Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. 2014
  2. Published

    Antioxidant supplementation reduces genomic aberrations in human induced pluripotent stem cells

    Ji, J., Sharma, V., Qi, S., Guarch, M. E., Zhao, P., Luo, Z., Fan, W., Wang, Y., Mbabaali, F., Neculai, D., Esteban, M. A., McPherson, J. D. & Batada, N. N., 14 Jan 2014, In : Stem Cell Reports. 2, 1, p. 44-51 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    Gene Sets Net Correlations Analysis (GSNCA): A multivariate differential coexpression test for gene sets

    Rahmatallah, Y., Emmert-Streib, F. & Glazko, G., 1 Feb 2014, In : Bioinformatics. 30, 3, p. 360-368 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Published

    Structure and barrier properties of human embryonic stem cell-derived retinal pigment epithelial cells are affected by extracellular matrix protein coating

    Sorkio, A., Hongisto, H., Kaarniranta, K., Uusitalo, H., Juuti-Uusitalo, K. & Skottman, H., 1 Feb 2014, In : Tissue Engineering Part A. 20, 3-4, p. 622-634 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Published

    Small-molecule induction promotes corneal epithelial cell differentiation from human induced pluripotent stem cells

    Mikhailova, A., Ilmarinen, T., Uusitalo, H. & Skottman, H., 11 Feb 2014, In : Stem Cell Reports. 2, 2, p. 219-231 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  6. Published

    NetBioV: An R package for visualizing large network data in biology and medicine

    Tripathi, S., Dehmer, M. & Emmert-Streib, F., 2 Apr 2014, In : Bioinformatics. 30, 19, p. 2834-2836 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  7. Published

    AROS has a context-dependent effect on SIRT1

    Kokkola, T., Suuronen, T., Molnár, F., Määttä, J., Salminen, A., Jarho, E. M. & Lahtela-Kakkonen, M., 2 May 2014, In : FEBS Letters. 588, 9, p. 1523-1528 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  8. Published

    Light-fuelled transport of large dendrimers and proteins

    Koskela, J. E., Liljeström, V., Lim, J., Simanek, E. E., Ras, R. H. A., Priimagi, A. & Kostiainen, M. A., 14 May 2014, In : Journal of the American Chemical Society. 136, 19, p. 6850-6853 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Published

    Blood microRNA profile associates with the levels of serum lipids and metabolites associated with glucose metabolism and insulin resistance and pinpoints pathways underlying metabolic syndrome. The cardiovascular risk in Young Finns Study.

    Raitoharju, E., Seppälä, I., Oksala, N., Lyytikäinen, L. P., Raitakari, O., Viikari, J., Ala-Korpela, M., Soininen, P., Kangas, A. J., Waldenberger, M., Klopp, N., Illig, T., Leiviskä, J., Loo, B. M., Hutri-Kähönen, N., Kähönen, M., Laaksonen, R. & Lehtimäki, T., 25 Jun 2014, In : Molecular and Cellular Endocrinology. 391, 1-2, p. 41-49 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    Calcium transients closely reflect prolonged action potentials in iPSC models of inherited cardiac arrhythmia

    Spencer, C. I., Baba, S., Nakamura, K., Hua, E. A., Sears, M. A. F., Fu, C. C., Zhang, J., Balijepalli, S., Tomoda, K., Hayashi, Y., Lizarraga, P., Wojciak, J., Scheinman, M. M., Aalto-Setälä, K., Makielski, J. C., January, C. T., Healy, K. E., Kamp, T. J., Yamanaka, S. & Conklin, B. R., 12 Aug 2014, In : Stem Cell Reports. 3, 2, p. 269-281 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

    Global analysis of human nonreceptor tyrosine kinase specificity using high-density peptide microarrays

    Deng, Y., Alicea-Velázquez, N. L., Bannwarth, L., Lehtonen, S. I., Boggon, T. J., Cheng, H. C., Hytönen, V. P. & Turk, B. E., 3 Oct 2014, In : Journal of Proteome Research. 13, 10, p. 4339-4346 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  12. Published

    Connection between absorption properties and conformational changes in Deinococcus radiodurans phytochrome

    Takala, H., Lehtivuori, H., Hammarén, H., Hytönen, V. P. & Ihalainen, J. A., 18 Nov 2014, In : Biochemistry. 53, 45, p. 7076-7085 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

    Comparative evaluation of gene set analysis approaches for RNA-Seq data

    Rahmatallah, Y., Emmert-Streib, F. & Glazko, G., 5 Dec 2014, In : BMC Bioinformatics. 15, 1, 397.

