Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. 1995
  2. Synthesis of chlorinated 5-hydroxy 4-methyl-2(5H)-furanones and mucochloric acid

    Franzén, R. & Kronberg, L., 29 May 1995, In : Tetrahedron Letters. 36, 22, p. 3905-3908 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. 1996
  4. Solution structure of nodularin: An inhibitor of serine/threonine- specific protein phosphatases

    Annila, A., Lehtimäki, J., Mattila, K., Eriksson, J. E., Sivonen, K., Rantala, T. T. & Drakenberg, T., 1996, In : Journal of Biological Chemistry. 271, 28, p. 16695-16702 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. 2000
  6. Utilization of Grignard reagents in solid-phase synthesis: A review of the literature

    Franzén, R. G., 28 Jan 2000, In : Tetrahedron. 56, 5, p. 685-691 7 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  7. Preparation of 5-substituted 2-carboxyindoles on solid support

    Tois, J., Franzén, R., Aitio, O., Huikko, K. & Taskinen, J., 1 Apr 2000, In : Tetrahedron Letters. 41, 14, p. 2443-2446 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  8. 2003
  9. Modeling of anaerobic degradation of solid slaughterhouse waste: Inhibition effects of long-chain fatty acids or ammonia

    Lokshina, L. Y., Vavilin, V. A., Salminen, E. & Rintala, J., Apr 2003, In : Applied Biochemistry and Biotechnology. 109, 1-3, p. 15-32 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. 2007
  11. Responses of methane oxidation to temperature and water content in cover soil of a boreal landfill

    Einola, J. K. M., Kettunen, R. H. & Rintala, J. A., May 2007, In : Soil Biology and Biochemistry. 39, 5, p. 1156-1164 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  12. 2008
  13. Structural information content of networks: Graph entropy based on local vertex functionals

    Dehmer, M. & Emmert-Streib, F., Apr 2008, In : Computational Biology and Chemistry. 32, 2, p. 131-138 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. 2009
  15. Unite and conquer: Univariate and multivariate approaches for finding differentially expressed gene sets

    Glazko, G. V. & Emmert-Streib, F., Sep 2009, In : Bioinformatics. 25, 18, p. 2348-2354 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. 2010
  17. Published

    Surface science analysis and surface modification methods for biomaterials research

    Kanninen, L., Jokinen, N., Lahtonen, K., Jussila, P., Ali-Löytty, H., Hirsimäki, M., Leppiniemi, J., Hytönen, V., Kulomaa, M., Ahola, N., Paakinaho, K., Kellomäki, M. & Valden, M., 1 Jan 2010, In : European Cells and Materials. 20, SUPPL. 3, p. 133 1 p.

    Research output: Contribution to journalArticleScientificpeer-review

  18. Revealing differences in gene network inference algorithms on the network level by ensemble methods

    Altay, G. & Emmert-Streib, F., 25 May 2010, In : Bioinformatics. 26, 14, p. 1738-1744 7 p., btq259.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Efficient production of NV colour centres in nanodiamonds using high-energy electron irradiation

    Dantelle, G., Slablab, A., Rondin, L., Lainé, F., Carrel, F., Bergonzo, P., Perruchas, S., Gacoin, T., Treussart, F. & Roch, J. F., Sep 2010, In : Journal of Luminescence. 130, 9, p. 1655-1658 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  20. 2011
  21. Published

    The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase

    Kaila, V. R. I., Sharma, V. & Wikström, M., Jan 2011, In : Biochimica et Biophysica Acta: Bioenergetics. 1807, 1, p. 80-84 5 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Detection of DNA hybridisation in a diluted serum matrix by surface plasmon resonance and film bulk acoustic resonators

    Auer, S., Nirschl, M., Schreiter, M. & Vikholm-Lundin, I., May 2011, In : Analytical and Bioanalytical Chemistry. 400, 5, p. 1387-1396 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Published

    Trans-interaction of nephrin and Neph1/Neph3 induces cell adhesion that associates with decreased tyrosine phosphorylation of nephrin

    Heikkilä, E., Ristola, M., Havana, M., Jones, N., Holthöfer, H. & Lehtonen, S., 1 May 2011, In : BIOCHEMICAL JOURNAL. 435, 3, p. 619-628 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. Published

    BACOM: In silico detection of genomic deletion types and correction of normal cell contamination in copy number data

    Yu, G., Zhang, B., Bova, G. S., Xu, J., Shih, I. M. & Wang, Y., Jun 2011, In : Bioinformatics. 27, 11, p. 1473-1480 8 p., btr183.

