-835 15 p.

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GDNF Overexpression from the Native Locus Reveals its Role in the Nigrostriatal Dopaminergic System Function

Kumar, A., Kopra, J. J., Varendi, K., Porokuokka, L. L., Panhelainen, A. E., Kuure, S. H., Marshall, P. O. L., Karalija, N., Härma, M-A., Vilenius, C. L., Lilleväli, K., Tekko, T., Mijatovic, J., Pulkkinen, N., Jakobson, M., Jakobson, M., Ola, R., Palm, E., Lindahl, M. S., Strömberg, I. & 4 othersVõikar, V., Piepponen, T. P., Saarma, M. & Andressoo, J-O., 2015, In : PLoS Genetics. 11, 12, 24 p., e1005710.

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Identification of cytoplasmic proteins interacting with unliganded estrogen receptor and in human breast cancer cells

Stellato, C., Nassa, G., Tarallo, R., Giurato, G., Ravo, M., Rizzo, F., Marchese, G., Alexandrova, E., Cordella, A., Baumann, M., Nyman, T. A., Weisz, A. & Ambrosino, C., 2015, In : Proteomics (Weinheim). 15, 11, p. 1801-1807 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer

Heinonen, H., Lepikhova, T., Sahu, B., Pehkonen, H. M., Pihlajamaa, P., Louhimo, R., Gao, P., Wei, G-H., Hautaniemi, S., Jänne, O. A. & Monni, O. M., 2015, In : International Journal of Cancer. 137, 10, p. 2374-2383 10 p.

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In Vivo Tomographic Imaging of Deep-Seated Cancer Using Fluorescence Lifetime Contrast

Rice, W. L., Shcherbakova, D. M., Verkhusha, V. V. & Kumar, A. T. N., 1 Apr 2015, In : Cancer Research. 75, 7, p. 1236-1243 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Mass-Tag Enhanced Immuno-Laser Desorption/Ionization Mass Spectrometry for Sensitive Detection of Intact Protein Antigens

Lorey, M., Adler, B., Yan, H., Soliymani, R., Ekström, S., Yli-Kauhaluoma, J., Laurell, T. & Baumann, M., 19 May 2015, In : Analytical Chemistry. 87, 10, p. 5255-5262 8 p.

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Matrix metalloproteinase 8 degrades apolipoprotein A-I and reduces its cholesterol efflux capacity

Salminen, A., Astrom, P., Metso, J., Soliymani, R., Salo, T., Jauhiainen, M., Pussinen, P. J. & Sorsa, T., Apr 2015, In : FASEB Journal. 29, 4, p. 1435-1445 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

Rumyantsev, K. A., Shcherbakova, D. M., Zakharova, N. I., Emelyanov, A. V., Turoverov, K. K. & Verkhusha, V. V., 18 Dec 2015, In : Scientific Reports. 5, 10 p., 18348.

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Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins

Shcherbakova, D. M., Baloban, M., Pletnev, S., Malashkevich, V. N., Xiao, H., Dauter, Z. & Verkhusha, V. V., 19 Nov 2015, In : Chemistry & Biology. 22, 11, p. 1540-1551 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Multiparametric Flow Cytometry Using Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes

Telford, W. G., Shcherbakova, D. M., Buschke, D., Hawley, T. S. & Verkhusha, V. V., 26 Mar 2015, In : PLoS One. 10, 3, 13 p., 0122342.

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Origins and Impacts of New Mammalian Exons

Merkin, J. J., Chen, P., Alexis, M. S., Hautaniemi, S. K. & Burge, C. B., 31 Mar 2015, In : Cell Reports. 10, 12, p. 1992-2005 14 p.

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Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex

Ekumi, K., Paculova, H., Lenasi, T., Pospichalova, V., Boesken, C. A., Rybarikova, J., Bryja, V., Geyer, M., Blazek, D. & Barboric, M., 11 Mar 2015, In : Nucleic Acids Research. 43, 5, p. 2575-2589 15 p.

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Proteomic analysis of the palmitoyl protein thioesterase 1 interactome in SH-SY5Y human neuroblastoma cells

Scifo, E., Szwajda, A., Soliymani, R., Pezzini, F., Bianchi, M., Dapkunas, A., Debski, J., Uusi-Rauva, K., Dadlez, M., Gingras, A-C., Tyynelä, J., Simonati, A., Jalanko, A., Baumann, M. H. & Lalowski, M., 18 Jun 2015, In : Journal of Proteomics. 123, p. 42-53 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Quantitative analysis of PPT1 interactome in human neuroblastoma cells

Scifo, E., Szwajda, A., Soliymani, R., Pezzini, F., Bianchi, M., Dapkunas, A., Debski, J., Uusi-Rauvala, K., Dadlez, M., Gingras, A-C., Tyynelä, J., Simonati, A., Jalanko, A., Baumann, M. & Lalowski, M., 2015, In : Data in Brief. 4, p. 207-216 10 p.