    Research output: Contribution to journalArticleScientificpeer-review

  14. 2015
  15. Published

    Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning

    Lehtonen, S. I., Taskinen, B., Ojala, E., Kukkurainen, S., Rahikainen, R., Riihimäki, T. A., Laitinen, O. H., Kulomaa, M. S. & Hytönen, V. P., 2015, In : Protein Engineering Design and Selection. 28, 1, p. 23-28 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. Published

    Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate

    Kulig, W., Jurkiewicz, P., Olzyńska, A., Tynkkynen, J., Javanainen, M., Manna, M., Rog, T., Hof, M., Vattulainen, I. & Jungwirth, P., 2015, In : Biochimica et Biophysica Acta: Biomembranes. 1848, 2, p. 422-432 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  17. Interaction with serum albumin as a factor of the photodynamic efficacy of novel bacteriopurpurinimide derivatives

    Akimova, A. V., Rychkov, G. N., Grin, M. A., Filippova, N. A., Golovina, G. V., Durandin, N. A., Vinogradov, A. M., Kokrashvili, T. A., Mironov, A. F., Shtil, A. A. & Kuzmin, V. A., 2015, In : ACTA NATURAE. 7, 1, p. 109-116 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  18. Published

    Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data

    Häkkinen, A. & Ribeiro, A. S., 1 Jan 2015, In : Bioinformatics. 31, 1, p. 69-75 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Published

    Oxidation half-reaction of aqueous nucleosides and nucleotides via photoelectron spectroscopy augmented by ab initio calculations

    Schroeder, C. A., Pluharová, E., Seidel, R., Schroeder, W. P., Faubel, M., Slavíçek, P., Winter, B., Jungwirth, P. & Bradforth, S. E., 14 Jan 2015, In : Journal of the American Chemical Society. 137, 1, p. 201-209 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    Multi-stable dynamics of the non-adiabatic repressilator

    Potapov, I., Zhurov, B. & Volkov, E., 6 Mar 2015, In : Journal of the Royal Society. Interface. 12, 104, 20141315.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase

    Sharma, V., Ala-Vannesluoma, P., Vattulainen, I., Wikström, M. & Róg, T., 17 Apr 2015, In : Biochimica et Biophysica Acta: Bioenergetics. 1847, 8, p. 690-697 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Apolipoprotein A-I mimetic peptide 4F blocks sphingomyelinase-induced LDL aggregation

    Nguyen, S. D., Javanainen, M., Rissanen, S., Zhao, H., Huusko, J., Kivelä, A. M., Ylä-Herttuala, S., Navab, M., Fogelman, A. M., Vattulainen, I., Kovanen, P. T. & Öörni, K., 1 Jun 2015, In : Journal of Lipid Research. 56, 6, p. 1206-1221 16 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Published

    Using shRNA experiments to validate gene regulatory networks

    Olsen, C., Fleming, K., Prendergast, N., Rubio, R., Emmert-Streib, F., Bontempi, G., Quackenbush, J. & Haibe-Kains, B., 1 Jun 2015, In : Genomics Data. 4, p. 123-126 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. Published

    A robust AMMI model for the analysis of genotype-by-environment data

    Rodrigues, P. C., Monteiro, A. & Lourenço, V. M., 1 Jul 2015, In : Bioinformatics. 32, 1, p. 58-66 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    Cholesterol under oxidative stress: How lipid membranes sense oxidation as cholesterol is being replaced by oxysterols