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb3

    Sharma, V., Wikström, M. & Kaila, V. R. I., Jul 2011, In : Biochimica et Biophysica Acta: Bioenergetics. 1807, 7, p. 813-818 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

    Laser-induced primary and secondary hemostasis dynamics and mechanisms in relation to selective photothermolysis of port wine stains

    Heger, M., Salles, I. I., Bezemer, R., Cloos, M. A., Mordon, S. R., Bégu, S., Deckmyn, H. & Beek, J. F., Sep 2011, In : JOURNAL OF DERMATOLOGICAL SCIENCE. 63, 3, p. 139-147 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    Modification of olivomycin A at the side chain of the aglycon yields the derivative with perspective antitumor characteristics

    Tevyashova, A. N., Shtil, A. A., Olsufyeva, E. N., Luzikov, Y. N., Reznikova, M. I., Dezhenkova, L. G., Isakova, E. B., Bukhman, V. M., Durandin, N. A., Vinogradov, A. M., Kuzmin, V. A. & Preobrazhenskaya, M. N., 15 Dec 2011, In : BIOORGANIC AND MEDICINAL CHEMISTRY. 19, 24, p. 7387-7393 7 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  28. Published

    Structural Measures for Network Biology Using QuACN

    Mueller, L. A. J., Kugler, K. G., Graber, A., Emmert-Streib, F. & Dehmer, M., 24 Dec 2011, In : BMC Bioinformatics. 12, 1, 492.

    Research output: Contribution to journalArticleScientificpeer-review

  29. 2012
  30. Published

    Osteogenic medium is superior to growth factors in differentiation of human adipose stem cells towards boneforming cells in 3D culture

    Tirkkonen, L., Haimi, S., Huttunen, S., Wolff, J., Pirhonen, E., Sándor, G. K. & Miettinen, S., 2012, In : European Cells and Materials. 25, p. 144-158 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  31. Published

    Structure-function analysis indicates that sumoylation modulates DNA-binding activity of STAT1

    Grönholm, J., Vanhatupa, S., Ungureanu, D., Väliaho, J., Laitinen, T., Valjakka, J. & Silvennoinen, O., 2012, In : BMC BIOCHEMISTRY. 13, 1, 20.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Lipid hydration and mobility: An interplay between fluorescence solvent relaxation experiments and molecular dynamics simulations

    Jurkiewicz, P., Cwiklik, L., Jungwirth, P. & Hof, M., Jan 2012, In : Biochimie. 94, 1, p. 26-32 7 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  33. Published

    Human adipose tissue extract induces angiogenesis and adipogenesis in vitro

    Sarkanen, J. R., Kaila, V., Mannerström, B., Räty, S., Kuokkanen, H., Miettinen, S. & Ylikomi, T., 1 Jan 2012, In : Tissue Engineering Part A. 18, 1-2, p. 17-25 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    Production of l-xylose from l-xylulose using Escherichia coli l-fucose isomerase

    Usvalampi, A., Turunen, O., Valjakka, J., Pastinen, O., Leisola, M. & Nyyssölä, A., 5 Jan 2012, In : ENZYME AND MICROBIAL TECHNOLOGY. 50, 1, p. 71-76 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Counterion condensation in short cationic peptides: Limiting mobilities beyond the Onsager-Fuoss theory

    Wernersson, E., Heyda, J., Kubíčková, A., Křížek, T., Coufal, P. & Jungwirth, P., Mar 2012, In : ELECTROPHORESIS. 33, 6, p. 981-989 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    Histone H2B ubiquitin ligases RNF20 and RNF40 in androgen signaling and prostate cancer cell growth

    Jääskeläinen, T., Makkonen, H., Visakorpi, T., Kim, J., Roeder, R. G. & Palvimo, J. J., 5 Mar 2012, In : Molecular and Cellular Endocrinology. 350, 1, p. 87-98 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  37. Published

    Neuroprotective effect of RO-20-1724-a phosphodiesterase4 inhibitor against intracerebroventricular streptozotocin induced cognitive deficit and oxidative stress in rats

