Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. 2020
  2. Published

    Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup

    Palma, C. S. D., Kandavalli, V., Bahrudeen, M. N. M., Minoia, M., Chauhan, V., Dash, S. & Ribeiro, A. S., 2020, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1863, 5, 13 p., 194515.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Published

    High-content imaging and structure-based predictions reveal functional differences between Niemann-Pick C1 variants

    Vanharanta, L., Peränen, J., Pfisterer, S. G., Enkavi, G., Vattulainen, I. & Ikonen, E., 2020, In : Traffic. 21, 5, p. 386-397 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Published

    Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex

    Liekkinen, J., Enkavi, G., Javanainen, M., Olmeda, B., Pérez-Gil, J. & Vattulainen, I., 2020, In : JOURNAL OF MOLECULAR BIOLOGY. 432, 10, p. 3251-3268 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. 2019
  6. Published

    Sodium channels enable fast electrical signaling and regulate phagocytosis in the retinal pigment epithelium

    Johansson, J. K., Karema-Jokinen, V. I., Hakanen, S., Jylhä, A., Uusitalo, H., Vihinen-Ranta, M., Skottman, H., Ihalainen, T. O. & Nymark, S., 15 Aug 2019, In : BMC BIOLOGY. 17, 1, 63.

    Research output: Contribution to journalArticleScientificpeer-review

  7. 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

  8. 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

  9. Published

    Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression

    Startceva, S., Kandavalli, V. K., Visa, A. & Ribeiro, A. S., 1 Feb 2019, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1862, 2, p. 119-128 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. 2018
  11. Published

    Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins

    Laulumaa, S., Nieminen, T., Raasakka, A., Krokengen, O. C., Safaryan, A., Hallin, E. I., Brysbaert, G., Lensink, M. F., Ruskamo, S., Vattulainen, I. & Kursula, P., 25 Jun 2018, In : BMC Structural Biology. 18, 1, 8.

    Research output: Contribution to journalArticleScientificpeer-review

  12. Published

    The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures

    Neeli-Venkata, R., Oliveira, S. M. D., Martins, L., Startceva, S., Bahrudeen, M., Fonseca, J. M., Minoia, M. & Ribeiro, A. S., 18 May 2018, In : Physical Biology. 15, 5, 056002.

    Research output: Contribution to journalArticleScientificpeer-review

  13. 2017
  14. 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

  15. Published

    sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

    Tripathi, S., Lloyd-Price, J., Ribeiro, A., Yli-Harja, O., Dehmer, M. & Emmert-Streib, F., 4 Jul 2017, In : BMC Bioinformatics. 18, 1, 325.

    Research output: Contribution to journalArticleScientificpeer-review

  16. 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

  17. 2016
  18. 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

  19. 2015
  20. Published

    Biogenesis of Nascent High Density Lipoprotein Particles

    Koivuniemi, A. & Vattulainen, I., 9 Jul 2015, In : Structure. 23, 7, p. 1153-1154 2 p., 3212.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

    Matos Simoes, R. D., Dalleau, S., Williamson, K. E. & Emmert-Streib, F., 14 May 2015, In : BMC Systems Biology. 9, 21.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction

    Moriya, T., Acar, E., Cheng, R. H. & Ruotsalainen, U., 3 Apr 2015, In : Journal of Structural Biology. 191, 3, p. 318–331 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. 2014
  24. 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

  25. 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

  26. Published

    Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy

    Rangl, M., Leitner, M., Riihimäki, T., Lehtonen, S., Hytönen, V. P., Gruber, H. J., Kulomaa, M., Hinterdorfer, P. & Ebner, A., Feb 2014, In : Journal of Molecular Recognition. 27, 2, p. 92-97 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  27. 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

  28. 2013
  29. Published

    The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase

    Anantharajan, J., Koski, M. K., Kursula, P., Hieta, R., Bergmann, U., Myllyharju, J. & Wierenga, R. K., 3 Dec 2013, In : Structure. 21, 12, p. 2107-2118 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  30. 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

  31. 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

  32. 2012
  33. Published

    Characteristics of complex formation between monomeric and dimeric bisbenzimidazoles and AT-containing polynucleotide

    Lisitsyna, E. S., Durandin, N. A., Ivanov, A. A., Streltsov, S. A., Susova, O. Y., Shtil, A. A., Zhuze, A. L. & Kuzmin, V. A., Nov 2012, In : MOLECULAR BIOLOGY. 46, 6, p. 823-827 5 p.

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma.

    de Matos Simoes, R., Tripathi, S. & Emmert-Streib, F., 14 May 2012, In : BMC Systems Biology. 6, 38.

    Research output: Contribution to journalArticleScientificpeer-review

  35. 2011
  36. 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

  37. 2010
  38. Inferring the conservative causal core of gene regulatory networks

    Altay, G. & Emmert-Streib, F., 28 Sep 2010, In : BMC Systems Biology. 4, 132.

    Research output: Contribution to journalArticleScientificpeer-review

  39. 2009
  40. Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae

    Emmert-Streib, F. & Dehmer, M., 20 Jul 2009, In : BMC Systems Biology. 3, 76.

    Research output: Contribution to journalArticleScientificpeer-review

  41. Information processing in the transcriptional regulatory network of yeast: Functional robustness

    Emmert-Streib, F. & Dehmer, M., 19 Mar 2009, In : BMC Systems Biology. 3, 35.

    Research output: Contribution to journalArticleScientificpeer-review

  42. 2008
  43. 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

  44. 2007
  45. A topological algorithm for identification of structural domains of proteins

    Emmert-Streib, F. & Mushegian, A., 3 Jul 2007, In : BMC Bioinformatics. 8, 237.

    Research output: Contribution to journalArticleScientificpeer-review