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Articles and white papers

At SBW, we believe the best way to valiate our methods and services includes a publication in a peer-reviewd scientific journal.

Accepted publications including SBW employees co-authoring since 2005

  1. Madetoja, J., Madetoja, M., Mäkinen, J., Riuttala, E., Jokinen, J. Blood Sampling from the Tail Vein, in Comparison with Two Other Techniques, Causes Less Stress to Mice. Submitted, 2008.
  2. Aulchenko, Y., et al. Major loci determining lipid levels and coronary heart disease risk in 16 population-based European cohorts. Nature Genetics. In press, 2008.
  3. Jakkula, E., et al. The genome-wide patterns of variation confirms significant substructure in a founder population. American Journal of Human Genetics. Am J Hum Genet. 12:787-794, 2008.
  4. Petsalo, Aleksanteri, Turpeinen, Miia, Pelkonen, Olavi, Tolonen, Ari. Analysis of nine drugs and their cytochrome P450 specific probe metabolites from urine by liquid chromatography-tandem mass spectrometry utilizing sub 2 µm particle size column. Journal of Chromatography A. In press, 2008.
  5. Ruosaari, S., et al. Pathways affected by asbestos exposure in normal and tumour tissue of lung cancer patients. BMC Medical Genomics 1:55, 2008.
  6. Tolonen, Ari, Turpeinen, Miia, Pelkonen, Olavi. Liquid chromatography-mass spectrometry in in vitro drug metabolite screening. Drug Discovery Today. In press, 2008.
  7. Volotinen, Marjo, Mäenpää, Jukka, Kautiainen, Hannu, Tolonen, Ari,  Uusitalo, Jouko, Nilsson, Mats, Ropo, Auli, Vapaatalo, Heikki, Aine, Esko. Ophthalmic timolol in a hydrogel vehicle leads to minor inter-individual variation in timolol concentration in aqueous humor. European Journal of Pharmaceutical Sciences. In press, 2008.
  8. Alhopuro, P., et al. Unregulated smooth-muscle myosin in human intestinal neoplasia. Proc Natl Acad Sci U S A, 2008. 105(14): p. 5513-8.
  9. Hayeshi, Rose, Hilgendorf, Constanze, Artursson, Per, Augustijns, Patrick, Brodin, Birger, Fischer, Karen, Hovenkamp, Egbert, Korjamo, Timo, Masungi, Chantal, Maubon, Nathalie, Mols, Raf, Monkkonen, Jukka, Müllertz, Anette, O’Driscoll, Caitriona, Oppers - Tiemissen, H.M., Ragnarsson, Eva, Rooseboom, Martijn, and Ungell, Anna-Lena. Comparison of drug transporter gene expression and functionality in Caco-2 cells from 10 different laboratories. European Journal of Pharmaceutical Sciences, 2008. 35, 383-396.
  10. Hilli, Johanna, Korhonen, Tuomas, Turpeinen, Miia, Hokkanen, Juho, Mattila, Sampo, Laine, Kari. The Effect of Oral Contraceptives on the Pharmacokinetics of Melatonin in Healthy Subjects With CYP1A2 g.-163C>A Polymorphism. Journal of Clinical Pharmacology, 2008. 48, 986-994.
  11. Ilmarinen, T., et al. Functional interaction of AIRE with PIAS1 in transcriptional regulation. Mol Immunol, 2008. 45(7): p. 1847-62.
  12. Ihalmo, P., Wessman, M., Kaunisto, M.A., Kilpikari, R., Parkkonen, M., Forsblom, C., Holthöfer, H., Groop, P.H.; FinnDiane Study Group. Association analysis of podocyte slit diaphragm genes as candidates for diabetic nephropathy. Diabetologia, 2008. Jan;51(1):86-90. Epub 2007 Oct 30.
  13. Korjamo, Timo, Heikkinen, Aki T, Waltari, Pekka, Mönkkönen, Jukka. The asymmetry of the unstirred water layer in permeability experiments. Pharmaceutical Research, 2008. 25, 1714-1722.
  14. Korjamo, Timo, Holappa, Jukka, Taimisto, Sanna, Savolainen, Jouko, Järvinen, Tomi, Mönkkönen, Jukka. Effect of N-betainate and N-piperazine derivatives of chitosan on paracellular permeability in Caco-2 cells. European Journal of Pharmaceutical Sciences, 2008. 35, 226-234.
  15. Korhonen, Tuomas, Turpeinen, Miia, Tolonen, Ari, Laine, Kari, Pelkonen, Olavi. Identification of the human cytochrome P450 enzymes involved in the in vitro biotransformation of lynestrenol and norethindrone. Journal of Steroid Biochemistry and Molecular Biology, 2008. 110, 56-66.
