Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. Published

    Non-intersecting leaf insertion algorithm for tree structure models

    Åkerblom, M., Raumonen, P., Casella, E., Disney, M. I., Danson, F. M., Gaulton, R., Schofield, L. A. & Kaasalainen, M., 6 Apr 2018, In : Interface Focus. 8, 2, 20170045.

    Research output: Contribution to journalArticleScientificpeer-review

  2. 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

  3. 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

  4. Published

    Methods for simultaneous robot-world-hand–eye calibration: A comparative study

    Ali, I., Suominen, O., Gotchev, A. & Morales, E. R., 2 Jun 2019, In : Sensors (Switzerland). 19, 12, 2837.

    Research output: Contribution to journalArticleScientificpeer-review

  5. 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

  6. 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

  7. 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

  8. 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

  9. Published

    Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition

    Bilkova, E., Pleskot, R., Rissanen, S., Sun, S., Czogalla, A., Cwiklik, L., Róg, T., Vattulainen, I., Cremer, P. S., Jungwirth, P. & Coskun, Ü., 22 Mar 2017, In : Journal of the American Chemical Society. 139, 11, p. 4019-4024 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    Alzheimer's disease and alpha-synuclein pathology in the olfactory bulbs of infants, children, teens and adults ≤ 40 years in Metropolitan Mexico City. APOE4 carriers at higher risk of suicide accelerate their olfactory bulb pathology

    Calderón-Garcidueñas, L., González-Maciel, A., Reynoso-Robles, R., Kulesza, R. J., Mukherjee, P. S., Torres-Jardón, R., Rönkkö, T. & Doty, R. L., 1 Oct 2018, In : Environmental Research. 166, p. 348-362 15 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

    Molecular-Scale Ligand Effects in Small Gold-Thiolate Nanoclusters

    Chevrier, D. M., Raich, L., Rovira, C., Das, A., Luo, Z., Yao, Q., Chatt, A., Xie, J., Jin, R., Akola, J. & Zhang, P., 14 Nov 2018, In : Journal of the American Chemical Society. 140, 45, p. 15430-15436 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. Published

    Weighing trees with lasers: Advances, challenges and opportunities

    Disney, M. I., Boni Vicari, M., Burt, A., Calders, K., Lewis, S. L., Raumonen, P. & Wilkes, P., 6 Apr 2018, In : Interface Focus. 8, 2, 20170048.

    Research output: Contribution to journalArticleScientificpeer-review

  19. 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

  20. 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

  21. 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

  22. Published

    Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis

    Euro, L., Haapanen, O., Róg, T., Vattulainen, I., Suomalainen, A. & Sharma, V., 7 Mar 2017, In : Biochemistry. 56, 9, p. 1227-1238 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Published

    Azopolymer photopatterning for directional control of angiogenesis

    Fedele, C., De Gregorio, M., Netti, P. A., Cavalli, S. & Attanasio, C., 1 Nov 2017, In : Acta Biomaterialia. 63, p. 317-325 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. Published

    Comparison of different coating techniques on the properties of FucoPol films

    Ferreira, A. R. V., Haapanen, J., Mäkelä, J. M., Bratvold, J. E., Nilsen, O., Tuominen, M., Alves, V. D. & Coelhoso, I. M., 1 Oct 2017, In : International Journal of Biological Macromolecules. 103, p. 268-274 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. 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

  26. 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

  27. Published

    Photo-antimicrobial efficacy of zinc complexes of porphyrin and phthalocyanine activated by inexpensive consumer LED lamp

    George, L., Hiltunen, A., Santala, V. & Efimov, A., 1 Jun 2018, In : Journal of Inorganic Biochemistry. 183, p. 94-100 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. 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

  29. 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

  30. 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

  31. Published

    Connection of Collimation, Asymmetric Beaming, and Independent Transmission-Reflection Processes in Concentric-Groove Gratings Supporting Spoof Surface Plasmons

    Habib, M., Serebryannikov, A. E., Caglayan, H., Vandenbosch, G. A. E. & Ozbay, E., Jun 2019, In : Plasmonics. 14, 3, p. 721-729 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  32. 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

  33. Published

    Molecular mechanism for inhibition of twinfilin by phosphoinositides

    Hakala, M., Kalimeri, M., Enkavi, G., Vattulainen, I. & Lappalainen, P., 1 Jan 2018, In : Journal of Biological Chemistry. 293, 13, p. 4818-4829 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. Published

    Hexaphyrin as a Potential Theranostic Dye for Photothermal Therapy and 19F Magnetic Resonance Imaging

    Higashino, T., Nakatsuji, H., Fukuda, R., Okamoto, H., Imai, H., Matsuda, T., Tochio, H., Shirakawa, M., Tkachenko, N. V., Hashida, M., Murakami, T. & Imahori, H., 24 Mar 2017, In : ChemBioChem. 18, 10, p. 951-959 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  40. 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

  41. Published

    An architectural understanding of natural sway frequencies in trees

    Jackson, T., Shenkin, A., Moore, J., Bunce, A., van Emmerik, T., Kane, B., Burcham, D., James, K., Selker, J., Calders, K., Origo, N., Disney, M., Burt, A., Wilkes, P., Raumonen, P., Gonzalez de Tanago Menaca, J., Lau, A., Herold, M., Goodman, R. C., Fourcaud, T. & Malhi, Y., 28 Jun 2019, In : Journal of the Royal Society. Interface. 16, 155, 1 p.

    Research output: Contribution to journalArticleScientificpeer-review

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. Published

    Uncertainty in multispectral lidar signals caused by incidence angle effects

    Kaasalainen, S., Åkerblom, M., Nevalainen, O., Hakala, T. & Kaasalainen, M., 6 Apr 2018, In : Interface Focus. 8, 2, 20170033.

    Research output: Contribution to journalArticleScientificpeer-review

  48. Tunable Plasmonic Silver Nanodomes for Surface-Enhanced Raman Scattering

    Kahraman, M., Ozbay, A., Yuksel, H., Solmaz, R., Demir, B. & Caglayan, H., 5 Apr 2017, (Accepted/In press) In : Plasmonics. p. 1-11 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  49. 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

  50. 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

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