Tampere University of Technology

TUTCRIS Research Portal

Publications

  1. Published

    Using multi-step proposal distribution for improved MCMC convergence in Bayesian network structure learning

    Larjo, A. & Lähdesmäki, H., 27 Dec 2015, In : Eurasip Journal on Bioinformatics and Systems Biology. 2015, 1, 6.

    Research output: Contribution to journalArticleScientificpeer-review

  2. 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

  3. Published

    Structured orthogonal families of one and two strata prime basis factorial models

    Rodrigues, P. C., Moreira, E. E., Jesus, V. M. & Mexia, J. T., 2014, In : Statistical Papers. 55, 3, p. 603-614 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Published

    Signal focusing through active transport

    Godec, A. & Metzler, R., 2 Jul 2015, In : Physical Review E. 92, 1, 6 p., 010701.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Published

    Search reliability and search efficiency of combined Lévy-Brownian motion: Long relocations mingled with thorough local exploration

    Palyulin, V. V., Chechkin, A. V., Klages, R. & Metzler, R., 8 Sep 2016, In : Journal of Physics A: Mathematical and Theoretical. 49, 39, 394002.

    Research output: Contribution to journalArticleScientificpeer-review

  6. 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

  7. 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

  8. 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

  9. Published

    Reorientational versus Kerr dark and gray solitary waves using modulation theory

    Assanto, G., Marchant, T. R., Minzoni, A. A. & Smyth, N. F., 9 Dec 2011, In : Physical Review E. 84, 6, 066602.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    Quantifying the non-ergodicity of scaled Brownian motion

    Safdari, H., Cherstvy, A. G., Chechkin, A. V., Thiel, F., Sokolov, I. M. & Metzler, R., 18 Sep 2015, In : Journal of Physics A: Mathematical and Theoretical. 48, 37, 375002.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

    Performance of Variable Partial Factor approach in a slope design

    Knuuti, M. & Länsivaara, T., 2019, 13th International Conference on Applications of Statistics and Probability in Civil Engineering(ICASP13), Seoul, South Korea, May 26-30, 2019.

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

  12. Published

    Parity-time-symmetric solitons in trapped Bose-Einstein condensates and the influence of varying complex potentials: A variational approach

    Devassy, L., Jisha, C. P., Alberucci, A. & Kuriakose, V. C., 19 Aug 2015, In : Physical Review E. 92, 2, 12 p., 022914.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

    Optimization and universality of Brownian search in a basic model of quenched heterogeneous media

    Godec, A. & Metzler, R., 21 May 2015, In : Physical Review E. 91, 5, 052134.

    Research output: Contribution to journalArticleScientificpeer-review

  14. Published

    Nonlinear continuous-wave optical propagation in nematic liquid crystals: Interplay between reorientational and thermal effects

    Alberucci, A., Laudyn, U. A., Piccardi, A., Kwasny, M., Klus, B., Karpierz, M. A. & Assanto, G., 11 Jul 2017, In : Physical Review E. 96, 1, 012703.

    Research output: Contribution to journalArticleScientificpeer-review

  15. 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

  16. Published

    Majorization-minimization for manifold embedding

    Yang, Z., Peltonen, J. & Kaski, S., 2015, In : Journal of Machine Learning Research. 38, p. 1088-1097 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  17. Published

    Investigation of an entropic stabilizer for the lattice-Boltzmann method

    Mattila, K. K., Hegele, L. A. & Philippi, P. C., 19 Jun 2015, In : Physical Review E. 91, 6, 063010.

    Research output: Contribution to journalArticleScientificpeer-review

  18. 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

  19. Published

    Information retrieval perspective to meta-visualization

    Peltonen, J. & Lin, Z., 2013, In : Journal of Machine Learning Research. 29, p. 165-180 16 p.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    High-Reynolds-number turbulent cavity flow using the lattice Boltzmann method

    Hegele, L. A., Scagliarini, A., Sbragaglia, M., Mattila, K. K., Philippi, P. C., Puleri, D. F., Gounley, J. & Randles, A., 4 Oct 2018, In : Physical Review E. 98, 4, 13 p., 043302.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

    Hermitian one-particle density matrix through a semiclassical gradient expansion

    Bencheikh, K. & Räsänen, E., 9 Dec 2015, In : Journal of Physics A: Mathematical and Theoretical. 49, 1, 015205.