  16. Kublbeck, Jenni, Jyrkkärinne, Johanna, Poso, Antti, Turpeinen, Miia, Sippl, Wolfgang, Honkakoski, Paavo, Windshugel, Björn. Discovery of substituted sulfonamides and thiazolidin-4-one derivatives as agonists of human constitutive androstane receptor. Biochemical Pharmacology, 2008. 76, 1288-1297.
  17. Kumar, K.K., Shelokar, P.S. An SVM method using evolutionary information for the identification of allergenic proteins, Bioinformation, 2008. 2(6), 253-256.
  18. Lehto, M., Mäyränpää, M.I., Pellinen, T., Ihalmo, P., Lehtonen, S., Kovanen, P.T., Groop, P.H., Ivaska, J., Olkkonen, V.M. The R-Ras interaction partner ORP3 regulates cell adhesion. J Cell Sci., 2008. Mar 1;121(Pt 5):695-705. Epub 2008 Feb 12.
  19. Pelkonen, Olavi, Tolonen, Ari, Turpeinen, Miia, Uusitalo, Jouko. In vitro metabolism in preclinical drug development, In Preclinical Development Handbook, Edited by Shayne C. Gad, John Wiley & Sons Inc. 2008.
  20. Petrova, T.V., et al. Transcription factor PROX1 induces colon cancer progression by promoting the transition from benign to highly dysplastic phenotype. Cancer Cell, 2008. 13(5): p. 407-19.
  21. Pietilainen, K.H., et al. Global transcript profiles of fat in monozygotic twins discordant for BMI: pathways behind acquired obesity. PLoS Med, 2008. 5(3): p. e51.
  22. Pontynen, N., et al. Critical immunological pathways are downregulated in APECED patient dendritic cells. J Mol Med, 2008.
  23. Pugalenthi, Ganesan K., Kumar, Krishna, Suganthana, P.N., Gangal, Rajeev. Identification of catalytic residues from protein structure using support vector machine with sequence and structural features. Biochem Biophys Res Commun, 2008. Jan 16. [Epub ahead of print].
  24. Rahnasto, Minna, Wittekindt, Carsten, Juvonen, Risto, Turpeinen, Miia, Petsalo, Aleksanteri, Pelkonen, Olavi, Poso, Antti, Stahl, Gunther, Höltje, Hans-Dieter, Raunio, Hannu. Identification of inhibitors of the nicotine metabolising CYP2A6 enzyme - an in silico approach. The Pharmacogenomics Journal, 2008. 8, 328-338.
  25. Sanchez-Niño, M.D., Sanz, A.B., Ihalmo, P., Lassila, M., Holthofer, H., Mezzano, S., Aros, C., Groop, P.H., Saleem, M.A., Mathieson, P.W., Langham, R., Kretzler, M., Nair, V., Lemley, K.V., Nelson, R.G., Mervaala, E., Mattinzoli, D., Rastaldi, M.P., Ruiz-Ortega, M., Martin-Ventura, J.L., Egido, J., Ortiz, A. The MIF Receptor CD74 in Diabetic Podocyte Injury. J Am Soc Nephrol, 2008. Oct 8. [Epub ahead of print]
  26. Scheinin, I., et al. CanGEM: mining gene copy number changes in cancer. Nucleic Acids Res, 2008. 36(Database issue): p. D830-5.
  27. von Schantz, C., et al. Brain gene expression profiles of Cln1 and Cln5 deficient mice unravels common molecular pathways underlying neuronal degeneration in NCL diseases. BMC Genomics, 2008. 9: p. 146.
  28. Ihalmo, P., Schmid, H., Rastaldi, M.P., Mattinzoli, D., Langham, R.G., Luimula, P., Kilpikari, R., Lassila, M., Gilbert, R.E., Kerjaschki, D., Kretzler, M., Holthöfer, H. Expression of filtrin in human glomerular diseases. Nephrol Dial Transplant, 2007. Jul;22(7):1903-9. Epub 2007 Apr 18.
  29. Karppinen, Katja, Hokkanen, Juho, Tolonen, Ari, Mattila, Sampo, Hohtola, Anja. Biosynthesis of hyperforin and adhyperforin from amino acid precursors in shoot cultures of Hypericum perforatum. Phytochemistry, 2007. 68, 1038 -1045.
  30. Kiialainen, A., et al. Transcript profiles of dendritic cells of PLOSL patients link demyelinating CNS disorders with abnormalities in pathways of actin bundling and immune response. J Mol Med, 2007. 85(9): p. 971-83.
  31. Korjamo T., Kemiläinen H., Heikkinen A.T., Mönkkönen J. Decrease in intracellular concentration causes the shift in Km value of efflux pump substrates. Drug Metab Dispos., 2007. 35,:1574-1579.
