Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. 1993
  2. Melting of copper clusters

    Valkealahti, S. & Manninen, M., 1 Jan 1993, In : Computational Materials Science. 1, 2, p. 123-134 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. 2006
  4. Algorithmic computation of knot polynomials of secondary structure elements of proteins

    Emmert-Streib, F., 1 Oct 2006, In : Journal of Computational Biology. 13, 8, p. 1503-1512 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. A similarity measure for graphs with low computational complexity

    Dehmer, M., Emmert-Streib, F. & Kilian, J., 1 Nov 2006, In : Applied Mathematics and Computation. 182, 1, p. 447-459 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  6. 2007
  7. Topological mappings between graphs, trees and generalized trees

    Emmert-Streib, F. & Dehmer, M., 15 Mar 2007, In : Applied Mathematics and Computation. 186, 2, p. 1326-1333 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  8. Comparing large graphs efficiently by margins of feature vectors

    Dehmer, M. & Emmert-Streib, F., 15 May 2007, In : Applied Mathematics and Computation. 188, 2, p. 1699-1710 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Information theoretic measures of UHG graphs with low computational complexity

    Emmert-Streib, F. & Dehmer, M., 15 Jul 2007, In : Applied Mathematics and Computation. 190, 2, p. 1783-1794 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Structural similarity of directed universal hierarchical graphs: A low computational complexity approach

    Dehmer, M. & Emmert-Streib, F., 1 Dec 2007, In : Applied Mathematics and Computation. 194, 1, p. 7-20 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  11. 2008
  12. A comparative analysis of multidimensional features of objects resembling sets of graphs

    Dehmer, M., Emmert-Streib, F. & Gesell, T., 15 Feb 2008, In : Applied Mathematics and Computation. 196, 1, p. 221-235 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. 2009
  14. 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

  15. 2010
  16. 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

  17. 2011
  18. Published

    The different levels of magneto-mechanical coupling in energy conversion machines and devices

    Belahcen, A., Kouhia, R. & Fonteyn, K., 2011, Proceedings of the 4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011. p. 472-483 12 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  19. 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

  20. Published

    Machine learning: How it can help nanocomputing

    Uusitalo, M. A., Peltonen, J. & Ryhänen, T., Aug 2011, In : Journal of Computational and Theoretical Nanoscience. 8, 8, p. 1347-1363 17 p.

    Research output: Contribution to journalReview ArticleScientificpeer-review

  21. 2012
  22. Published

    Evolutionary dynamics of the spatial Prisoner's Dilemma with self-inhibition

    Emmert-Streib, F., 5 Feb 2012, In : Applied Mathematics and Computation. 218, 11, p. 6482-6488 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Published

    Universal construction mechanism for networks from one-dimensional symbol sequences

    Emmert-Streib, F., 15 Oct 2012, In : Applied Mathematics and Computation. 219, 3, p. 1020-1030 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. 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

  25. 2013
  26. Published

    Density functional theory study of FePdn (n = 2-14) clusters and interactions with small molecules

    Ma, L., Wang, J., Hao, Y. & Wang, G., Feb 2013, In : Computational Materials Science. 68, p. 166-173 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

    Growth behavior and magnetic properties of spherical uranium oxide nanoclusters

    Ma, L. & Ray, A. K., Feb 2013, In : Journal of Computational and Theoretical Nanoscience. 10, 2, p. 334-340 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

    An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants

    Dehmer, M., Grabner, M., Mowshowitz, A. & Emmert-Streib, F., Aug 2013, In : Advances in Computational Mathematics. 39, 2, p. 311-325 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  29. 2014
  30. Published

    A full-potential linearized augmented plane wave study of the interaction of CO2 with α-Pu (020) surface nanolayers

    Wang, J. & Ray, A. K., 2014, In : Journal of Computational and Theoretical Nanoscience. 11, 7, p. 1710-1717 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  31. Published

    A microscopic view of the mechanisms of active transport across the cellular membrane

    Enkavi, G., Li, J., Wen, P., Thangapandian, S., Moradi, M., Jiang, T., Han, W. & Tajkhorshid, E., 2014, In : Annual Reports in Computational Chemistry. 10, p. 77-125 49 p.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Magnetic origin of the chemical balance in alloyed Fe-Cr stainless steels: First-principles and Ising model study

    Airiskallio, E., Nurmi, E., Väyrynen, I. J., Kokko, K., Ropo, M., Punkkinen, M. P. J., Johansson, B. & Vitos, L., 2014, In : Computational Materials Science. 92, p. 135-140 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  33. 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