    Sharma, V., Bala, A., Deshmukh, R., Bedi, K. L. & Sharma, P. L., Apr 2012, In : PHARMACOLOGY BIOCHEMISTRY AND BEHAVIOR. 101, 2, p. 239-245 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  38. Published

    Molecular mechanisms of ion-specific effects on proteins

    Rembert, K. B., Paterová, J., Heyda, J., Hilty, C., Jungwirth, P. & Cremer, P. S., 20 Jun 2012, In : Journal of the American Chemical Society. 134, 24, p. 10039-10046 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

    Endocrine prevention and treatment of prostate cancer

    Tammela, T. L. J., 5 Sep 2012, In : Molecular and Cellular Endocrinology. 360, 1-2, p. 59-67 9 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  40. Published

    Biophysics of lipid bilayers containing oxidatively modified phospholipids: Insights from fluorescence and EPR experiments and from MD simulations

    Jurkiewicz, P., Olzyńska, A., Cwiklik, L., Conte, E., Jungwirth, P., Megli, F. M. & Hof, M., Oct 2012, In : Biochimica et Biophysica Acta: Biomembranes. 1818, 10, p. 2388-2402 15 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  41. Published

    Gene set analysis for self-contained tests: Complex null and specific alternative hypotheses

    Rahmatallah, Y., Emmert-Streib, F. & Glazko, G., Dec 2012, In : Bioinformatics. 28, 23, p. 3073-3080 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  42. 2013
  43. Published

    Hollow fibers of poly(lactide-co-glycolide) and poly(ε-caprolactone) blends for vascular tissue engineering applications

    Diban, N., Haimi, S., Bolhuis-Versteeg, L., Teixeira, S., Miettinen, S., Poot, A., Grijpma, D. & Stamatialis, D., 2013, In : Acta Biomaterialia. 9, 5, p. 6450-6458 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone

    Ylilauri, M., Mattila, E., Nurminen, E. M., Käpylä, J., Niinivehmas, S. P., Määttä, J. A., Pentikäinen, U., Ivaska, J. & Pentikäinen, O. T., 2013, In : Biochimica et biophysica acta: proteins and proteomics. 1834, 10, p. 1988-1997 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  45. Published

    Visualizing functional motions of membrane transporters with molecular dynamics simulations

    Shaikh, S. A., Li, J., Enkavi, G., Wen, P. C., Huang, Z. & Tajkhorshid, E., 29 Jan 2013, In : Biochemistry. 52, 4, p. 569-587 19 p.

    Research output: Contribution to journalArticleScientificpeer-review

  46. Published

    How the amyloid-β peptide and membranes affect each other: An extensive simulation study

    Poojari, C., Kukol, A. & Strodel, B., Feb 2013, In : Biochimica et Biophysica Acta: Biomembranes. 1828, 2, p. 327-339 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    Resonance assignments of the 56 kDa chimeric avidin in the biotin-bound and free forms

    Tossavainen, H., Helppolainen, S. H., Määttä, J. A. E., Pihlajamaa, T., Hytönen, V. P., Kulomaa, M. S. & Permi, P., Apr 2013, In : BIOMOLECULAR NMR ASSIGNMENTS. 7, 1, p. 35-38 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  48. Published

    Non-coding RNAs in DNA damage and repair

    Sharma, V. & Misteli, T., 27 Jun 2013, In : FEBS Letters. 587, 13, p. 1832-1839 8 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  49. Published

    The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins

    Leppiniemi, J., Meir, A., Kahkonen, N., Kukkurainen, S., Maatta, J. A., Ojanen, M., Janis, J., Kulomaa, M. S., Livnah, O. & Hytonen, V. P., Jul 2013, In : PROTEIN SCIENCE. 22, 7, p. 980-994 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  50. Published

    Development and characterization of poly(ε-caprolactone) hollow fiber membranes for vascular tissue engineering

    Diban, N., Haimi, S., Bolhuis-Versteeg, L., Teixeira, S., Miettinen, S., Poot, A., Grijpma, D. & Stamatialis, D., 1 Jul 2013, In : Journal of Membrane Science. 438, p. 29-37 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  51. Published

    Identification, prioritization, and evaluation of glycoproteins for aggressive prostate cancer using quantitative glycoproteomics and antibody-based assays on tissue specimens

