Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. 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

  2. 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

  3. 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

  4. Published

    Comparative analysis of tissue reconstruction algorithms for 3D histology

    Kartasalo, K., Latonen, L., Vihinen, J., Visakorpi, T., Nykter, M. & Ruusuvuori, P., 1 Sep 2018, In : Bioinformatics. 34, 17, p. 3013-3021 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Published

    Soft hydrazone crosslinked hyaluronan- and alginate-based hydrogels as 3D supportive matrices for human pluripotent stem cell-derived neuronal cells

    Karvinen, J., Joki, T., Ylä-Outinen, L., Koivisto, J. T., Narkilahti, S. & Kellomäki, M., 1 Mar 2018, In : Reactive and Functional Polymers. 124, p. 29-39 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  6. 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

  7. Published

    Bioimpedance Sensor Array for Long-Term Monitoring of Wound Healing from Beneath the Primary Dressings and Controlled Formation of H2O2 Using Low-Intensity Direct Current

    Kekonen, A., Bergelin, M., Johansson, M., Kumar Joon, N., Bobacka, J. & Viik, J., 31 May 2019, In : Sensors. 19, 11

    Research output: Contribution to journalArticleScientificpeer-review

  8. 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

  9. Published

    Alpha radiation-induced luminescence by am-241 in aqueous nitric acid solution

    Kerst, T., Malmbeck, R., lal Banik, N. L. & Toivonen, J., 1 Apr 2019, In : Sensors (Switzerland). 19, 7, 1602.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    Effect of N/S ratio on anoxic thiosulfate oxidation in a fluidized bed reactor: Experimental and artificial neural network model analysis

    Khanongnuch, R., Di Capua, F., Lakaniemi, A-M., Rene, E. R. & Lens, P. N. L., 2018, In : Process Biochemistry. 68, p. 171-181

    Research output: Contribution to journalArticleScientificpeer-review

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  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. 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

  18. 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

  19. 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

  20. 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

  21. Published

    An efficient auxin-inducible degron system with low basal degradation in human cells

    Li, S., Prasanna, X., Salo, V. T., Vattulainen, I. & Ikonen, E., 1 Sep 2019, In : Nature Methods. 16, 9, p. 866-869 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks

    Liimatainen, K., Kananen, L., Latonen, L. & Ruusuvuori, P., 15 Feb 2019, In : BMC Bioinformatics. 20, 1, 80.

    Research output: Contribution to journalArticleScientificpeer-review

  23. 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

  24. Published

    Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation

    Manna, M., Javanainen, M., Martinez-Seara Monne, H., Gabius, H-J., Rog, T. & Vattulainen, I., 1 May 2017, In : Biochimica et Biophysica Acta: Biomembranes. 1859, 5, p. 870-878 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes

    Manna, M., Nieminen, T. & Vattulainen, I., 6 May 2019, In : ANNUAL REVIEW OF BIOPHYSICS. 48, p. 421-439 19 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  26. 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

  27. Published

    SCIP: a single-cell image processor toolbox

    Martins, L., Neeli-Venkata, R., Oliveira, S. M. D., Häkkinen, A., Ribeiro, A. S. & Fonseca, J. M., 15 Dec 2018, In : Bioinformatics. 34, 24, p. 4318-4320 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    An activity recognition framework deploying the random forest classifier and a single optical heart rate monitoring and triaxial accelerometer wrist-band

    Mehrang, S., Pietilä, J. & Korhonen, I., 22 Feb 2018, In : Sensors. 18, 2, 613.

    Research output: Contribution to journalArticleScientificpeer-review

  29. 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

  30. 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

  31. Published

    Hierarchical Self-Assembly of Halogen-Bonded Block Copolymer Complexes into Upright Cylindrical Domains

    Milani, R., Houbenov, N., Fernandez-Palacio, F., Cavallo, G., Luzio, A., Haataja, J., Giancane, G., Saccone, M., Priimägi, A., Metrangolo, P. & Ikkala, O., 9 Mar 2017, In : CheM. 2, 3, p. 417-426 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative

    Mobarak, E., Javanainen, M., Kulig, W., Honigmann, A., Sezgin, E., Aho, N., Eggeling, C., Rog, T. & Vattulainen, I., Nov 2018, In : Biochimica et Biophysica Acta - Biomembranes. 1860, 11, p. 2436-2445

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles

    Mokkila, S., Postila, P. A., Rissanen, S., Juhola, H., Vattulainen, I. & Róg, T., 21 Jun 2017, In : ACS Chemical Neuroscience. 8, 6, p. 1242-1250 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  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

    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

  36. 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

  37. Published

    Dynamics of a True Moving Bed separation process: Linear model identification and advanced process control

    Nogueira, I. B. R., Ribeiro, A. M., Martins, M. A. F., Rodrigues, A. E., Koivisto, H. & Loureiro, J. M., 30 Jun 2017, In : Journal of Chromatography A. 1504

    Research output: Contribution to journalArticleScientificpeer-review

  38. 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

  39. Published

    Bioactive glass induced osteogenic differentiation of human adipose stem cells is dependent on cell attachment mechanism and mitogen-activated protein kinases

    Ojansivu, M., Wang, X., Hyväri, L., Kellomäki, M., Hupa, L., Vanhatupa, S. & Miettinen, S., 2018, In : European Cells and Materials. 35, p. 53-71 19 p.

    Research output: Contribution to journalArticleScientificpeer-review

  40. 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

  41. 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

  42. Published

    Positioning information privacy in intelligent transportation systems: An overview and future perspective

    Ometov, A., Bezzateev, S., Davydov, V., Shchesniak, A., Masek, P., Lohan, E. S. & Koucheryavy, Y., 1 Apr 2019, In : Sensors. 19, 7, 1603.

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    Physiologically-relevant levels of sphingomyelin, but not GM1, induces a β-sheet-rich structure in the amyloid-β(1-42) monomer

    Owen, M. C., Kulig, W., Poojari, C., Rog, T. & Strodel, B., Sep 2018, In : Biochimica et Biophysica Acta - Biomembranes. 1860, 9, p. 1709-1720

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    Acquiring respiration rate from photoplethysmographic signal by recursive bayesian tracking of intrinsic modes in time-frequency spectra

    Pirhonen, M., Peltokangas, M. & Vehkaoja, A., 1 Jun 2018, In : Sensors. 18, 6, 1693.

    Research output: Contribution to journalArticleScientificpeer-review

  45. Published

    Characterisation and in vitro and in vivo evaluation of supercritical-CO2-foamed β-TCP/PLCL composites for bone applications

    Pitkänen, S., Paakinaho, K., Pihlman, H., Ahola, N., Hannula, M., Asikainen, S., Manninen, M., Morelius, M., Keränen, P., Hyttinen, J., Kellomäki, M., Laitinen-Vapaavuori, O. & Miettinen, S., 5 Aug 2019, In : European cells & materials. 38, p. 35-50 16 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

    Behavior of the DPH fluorescence probe in membranes perturbed by drugs

    Poojari, C., Wilkosz, N., Lira, R. B., Dimova, R., Jurkiewicz, P., Petka, R., Kepczynski, M. & Róg, T., 1 Sep 2019, In : Chemistry and Physics of Lipids. 223, 104784.

    Research output: Contribution to journalArticleScientificpeer-review

  48. 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

  49. 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

  50. 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