    Research output: Contribution to journalArticleScientificpeer-review

  22. 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

  23. 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

  24. Published

    Generative modeling for maximizing precision and recall in information visualization

    Peltonen, J. & Kaski, S., 2011, In : Journal of Machine Learning Research. 15, p. 579-587 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

    Forecasting mortality rate by singular spectrum analysis

    Mahmoudvand, R., Alehosseini, F. & Rodrigues, P. C., 1 Nov 2015, In : REVSTAT STATISTICAL JOURNAL. 13, 3, p. 193-206 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

    First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids

    Ropo, M., Schneider, M., Baldauf, C. & Blum, V., 16 Feb 2016, In : Scientific Data. 3, 160009.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Fault tolerance of information processing in gene networks

    Emmert-Streib, F. & Dehmer, M., 15 Feb 2009, In : Physica A: Statistical Mechanics and Its Applications. 388, 4, p. 541-548 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Exploratory analysis of spatiotemporal patterns of cellular automata by clustering compressibility

    Emmert-Streib, F., 8 Feb 2010, In : Physical Review E. 81, 2, 026103.

    Research output: Contribution to journalArticleScientificpeer-review

  29. 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

  30. Published

    Ergodicity breaking, ageing, and confinement in generalized diffusion processes with position and time dependent diffusivity

    Cherstvy, A. G. & Metzler, R., 15 May 2015, In : Journal of Statistical Mechanics: Theory and Experiment. 2015, 5, P05010.

    Research output: Contribution to journalArticleScientificpeer-review

  31. Published

    Dynamics of intracranial electroencephalographic recordings from epilepsy patients using univariate and bivariate recurrence networks

    Subramaniyam, N. P. & Hyttinen, J., 27 Feb 2015, In : Physical Review E. 91, 2, 022927.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Published

    Dynamics of coupled repressilators: The role of mRNA kinetics and transcription cooperativity

    Potapov, I., Volkov, E. & Kuznetsov, A., 4 Mar 2011, In : Physical Review E. 83, 3, 031901.

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Diffusion through thin membranes: Modeling across scales

    Aho, V., Mattila, K., Kühn, T., Kekäläinen, P., Pulkkinen, O., Minussi, R. B., Vihinen-Ranta, M. & Timonen, J., 12 Apr 2016, In : Physical Review E. 93, 4, 043309.

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    Conformational properties of complex polymers: Rosette versus star-like structures

    Blavatska, V. & Metzler, R., 7 Apr 2015, In : Journal of Physics A: Mathematical and Theoretical. 48, 13, 135001.

    Research output: Contribution to journalArticleScientificpeer-review

  35. 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

  36. Published

    Clustering-based method for developing a genomic copy number alteration signature for predicting the metastatic potential of prostate cancer

    Pearlman, A., Campbell, C., Brooks, E., Genshaft, A., Shajahan, S., Ittman, M., Bova, G. S., Melamed, J., Holcomb, I., Schneider, R. J. & Ostrer, H., 2012, In : JOURNAL OF PROBABILITY AND STATISTICS. 873570.

    Research output: Contribution to journalArticleScientificpeer-review

  37. 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

  38. 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

  39. Published

    A stochastic model for survival of early prostate cancer with adjustments for leadtime, length bias, and over-detection

    Wu, G. H. M., Auvinen, A., Yen, A. M. F., Hakama, M., Walter, S. D. & Chen, H. H., Jan 2012, In : Biometrical Journal. 54, 1, p. 20-44 25 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. Published

    Aging scaled Brownian motion

    Safdari, H., Chechkin, A. V., Jafari, G. R. & Metzler, R., 7 Apr 2015, In : Physical Review E. 91, 4, 042107.

    Research output: Contribution to journalArticleScientificpeer-review

  42. Published

    Ageing first passage time density in continuous time random walks and quenched energy landscapes

    Krüsemann, H., Godec, A. & Metzler, R., 17 Jul 2015, In : Journal of Physics A: Mathematical and Theoretical. 48, 28, 285001.

    Research output: Contribution to journalArticleScientificpeer-review

  43. Published

    A comparison between joint regression analysis and the AMMI model: A case study with barley

    Pereira, D. G., Rodrigues, P. C., Mejza, S. & Mexia, J. T., Feb 2012, In : JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION. 82, 2, p. 193-207 15 p.

    Research output: Contribution to journalArticleScientificpeer-review