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Serine 62-Phosphorylated MYC Associates with Nuclear Lamins and Its Regulation by CIP2A Is Essential for Regenerative Proliferation

Myant, K., Qiao, X., Halonen, T., Come, C., Laine, A., Janghorban, M., Partanen, J. I., Cassidy, J., Ogg, E-L., Cammareri, P., Laitera, T., Okkeri, J., Klefstrom, J., Sears, R. C., Sansom, O. J. & Westermarck, J., 11 Aug 2015, In : Cell Reports. 12, 6, p. 1019-1031 13 p.

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Subnuclear domain proteins in cancer cells support the functions of RUNX2 in the DNA damage response

Yang, S., Christiano Quaresma, A. J., Nickerson, J. A., Green, K. M., Shaffer, S. A., Imbalzano, A. N., Martin-Buley, L. A., Lian, J. B., Stein, J. L., van Wijnen, A. J. & Stein, G. S., 15 Feb 2015, In : Journal of Cell Science. 128, 4, p. 728-740 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Substrate Efflux Propensity Is the Key Determinant of Ca2+-independent Phospholipase A-beta (iPLA beta)-mediated Glycerophospholipid Hydrolysis

Batchu, K. C., Hokynar, K., Jeltsch, M., Somerharju, P. & Mattonet, K., 17 Apr 2015, In : Journal of Biological Chemistry. 290, 16, p. 10093-10103 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Suppression of RNAi by dsRNA-Degrading RNaseIII Enzymes of Viruses in Animals and Plants

Weinheimer, I., Jiu, Y., Rajamäki, M., Matilainen, O., Kallijärvi, J., Cuellar, W., Lu, R., Saarma, M., Holmberg, C. I., Jäntti, J. & Valkonen, J., 6 Mar 2015, In : PLoS Pathogens. 11, 3, 25 p., e1004711.

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Ultrafast excited-state dynamics and fluorescence deactivation of near-infrared fluorescent proteins engineered from bacteriophytochromes

Zhu, J., Shcherbakova, D. M., Hontani, Y., Verkhusha, V. V. & Kennis, J. T. M., 6 Aug 2015, In : Scientific Reports. 5, 8 p., 12840.

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Workflow for automated quantification of cerebromicrovascular gelatinase activity

Mattila, O. S., Rantanen, V., Saksi, J., Strbian, D., Pikkarainen, T., Hautaniemi, S. & Lindsberg, P. J., Jan 2015, In : Microvascular Research. 97, p. 19-24 6 p.

Research output: Contribution to journalArticleScientificpeer-review

2014

Adipocyte morphology and implications for metabolic derangements in acquired obesity

Heinonen, S., Saarinen, L., Naukkarinen, J., Rodriguez, A., Fruhbeck, G., Hakkarainen, A., Lundbom, J., Lundbom, N., Vuolteenaho, K., Moilanen, E., Arner, P., Hautaniemi, S., Suomalainen, A., Kaprio, J., Rissanen, A. & Pietilainen, K. H., Nov 2014, In : International Journal of Obesity. 38, 11, p. 1423-1431 9 p.

Research output: Contribution to journalArticleScientificpeer-review

A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome

Stepanenko, O. V., Bublikov, G. S., Stepanenko, O. V., Shcherbakova, D. M., Verkhusha, V. V., Turoverov, K. K. & Kuznetsova, I. M., May 2014, In : The FEBS Journal. 281, 9, p. 2284-2298 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Anima: modular workflow system for comprehensive image data analysis

Rantanen, V., Valori, M. & Hautaniemi, S., 30 Jul 2014, In : Frontiers in Bioengineering and Biotechnology. 2, p. 25 25.

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Antigenic Differences between AS03 Adjuvanted Influenza A (H1N1) Pandemic Vaccines: Implications for Pandemrix-Associated Narcolepsy Risk

Vaarala, O., Vuorela, A., Partinen, M., Baumann, M., Freitag, T. L., Meri, S., Saavalainen, P., Jauhiainen, M., Soliymani, R., Kirjavainen, T., Olsen, P., Saarenpaa-Heikkila, O., Rouvinen, J., Roivainen, M., Nohynek, H., Jokinen, J., Julkunen, I. & Kilpi, T., 15 Dec 2014, In : PLoS One. 9, 12, 23 p., 114361.

