Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. 2014
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 2013
  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 2012
  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 2011
  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 2010
  43. 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

  44. 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

  45. 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

  46. 2009
  47. 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

  48. 2008
  49. 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

  50. 2007
  51. 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

  52. 2003
  53. 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

  54. 2000
  55. 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

  56. 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

  57. 1996
  58. 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

  59. 1995
  60. 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

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