  32. Mundra, Piyush Kumar, Kumar, Madhan, Kumar, K., Kumar, Krishna, Jayaraman, V.K., Kurkarni, B.D. Using Pseudo Amino Acid Composition to Predict Protein Sub nuclear Localization: Approached with PSSM. Pattern Recognition Letters, 2007. 28 1610–1615.
  33. Pakkasjarvi, N., et al. Neural precursor cells from a fatal human motoneuron disease differentiate despite aberrant gene expression. Dev Neurobiol, 2007. 67(3): p. 270-84.
  34. Pelkonen, Olavi, Turpeinen, Miia. In Vitro - In Vivo Extrapolation of Hepatic Clearance: Biological Tools, Scaling Factors, Model Assumptions and Correct Concentrations. Xenobiotica, 2007. 37, 1066-1089.
  35. Petsalo, Aleksanteri, Turpeinen, Miia, Tolonen, Ari. Identification of bupropion urinary metabolites by liquid chromatography-mass spectrometry. Rapid Communications in Mass Spectrometry, 2007. 21, 2547-2554.
  36. Raje, Dhananjay, Krishnan, Venkatesh, Bundela, Saurabh, Rekha Rao, M.S. Identification of closely linked SNP markers using information theory. CAMDA, 2007. (Critical Assessment of Microarray Data Analysis).
  37. Turpeinen, Miia, Ghiciuc, Cristina, Opritoui, Maria, Tursas, Larissa, Pelkonen, Olavi, Pasanen, Markku. Predictive value of animal models for human cytochrome P450 (CYP) mediated metabolism: comparative study in vitro. Xenobiotica, 2007. 37, 1367-1377.
  38. Turpeinen, Miia, Koivuviita, Niina, Tolonen, Ari, Reponen, Petri, Lundgren, Stefan, Miettunen, Jouko, Metsärinne, Kaj, Rane, Anders, Pelkonen, Olavi, Laine, Kari. Effect of kidney disease on the hepatic cytochrome P450 (CYP) 2B6 activity as measured by bupropion pharmacokinetics. British Journal of Clinical Pharmacology, 2007. 64, 165-173.
  39. Tolonen, Ari, Petsalo, Aleksanteri, Turpeinen, Miia, Uusitalo, Jouko, Pelkonen, Olavi. In vitro interaction cocktail assay for nine major cytochrome P450 enzymes with thirteen probe reactions and a single LC/MSMS run; analytical validation and further testing with monoclonal P450 antibodies. Journal of Mass Spectrometry, 2007. 42, 960-966.
  40. Volotinen, Marjo, Turpeinen, Miia, Tolonen, Ari, Uusitalo, Jouko, Mäenpää, Jukka, Pelkonen, Olavi. Timolol metabolism in human liver microsomes is mediated principally by CYP2D6. Drug Metabolism and Disposition, 2007. 35, 1135 - 1141 .
  41. Wick, N., et al. Transcriptomal comparison of human dermal lymphatic endothelial cells ex vivo and in vitro. Physiol Genomics, 2007. 28(2): p. 179-92.
  42. Wikman, H., et al. Gene expression and copy number profiling suggests the importance of allelic imbalance in 19p in asbestos-associated lung cancer. Oncogene, 2007. 26(32): p. 4730-7.
  43. Bjorklund, M., et al. Identification of pathways regulating cell size and cell-cycle progression by RNAi. Nature, 2006. 439(7079): p. 1009-13.
  44. Ek, Sari, Kartimo, Heikki, Mattila, Sampo, Tolonen, Ari. Characterization of phenolic compounds from Lingonberry (Vaccinium vitis-idaea). Journal of Agricultural and Food Chemistry, 2006. 54, 9834-9842.
  45. Härtter, Sebastian, Korhonen, Tuomas, Lundgren, Stefan,  Rane, Anders, Tolonen, Ari, Turpeinen, Miia, Laine, Kari. Effect of caffeine intake 12 or 24 hours prior to melatonin intake and CYP1A2*1F polymorphism on CYP1A2 phenotyping by melatonin. Basic & Clinical Pharmacology & Toxicology, 2006. 99, 300-304.
  46. Korjamo Timo, Mönkkönen Jukka, Uusitalo Jouko, Turpeinen Miia, Pelkonen Olavi, Honkakoski Paavo. Metabolic and efflux properties of Caco-2 cells stably transfected with nuclear receptors. Pharmaceutical Research, 2006. 23,1991-2001.
