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Information on the principal investigator and host institution

Information of the project and the call

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Integrative bioinformatics methods for high throughput molecular biology experimental data in the analysis or radiosensitivity of cells and tissues.

2013/08/M/ST6/00924

Keywords:

Radiosensitivity integrative bioinformatics

Descriptors:

  • ST6_11: Machine learning, statistical data processing and applications using signal processing (e.g. speech, image, video)
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Politechnika Śląska, Wydział Automatyki, Elektroniki i Informatyki

woj. śląskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Joanna Polańska 

Number of co-investigators in the project: 6

Call: HARMONIA 4 - announced on 2012-12-15

Amount awarded: 613 857 PLN

Project start date (Y-m-d): 2013-09-13

Project end date (Y-m-d): 2016-11-12

Project duration:: 38 months (the same as in the proposal)

Project status: Project settled

Information in the final report

  • Publication in academic press/journals (12)
  • Articles in post-conference publications (33)
  • Book publications / chapters in book publications (7)
  1. Initializing the EM algorithm for univariate Gaussian, multi-component, heteroscedastic mixture models by dynamic programming partitions
    Authors:
    Polanski A., Marczyk M., Pietrowska M., Widlak P., Polanska J.
    Academic press:
    International Journal of Computational Methods (rok: 2018, tom: 15, strony: 1850012 (21 pages)), Wydawca: World Scientific
    Status:
    Published
    DOI:
    10.1142/S0219876218500123 - link to the publication
  2. Potential protein activity modifications of amino acid variants in the human transcriptome
    Authors:
    Zyla J., Bulman R., Badie C., Bouffler S.
    Academic press:
    Acta Biochimica Polonica (rok: 2015, tom: 62(1), strony: 57-61), Wydawca: Polish Biochemical Society
    Status:
    Published
    DOI:
    10.18388/abp.2014_771 - link to the publication
  3. Age of diagnosis and gender modify the risk of 9q22, 14q13 polymorphisms for papillary thyroid carcinoma
    Authors:
    Kula D., Kalemba M., Puch Z., Polanska J., Handkiewicz-Junak D., Swierniak M., Rusinek D., Żebracka-Gala J., Kowalska M., Kowal M., Tyszkiewicz T., Piasna E., Czarniecka A., Pawlaczek A., Krajewska J., Szpak-Ulczok S., Jarząb B.
    Academic press:
    Endokrynologia Polska (rok: 2017, tom: 68(3), strony: 283-289), Wydawca: Via Medica Journals
    Status:
    Published
    DOI:
    10.5603/EP.2017.0021 - link to the publication
  4. Comprehensive analysis of MILE gene expression data set advances discovery of leukaemia type and subtype biomarkers
    Authors:
    Labaj W., Papiez A., Polanski A., Polanska J.
    Academic press:
    Interdisciplinary Sciences: Computational Life Sciences (rok: 2017, tom: 9, strony: 24–35), Wydawca: Springer Verlag
    Status:
    Published
    DOI:
    10.1007/s12539-017-0216-9 - link to the publication
  5. Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry
    Authors:
    Polanski A., Marczyk M., Pietrowska M., Widlak P., Polanska J.
    Academic press:
    Plos ONE (rok: 2015, tom: 10(7), strony: e0134256), Wydawca: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0134256 - link to the publication
  6. Transcriptomic and proteomic analysis of mouse radiation – induced acute myeloid leukaemia (AML)
    Authors:
    Badie C., Blachowicz A., Barjaktarovic Z., Finnon R., Michaux A., Sarioglu H., Brown N., Benotmane A., Tapio S., Polanska J., Bouffler S.
    Academic press:
    Oncotarget (rok: 2015, tom: 7 (26), strony: 40461-80), Wydawca: Impact Journals, LLC
    Status:
    Published
    DOI:
    10.18632/oncotarget.9626 - link to the publication
  7. BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm
    Authors:
    Papiez A., Marczyk M., Polanski A., Polanska J.
    Academic press:
    BMC Bioinformatics (rok: 2017, tom: bd, strony: bd), Wydawca: Springer
    Status:
    Submitted
    DOI:
    brak - link to the publication
  8. Low dose radiation accelerates ageing of the mur 1 ine T cell receptor repertoire in CBA/Ca mice
    Authors:
    Candéias S.M., Mika J., Finnon P., Verbiest T., Finnon R., Brown N., Bouffler S., Polanska J., Badie C.