    Kulig, W., Olzyńska, A., Jurkiewicz, P., Kantola, A. M., Komulainen, S., Manna, M., Pourmousa, M., Vazdar, M., Cwiklik, L., Rog, T., Khelashvili, G., Harries, D., Telkki, V. V., Hof, M., Vattulainen, I. & Jungwirth, P., 1 Jul 2015, In : Free Radical Biology and Medicine. 84, p. 30-41 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

    Bioactive glass ions as strong enhancers of osteogenic differentiation in human adipose stem cells

    Ojansivu, M., Vanhatupa, S., Björkvik, L., Häkkänen, H., Kellomäki, M., Autio, R., Ihalainen, J. A., Hupa, L. & Miettinen, S., 15 Jul 2015, In : Acta Biomaterialia. 21, p. 190-203 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    Surface Modified Biodegradable Electrospun Membranes as a Carrier for Human Embryonic Stem Cell-Derived Retinal Pigment Epithelial Cells

    Sorkio, A., Porter, P. J., Juuti-Uusitalo, K., Meenan, B. J., Skottman, H. & Burke, G. A., 1 Sep 2015, In : Tissue Engineering Part A. 21, 17-18, p. 2301-2314 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    Cancer incidence and mortality in patients treated either with RAI or thyroidectomy for hyperthyroidism

    Ryödi, E., Metso, S., Jaatinen, P., Huhtala, H., Saaristo, R., Välimäki, M. & Auvinen, A., 1 Oct 2015, In : Journal of Clinical Endocrinology and Metabolism. 100, 10, p. 3710-3717 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  29. Published

    Submolecular Plasticization Induced by Photons in Azobenzene Materials

    Vapaavuori, J., Laventure, A., Bazuin, C. G., Lebel, O. & Pellerin, C., 28 Oct 2015, In : Journal of the American Chemical Society. 137, 42, p. 13510-13517 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  30. Published

    A BRCA1-interacting lncRNA regulates homologous recombination

    Sharma, V., Khurana, S., Kubben, N., Abdelmohsen, K., Oberdoerffer, P., Gorospe, M. & Misteli, T., 1 Nov 2015, In : EMBO REPORTS. 16, 11, p. 1520-1534 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  31. Published

    Gene expression analysis upon lncRNA DDSR1 knockdown in human fibroblasts

    Jia, L., Sun, Z., Wu, X., Misteli, T. & Sharma, V., 1 Dec 2015, In : Genomics Data. 6, p. 277-279 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Tuning the Plasmonic Extinction Resonances of Hexagonal Arrays of Ag Nanoparticles

    Ravi, A., Luthra, A., Teixeira, F. L., Berger, P. R. & Coe, J. V., 1 Dec 2015, In : Plasmonics. 10, 6, p. 1505-1512 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  33. 2016
  34. Published

    Cholesterol oxidation products and their biological importance

    Kulig, W., Cwiklik, L., Jurkiewicz, P., Rog, T. & Vattulainen, I., 2016, In : Chemistry and Physics of Lipids. 199, p. 144-160 17 p.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Morphological Differentiation Towards Neuronal Phenotype of SH-SY5Y Neuroblastoma Cells by Estradiol, Retinoic Acid and Cholesterol

    Teppola, H., Sarkanen, J. R., Jalonen, T. O. & Linne, M-L., 2016, In : Neurochemical Research. 41, 4, p. 731-747

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    Non-Brownian diffusion in lipid membranes: Experiments and simulations

    Metzler, R., Jeon, J. H. & Cherstvy, A. G., 2016, In : Biochimica et Biophysica Acta: Biomembranes. 215, p. 173–185

    Research output: Contribution to journalReview ArticleScientificpeer-review

  37. Published

    Role of charged lipids in membrane structures: Insight given by simulations

    Pöyry, S. & Vattulainen, I., 2016, In : Biochimica et Biophysica Acta: Biomembranes. p. 2322–2333 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations

    Rog, T. & Koivuniemi, A., 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 1, p. 97-103 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

    Human Adipose Stem Cells Differentiated on Braided Polylactide Scaffolds is a Potential Approach for Tendon Tissue Engineering

    Vuornos, K., Björninen, M., Talvitie, E., Paakinaho, K., Kellomäki, M., Huhtala, H., Miettinen, S., Seppänen-Kaijansinkko, R. & Haimi, S., 1 Mar 2016, In : Tissue Engineering Part A. 22, 5-6, p. 513-523 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  40. Published

    Characterizing rate limiting steps in transcription from RNA production times in live cells

    Häkkinen, A. & Ribeiro, A. S., 1 May 2016, In : Bioinformatics. 32, 9, p. 1346-1352 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  41. Published

    Robust statistical approaches for RSS-based floor detection in indoor localization

    Razavi, A., Valkama, M. & Lohan, E. S., 1 Jun 2016, In : Sensors. 16, 6, 793.