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Biclustering Methods: Biological Relevance and Application in Gene Expression Analysis

Oghabian, A., Kilpinen, S., Hautaniemi, S. & Czeizler, E., 20 Mar 2014, In : PLoS One. 9, 3, 10 p., 90801.

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Characterising metabolically healthy obesity in weight-discordant monozygotic twins

Naukkarinen, J., Heinonen, S., Hakkarainen, A., Lundbom, J., Vuolteenaho, K., Saarinen, L. A., Hautaniemi, S., Rodriguez, A., Fruehbeck, G., Pajunen, P., Hyotylainen, T., Oresic, M., Moilanen, E., Suomalainen Wartiovaara, A., Lundbom, N., Kaprio, J., Rissanen, A. & Pietiläinen, K. H., Jan 2014, In : Diabetologia. 57, 1, p. 167-176 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Dectin-1 Pathway Activates Robust Autophagy-Dependent Unconventional Protein Secretion in Human Macrophages

Ohman, T., Teirila, L., Lahesmaa-Korpinen, A-M., Cypryk, W., Veckman, V., Saijo, S., Wolff, H., Hautaniemi, S., Nyman, T. A. & Matikainen, S., 15 Jun 2014, In : Journal of Immunology. 192, 12, p. 5952-5962 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Diabetes drugs and neurological disorders: new views and therapeutic possibilities

Patrone, C., Eriksson, O. & Lindholm, D., Mar 2014, In : The Lancet diabetes & endocrinology. 2, 3, p. 256-262 7 p.

Research output: Contribution to journalArticleScientific

Fibroblast growth factor-21 enhances mitochondrial functions and increases the activity of PGC-1alpha in human dopaminergic neurons via Sirtuin-1

Mäkelä, J., Tselykh, T., Maiorana, F., Eriksson-Rosenberg, O., Do, H. T., Mudo, G., Korhonen, L., Belluardo, N. & Lindholm, D. B., 2014, In : SpringerPlus. 12 p., 3:2.

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Gene Expression Alterations in the Cerebellum and Granule Neurons of Cstb(-/-) Mouse Are Associated with Early Synaptic Changes and Inflammation

Joensuu, T., Tegelberg, S., Reinmaa, E., Segerstrale, M., Hakala, P., Pehkonen, H., Korpi, E. R., Vesterinen, J., Taira, T., Hovatta, I., Kopra, O. & Lehesjoki, A-E., 27 Feb 2014, In : PLoS One. 9, 2, 12 p., 89321.

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In vivo activation of the PI3K-Akt pathway in mouse beta cells by the EGFR mutation L858R protects against diabetes

Hakonen, E., Ustinov, J., Eizirik, D. L., Sariola, H., Miettinen, P. & Otonkoski, T., May 2014, In : Diabetologia. 57, 5, p. 970-979 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Kemiallisesti tuotetut kantasolut: Ikuisen nuoruuden lähde?

Baumann, M., Eriksson-Rosenberg, O. & Lindholm, D. B., 2014, In : Kemia - Kemi. 2, p. 52-54 3 p.

Research output: Contribution to journalArticleGeneral public

MED12 mutation frequency in unselected sporadic uterine leiomyomas

Heinonen, H-R., Sarvilinna, N. S., Sjoberg, J., Kampjarvi, K., Pitkanen, E., Vahteristo, P., Makinen, N. & Aaltonen, L. A., Oct 2014, In : Fertility and Sterility : official journal of the American Fertility Society . 102, 4, p. 1137-1142 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Meiosis: SYP Up Firmly and Cross Over Evenly

Kauppi, L., 6 Jan 2014, In : Current Biology. 24, 1, p. R20-R23 5 p.

Research output: Contribution to journalArticleScientific

mTORC1 Controls PNS Myelination along the mTORC1-RXR gamma-SREBP-Lipid Biosynthesis Axis in Schwann Cells

Norrmen, C., Figlia, G., Lebrun-Julien, F., Pereira, J. A., Troetzmueller, M., Koefeler, H. C., Rantanen, V., Wessig, C., van Deijk, A-L. F., Smit, A. B., Verheijen, M. H. G., Rueegg, M. A., Hall, M. N. & Suter, U., 23 Oct 2014, In : Cell Reports. 9, 2, p. 646-660 15 p.

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