  47. Leskelä, Hannu-Ville, Olkku, Anu, Lehtonen, Siri, Mahonen, Anitta, Koivunen, Jussi, Turpeinen, Miia, Uusitalo, Jouko, Pelkonen, Olavi, Kangas, Lauri, Selander, Katri, Lehenkari, Petri. Estrogen receptor alpha genotype confers interindividual variability of response to estrogen and testosterone in mesenchymal-stem-cell-derived osteoblasts. Bone, 2006. 39, 1026-1034.
  48. Mononen, N., et al. Profiling genetic variation along the androgen biosynthesis and metabolism pathways implicates several single nucleotide polymorphisms and their combinations as prostate cancer risk factors. Cancer Res, 2006. 66(2): p. 743-7.
  49. Petsalo, Aleksanteri, Jalonen, Jorma, Tolonen, Ari. Identification of flavonoids of Rhodiola rosea by liquid chromatography-tandem mass spectrometry; radical fragment ions and fragment ion intensities as indicators of glycosylation sites. Journal of Chromatography A, 2006. 1112, 224-231.
  50. Pätäri-Sampo, A., Ihalmo, P., Holthöfer, H. Molecular basis of the glomerular filtration: nephrin and the emerging protein complex at the podocyte slit diaphragm. Ann Med., 2006. 38(7):483-92. Review.
  51. Turpeinen, Miia, Korhonen, Laura, Tolonen, Ari, Uusitalo, Jouko, Juvonen, Risto, Raunio, Hannu, Pelkonen, Olavi.  Cytochrome P450 (CYP) inhibition screening: Comparison of three tests. European Journal of Pharmaceutical Sciences, 2006. 29(2) 130-138.
  52. Gangal, R., Sharma, P. Human pol II promoter prediction: time series descriptors and machine learning. Nucleic Acids Res., 2005. Mar 1;33(4):13326.
  53. György, Zsuzsanna, Tolonen, Ari, Neubauer, Peter, Hohtola, Anja. Enhanced biotransformation capacity of Rhodiola rosea callus cultures for glycosid production. Plant Cell, Tissue and Organ Culture, 2005. 83, 129-135.
  54. Korhonen, Tuomas, Tolonen, Ari, Uusitalo, Jouko, Lundgren, Stefan, Jalonen, Jorma, Laine, Kari. The role of CYP2C and CYP3A in the disposition of 3-ketodesogestrel after administration of desogestrel. British Journal of Clinical Pharmacology, 2005. 60, 69-75.
  55. Korjamo T.,  Honkakoski P., Toppinen M.R., Niva S., Reinisalo M., Palmgrén J.J., Mönkkönen J. Absorption properties and P-glycoprotein activity of modified Caco-2 cell lines. Eur J Pharm Sci., 2005. 26, 266-79.
  56. Nikali, K., et al. Infantile onset spinocerebellar ataxia is caused by recessive mutations in mitochondrial proteins Twinkle and Twinky. Hum Mol Genet, 2005. 14(20): p. 2981-90.
  57. Pakkasjarvi, N., et al. Indicative oligodendrocyte dysfunction in spinal cords of human fetuses suffering from a lethal motoneuron disease. J Neurobiol, 2005. 65(3): p. 269-81.
  58. Pelkonen, Olavi, Turpeinen, Miia, Uusitalo, Jouko, Rautio, Arja, Raunio, Hannu. Prediction of drug metabolism and interactions on the basis of in vitro investigations. Basic & Clinical Pharmacology & Toxicology, 2005. 96, 167-175.
  59. Shrivastava, Sudhir (Ed), Gangal R. Informatics in Proteomics, Chapter 10; Datamining in Proteomics, 2005. 208226. CRC Press LLC.
  60. Turpeinen, Miia, Uusitalo, Jouko, Jalonen, Jorma, Pelkonen, Olavi. Multiple P450 substrates in a single run: rapid and comprehensive in vitro interaction assay. European Journal of Pharmaceutical Sciences, 2005. 24(1), 123-132.
  61. Tolonen, Ari, Turpeinen, Miia, Uusitalo, Jouko, Pelkonen, Olavi. A simple method for differentiation of monoisotopic drug metabolites with hydrogen-deuterium exchange LC/MS. European Journal of Pharmaceutical Sciences, 2005. 25, 155-162.
  62. Turpeinen, Miia, Tolonen, Ari, Uusitalo, Jouko, Jalonen, Jorma, Pelkonen, Olavi, Laine, Kari. Effect of clopidrogel and ticlopidine on cytochrome P450 2B6 activity as measured by bupropion hydroxylation. Clinical Pharmacology & Therapeutics, 2005.  77(6), 553-559.
  63. Tolonen, Ari, Lehto, Tiina, Hannuksela, Minna, Savolainen, Markku. A method for determination of phosphatidylethanol from high density lipoproteins by reversed phase HPLC with TOF-MS detection. Analytical Biochemistry, 2005. 341, 83-88.