Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. Article › Scientific › Peer-reviewed
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Published

    Gloriosa superba Mediated Synthesis of Platinum and Palladium Nanoparticles for Induction of Apoptosis in Breast Cancer

    Rokade, S. S., Joshi, K. A., Mahajan, K., Patil, S., Tomar, G., Dubal, D. S., Parihar, V. S., Kitture, R., Bellare, J. R. & Ghosh, S., 2018, In : Bioinorganic Chemistry and Applications. 2018, 4924186.

    Research output: Contribution to journalArticleScientificpeer-review

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. Published

    Improved water services cooperation through clarification of rules and roles

    Inha, L. M., Katko, T. S. & Rajala, R. P., 19 Oct 2019, In : Water (Switzerland). 11, 10, 2172.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Influence of ions to modulate hydrazone and oxime reaction kinetics to obtain dynamically cross-linked hyaluronic acid hydrogels

    Wang, S., Nawale, G. N., Oommen, O. P., Hilborn, J. & Varghese, O. P., 21 Aug 2019, In : Polymer Chemistry. 10, 31, p. 4322-4327 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Inhibition of Aβ Amyloid Growth and Toxicity by Silybins: The Crucial Role of Stereochemistry

    Sciacca, M. F. M., Romanucci, V., Zarrelli, A., Monaco, I., Lolicato, F., Spinella, N., Galati, C., Grasso, G., D'Urso, L., Romeo, M., Diomede, L., Salmona, M., Bongiorno, C., Di Fabio, G., La Rosa, C. & Milardi, D., 16 Aug 2017, In : ACS Chemical Neuroscience. 8, 8, p. 1767-1778 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. 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

  24. 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

  25. 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

  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

    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

  28. 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

  29. Published

    M2M Communication Assessment in Energy-Harvesting and Wake-Up Radio Assisted Scenarios Using Practical Components

    Rinne, J., Keskinen, J., Berger, P. R., Lupo, D. & Valkama, M., 16 Nov 2018, In : Sensors (Basel, Switzerland). 18, 11

    Research output: Contribution to journalArticleScientificpeer-review

  30. 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

  31. 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

  32. 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

  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

    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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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