    Chen, J., Xi, J., Tian, Y., Bova, G. S. & Zhang, H., Aug 2013, In : Proteomics. 13, 15, p. 2268-2277 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  52. Published

    Mechanisms of acceleration and retardation of water dynamics by ions

    Stirnemann, G., Wernersson, E., Jungwirth, P. & Laage, D., 14 Aug 2013, In : Journal of the American Chemical Society. 135, 32, p. 11824-11831 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  53. Published

    Analysis of free, mono- and diacetylated polyamines from human urine by LC-MS/MS

    Häkkinen, M. R., Roine, A., Auriola, S., Tuokko, A., Veskimäe, E., Keinänen, T. A., Lehtimäki, T., Oksala, N. & Vepsäläinen, J., 15 Dec 2013, In : JOURNAL OF CHROMATOGRAPHY B: ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES. 941, p. 81-89 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  54. 2014
  55. Published

    Electrophoretic mobilities of neutral analytes and electroosmotic flow markers in aqueous solutions of Hofmeister salts

    Křížek, T., Kubíčková, A., Hladílková, J., Coufal, P., Heyda, J. & Jungwirth, P., 2014, In : ELECTROPHORESIS. 35, 5, p. 617-624 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  56. Published

    Functional and genetic analysis of the colon cancer network.

    Emmert-Streib, F., de Matos Simoes, R., Glazko, G., McDade, S., Haibe-Kains, B., Holzinger, A., Dehmer, M. & Campbell, F., 2014, In : BMC Bioinformatics. 15, Suppl 6, S6.

    Research output: Contribution to journalArticleScientificpeer-review

  57. Published

    Kinetics of bioconjugate nanoparticle label binding in a sandwich-type immunoassay

    Näreoja, T., Ebner, A., Gruber, H. J., Taskinen, B., Kienberger, F., Hänninen, P. E., Hytönen, V. P., Hinterdorfer, P. & Härmä, H., 2014, In : Analytical and Bioanalytical Chemistry. 406, 2, p. 493-503 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  58. Published

    Novel derivatives of bacteriochlorophyll a: Complex formation with albumin and the mechanism of tumor cell photodamage

    Akimova, A. V., Grin, M. A., Golovina, G. V., Kokrashvili, T. A., Vinogradov, A. M., Mironov, A. F., Rychkov, G. N., Shtil, A. A., Kuzmin, V. A. & Durandin, N. A., 2014, In : DOKLADY BIOCHEMISTRY AND BIOPHYSICS. 454, 1, p. 17-20 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  59. Published

    Recurrent thyroid cancers have more peritumoural lymphatic vasculature than nonrecurrent thyroid cancers

    Hakala, T., Sand, J., Kellokumpu-Lehtinen, P. L., Huhtala, H., Leinonen, R. & Kholová, I., 2014, In : European Journal of Clinical Investigation. 44, 9, p. 825-832 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  60. Published

    Report from the 2nd Summer School in Computational Biology organized by the Queen's University of Belfast

    Emmert-Streib, F., Zhang, S. D. & Hamilton, P., 2014, In : Genomics Data. 2, p. 37-39 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  61. Published

    Shiga-like toxin binds with high avidity to multivalent O-linked blood group P1 determinants on mucin-type fusion proteins

    Maria Cherian, R., Gaunitz, S., Nilsson, A., Liu, J., Karlsson, N. G. & Holgersson, J., Jan 2014, In : GLYCOBIOLOGY. 24, 1, p. 26-38 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  62. Published

    Natural thermal adaptation increases heat shock protein levels and decreases oxidative stress

    Oksala, N. K. J., Ekmekçi, F. G., Özsoy, E., Kirankaya, Ş., Kokkola, T., Emecen, G., Lappalainen, J., Kaarniranta, K. & Atalay, M., 1 Jan 2014, In : REDOX BIOLOGY. 3, p. 25-28 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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

  75. 2015
  76. 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

  77. 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

  78. 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

  79. 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

  80. 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

  81. 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

  82. 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

  83. 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

  84. 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

  85. 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

  86. 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

  87. 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

  88. 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

  89. 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

  90. 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

  91. 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

  92. 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

  93. 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

  94. 2016
  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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

  109. 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

  110. 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

  111. 2017
  112. 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

  113. 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

  114. 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

  115. 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

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