  34. 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

  35. Published

    Entropy bounds for dendrimers

    Chen, Z., Dehmer, M., Emmert-Streib, F. & Shi, Y., 1 Sep 2014, In : Applied Mathematics and Computation. 242, p. 462-472 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  36. 2015
  37. Published

    Van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads

    Karilainen, T., Cramariuc, O., Kuisma, M., Tappura, K. & Hukka, T. I., 2015, In : Journal of Computational Chemistry. 36, 9, p. 612-621 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  38. 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

  39. Published

    Graph distance measures based on topological indices revisited

    Dehmer, M., Emmert-Streib, F. & Shi, Y., 18 Jun 2015, In : Applied Mathematics and Computation. 266, p. 623-633 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  40. Published

    A robust AMMI model for the analysis of genotype-by-environment data

    Rodrigues, P. C., Monteiro, A. & Lourenço, V. M., 1 Jul 2015, In : Bioinformatics. 32, 1, p. 58-66 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  41. 2016
  42. Published

    Modeling probability densities with sums of exponentials via polynomial approximation

    Dumitrescu, B., Şicleru, B. C. & Avram, F., 2016, In : Journal of Computational and Applied Mathematics. 292, p. 513–525

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    On k-Hypermonogenic Functions and Their Mean Value Properties

    Eriksson, S-L. & Orelma, H., 2016, In : Complex Analysis and Operator Theory. 10, 2, p. 311-325 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  44. Published

    Two models for hydraulic cylinders in flexible multibody simulations

    Ylinen, A., Mäkinen, J. & Kouhia, R., 2016, Computational Methods for Solids and Fluids: Multiscale Analysis, Probability Aspects and Model Reduction. Springer, p. 463-493 31 p. (Computational Methods in Applied Sciences; vol. 41).

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  45. 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

  46. Published

    Introducing libeemd: a program package for performing the ensemble empirical mode decomposition

    Luukko, P. J. J., Helske, J. & Räsänen, E., 1 Jun 2016, In : Computational Statistics. 31, 2, p. 545-557 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files

    Stupnikov, A., Tripathi, S., De Matos Simoes, R., McArt, D., Salto-Tellez, M., Glazko, G., Dehmer, M. & Emmert-Streib, F., 1 Nov 2016, In : Bioinformatics. 32, 21, p. 3345-3347 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  48. 2017
  49. Published

    Homogeneous (α,k)-Polynomial Solutions of the Fractional Riesz System in Hyperbolic Space

    Orelma, H. & Vieira, N., 2017, In : Complex Analysis and Operator Theory. 11, 5, p. 1253–1267 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  50. Published

    Integral kernels for k-hypermonogenic functions

    Vuojamo, V. & Eriksson, S-L., 2017, In : Complex Variables and Elliptic Equations. 62, 9, p. 1-12 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  51. Published

    Chipless graphene tag and dual-CP reader for Internet of Things

    Dong, G., Shen, Y., He, H., Virkki, J. & Hu, S., 26 Sep 2017, 2017 International Applied Computational Electromagnetics Society Symposium in China, ACES-China 2017. IEEE

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  52. 2018
  53. Published

    Hypermonogenic Functions of Two Vector Variables

    Eriksson, S. L., Orelma, H. & Vieira, N., 2018, In : Complex Analysis and Operator Theory. 12, 2, p. 555–570 16 p.

    Research output: Contribution to journalArticleScientificpeer-review

  54. Published

    Multichannel Blind Sound Source Separation using Spatial Covariance Model with Level and Time Differences and Non-Negative Matrix Factorization

    Carabias Orti, J. J., Nikunen, J., Virtanen, T. & Vera-Candeas, P., Sep 2018, In : IEEE/ACM Transactions on Audio Speech and Language Processing. 26, 9, p. 1512-1527

    Research output: Contribution to journalArticleScientificpeer-review

  55. 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

  56. 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

  57. 2019
  58. Published

    An automated algorithm for reliable equation of state fitting of magnetic systems

    Levämäki, H., Tian, L-Y., Vitos, L. & Ropo, M., 2019, In : Computational Materials Science. 156, p. 121-128 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  59. Accepted/In press

    Cuts for 3-D magnetic scalar potentials: Visualizing unintuitive surfaces arising from trivial knots

    Stockrahm, A., Lahtinen, V., Kangas, J. J. J. & Kotiuga, P. R., 2019, (Accepted/In press) In : Computers and Mathematics with Applications.

    Research output: Contribution to journalArticleScientificpeer-review

  60. E-pub ahead of print

    Modeling mass transfer in fracture flows with the time domain-random walk method

    Kuva, J., Voutilainen, M. & Mattila, K., 2019, In : COMPUTATIONAL GEOSCIENCES.