    Research output: Contribution to journalArticleScientificpeer-review

  42. Published

    The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase

    Sharma, V. & Wikström, M., Aug 2016, In : Biochimica et Biophysica Acta: Bioenergetics. 1857, 8, p. 1111-1115

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria

    Kaurola, P., Sharma, V., Vonk, A., Vattulainen, I. & Róg, T., 1 Sep 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 9, p. 2116-2122 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    Efficient preparation and analysis of membrane and membrane protein systems

    Javanainen, M. & Martinez-Seara, H., Oct 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 10, p. 2468-2482

    Research output: Contribution to journalArticleScientificpeer-review

  45. Published

    Functionalized lipids and surfactants for specific applications

    Kepczynski, M. & Róg, T., Oct 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 10, p. 2362-2379

    Research output: Contribution to journalArticleScientificpeer-review

  46. Published

    Effects of σ factor competition are promoter initiation kinetics dependent

    Kandavalli, V. K., Tran, H. & Ribeiro, A. S., 1 Oct 2016, In : Biochimica et Biophysica Acta: Gene Regulatory Mechanisms. 1859, 10, p. 1281-1288 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1

    Kuleta, P., Sarewicz, M., Postila, P., Róg, T. & Osyczka, A., 1 Oct 2016, In : Biochimica et Biophysica Acta: Bioenergetics. 1857, 10, p. 1661-1668 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  48. Published

    Lipid membranes: Theory and simulations bridged to experiments

    Vattulainen, I. & Róg, T., 1 Oct 2016, In : Biochimica et Biophysica Acta: Biomembranes. 1858, 10, p. 2251-2253 3 p.

    Research output: Contribution to journalEditorialScientificpeer-review

  49. Published

    SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files

    Stupnikov, A., Tripathi, S., De Matos Simoes, R., McArt, D., Salto-Tellez, M., Glazko, G., Dehmer, M. & Emmert-Streib, F., 1 Nov 2016, In : Bioinformatics. 32, 21, p. 3345-3347 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  50. 2017
  51. Published

    Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle

    Grabon, A., Orłowski, A., Tripathi, A., Vuorio, J., Javanainen, M., Róg, T., Lönnfors, M., McDermott, M. I., Siebert, G., Somerharju, P., Vattulainen, I. & Bankaitis, V. A., 2017, In : Journal of Biological Chemistry. 292, 35, p. 14438-14455 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  52. Published

    Synthesis, Structural Characterization, Hirshfeld Surface and Antioxidant Activity Analysis of a Novel Organic Cation Antimonate Complex

    Lahbib, I., Valkonen, A., Rzaigui, M. & Smirani, W., 2017, In : Journal of Cluster Science. 28, 4, p. 2239–2252 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  53. Published

    GSAR: Bioconductor package for Gene Set analysis in R

    Rahmatallah, Y., Zybailov, B., Emmert-Streib, F. & Glazko, G., 24 Jan 2017, In : BMC Bioinformatics. 18, 1, 61.

    Research output: Contribution to journalArticleScientificpeer-review

  54. Published

    Polarization resolved photoluminescence in GaAs1−xBix/GaAs quantum wells

    Balanta, M. A. G., Orsi Gordo, V., Carvalho, A. R. H., Puustinen, J., Alghamdi, H. M., Henini, M., Galeti, H. V. A., Guina, M. & Galvão Gobato, Y., Feb 2017, In : Journal of Luminescence. 182, p. 49-52 4 p.

    Research output: Contribution to journalArticleScientificpeer-review