    Research output: Contribution to journalArticleScientificpeer-review

  61. Published

    Optimal energy decay for the wave-heat system on a rectangular domain

    Batty, C., Paunonen, L. & Seifert, D., 2019, In : SIAM JOURNAL ON MATHEMATICAL ANALYSIS. 51, 2, p. 808-819 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  62. Published

    Circularly Polarized Textile Tag Antenna for Wearable Passive UHF RFID Systems

    Kuang, Y., Ma, S., Ukkonen, L., Virkki, J. & Björninen, T., 18 Mar 2019, 2018 International Applied Computational Electromagnetics Society Symposium in China, ACES-China 2018. IEEE

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  63. Published

    Comparison of Human Head Phantoms with Different Complexities for Implantable Antenna Development

    Ma, S., Ukkonen, L., Sydänheimo, L. & Björninen, T., 18 Mar 2019, 2018 International Applied Computational Electromagnetics Society (ACES) Symposium: 29 July-1 Aug. 2018, China. IEEE

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  64. Published

    Hypermonogenic solutions and plane waves of the Dirac operator in Rp×Rq

    Guzmán Adán, A., Orelma, H. & Sommen, F., 1 Apr 2019, In : Applied Mathematics and Computation. 346, p. 1-14 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  65. Published

    Sound Event Detection in the DCASE 2017 Challenge

    Mesaros, A., Diment, A., Elizalde, B., Heittola, T., Vincent, E., Raj, B. & Virtanen, T., 1 Jun 2019, In : IEEE/ACM Transactions on Audio Speech and Language Processing. 27, 6, p. 992-1006 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  66. Published

    Visibility-Aware Part Coding for Vehicle Viewing Angle Estimation

    Yang, D., Qian, Y., Cai, D., Yan, S., Kämäräinen, J-K. & Chen, K., 1 Aug 2019, 9th International Conference on Information Science and Technology, ICIST 2019. IEEE, p. 65-70 6 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  67. Published

    Satisfiability of modal inclusion logic: Lax and strict semantics

    Hella, L., Kuusisto, A., Meier, A. & Vollmer, H., 1 Oct 2019, In : ACM TRANSACTIONS ON COMPUTATIONAL LOGIC. 21, 1, 7.

    Research output: Contribution to journalArticleScientificpeer-review

  68. Published

    On efficient network similarity measures

    Dehmer, M., Chen, Z., Shi, Y., Zhang, Y., Tripathi, S., Ghorbani, M., Mowshowitz, A. & Emmert-Streib, F., 1 Dec 2019, In : Applied Mathematics and Computation. 362, 124521.

    Research output: Contribution to journalArticleScientificpeer-review

  69. Published

    Graph entropy based on the number of spanning forests of c-cyclic graphs

    Wan, P., Tu, J., Dehmer, M., Zhang, S. & Emmert-Streib, F., 15 Dec 2019, In : Applied Mathematics and Computation. 363, 124616.

    Research output: Contribution to journalArticleScientificpeer-review

  70. 2020
  71. Published

    A novel epidemic model considering demographics and intercity commuting on complex dynamical networks

    Yin, Q., Wang, Z., Xia, C., Dehmer, M., Emmert-Streib, F. & Jin, Z., 2020, In : Applied Mathematics and Computation. 386, 21 p., 125517.

    Research output: Contribution to journalArticleScientificpeer-review

  72. Published

    Introducing Multi-Convexity in Path Constrained Trajectory Optimization for Mobile Manipulators

    Singh, A. K., Ahonen, A., Ghabcheloo, R. & Mueller, A., 2020, European Control Conference 2020, ECC 2020. IEEE, p. 1178-1185 8 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  73. Published

    Resilient Cooperative Voltage Control for Distribution Network with High Penetration Distributed Energy Resources

    Gusrialdi, A., Xu, Y., Qu, Z. & Simaan, M. A., 2020, European Control Conference 2020, ECC 2020. IEEE, p. 1533-1539 7 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  74. Published

    The watching system as a generalization of identifying code

    Ghorbani, M., Dehmer, M., Maimani, H., Maddah, S., Roozbayani, M. & Emmert-Streib, F., 2020, In : Applied Mathematics and Computation. 380, 7 p., 125302.

    Research output: Contribution to journalArticleScientificpeer-review

  75. Published

    Relations and bounds for the zeros of graph polynomials using vertex orbits

    Dehmer, M., Emmert-Streib, F., Mowshowitz, A., Ilić, A., Chen, Z., Yu, G., Feng, L., Ghorbani, M., Varmuza, K. & Tao, J., 1 Sep 2020, In : Applied Mathematics and Computation. 380, 125239.

    Research output: Contribution to journalArticleScientificpeer-review