    Academic press:
    Cellular and Molecular Life Sciences (rok: 2017, tom: 74, strony: 4339–4351), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00018-017-2581-2 - link to the publication
  9. Ranking metrics in Gene Set Enrichment Analysis: do they matter?
    Authors:
    Zyla J., Marczyk M., Weiner J., Polanska J.
    Academic press:
    BMC Bioinformatics (rok: 2017, tom: 18, strony: 256), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1186/s12859-017-1674-0 - link to the publication
  10. Seeking genetic signature of radiosensitivity - a novel method for data analysis in case of small sample sizes
    Authors:
    Zyla J., Finnon P., Bulman R., Bouffler S., Badie C., Polanska J.
    Academic press:
    Theoretical Biology and Medical Modelling (rok: 2014, tom: 11(S1), strony: S2), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1186/1742-4682-11-S1-S2 - link to the publication
  11. Strategies for optimizing the phase correction algorithms in Nuclear Magnetic Resonance spectroscopy
    Authors:
    Binczyk F., Tarnawski R., Polanska J.
    Academic press:
    BioMedical Engineering OnLine (rok: 2015, tom: 14(S2), strony: 5), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/1475-925X-14-S2-S5 - link to the publication
  12. Sources of high variance between probe signals in Affymetrix short oligonucleotide microarrays
    Authors:
    Jaksik R., Marczyk M., Polanska J., Rzeszowska-Wolny J.
    Academic press:
    Sensors (rok: 2014, tom: 14(1), strony: 532-548), Wydawca: MDPI AG, Basel, Switzerland
    Status:
    Published
    DOI:
    10.3390/s140100532 - link to the publication
  1. Discovery of polymorphisms responsible for radiosensitivity - preliminary analysis
    Authors:
    Zyla J., Badie C., Alsbeih G., Polanska J.
    Conference:
    48th Annual Meeting of the Polish Biochemical Society (rok: 2013, ), Wydawca: Polish Biochemical Society
    Data:
    konferencja 2-5.09.2013 Toruń, POLAND
    Status:
    Published
    DOI:
    link to the publication
  2. Impact of missing genotype imputation on the power of Genome Wide Association Studies
    Authors:
    Krol L., Alsbeih G., Badie C., Polanska J.
    Conference:
    International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) (rok: 2014, ), Wydawca: Copicentro Granada S.L, ISBN: 978-84-15814-84-9
    Data:
    konferencja 7-9.04.2014, Granada, SPAIN
    Status:
    Published
    DOI:
    link to the publication
  3. Integrating expression Data from Different Microarray Platforms in Search of Biomarkers of Radiosensitivity.
    Authors:
    Papiez A., Finnon P., Badie C., Bouffler S., Polanska J.
    Conference:
    International Work-Conference Bioinformatics and Biomedical Engineering (IWBBIO 2014) (rok: 2014, ), Wydawca: Copicentro Granada S.L, ISBN: 978-84-15814-84-9
    Data:
    konferencja 7-9.04.2014, Granada, SPAIN
    Status:
    Published
    DOI:
    link to the publication
  4. Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses?
    Authors:
    Dolbniak M., Zyla J., Kabacik S., Manning G., Badie C., Alsbeih G., Polanska J.
    Conference:
    6th International Conference on Bioinformatics Models, Methods and Algorithms BIOINFORMATICS 2015 (rok: 2015, ), Wydawca: SCITEPRESS – Science and Technology Publication, ISBN: 978-989-758-070-3
    Data:
    konferencja 12-15.01.2015, Lisbon, Portugal
    Status:
    Published
    DOI:
    link to the publication
  5. Low dose radiation accelerates ageing of the T cell receptor repertoire in mice
    Authors:
    Candéias S., Mika J., Finnon P., Verbiest T., Finnon R., Brown N., Bouffler S., Polanska J., Badie C.
    Conference:
    ERRS 2017 43rd Annual Meeting of the European Radiation Research Society GBS 2017 20th Annual Meeting of the Society (rok: 2017, ), Wydawca: Universitätsklinikum Essen
    Data:
    konferencja 17-21.09.2017
    Status:
    Published
    DOI:
    link to the publication
  6. Methods for quality control of low-resolution MALDI-ToF spectra
    Authors:
    Marczyk M., Polanska J.
    Conference:
    5th International Conference on Bioinformatics Models, Methods and Algorithms - BIOSTEC/Bioinformatics 2014 (rok: 2014, ), Wydawca: SCITEPRESS – Science and Technology Publications, ISBN: 978-989-758-012-3
    Data:
    konferencja 3-7.03.2014 Angers, FRANCE
    Status:
    Published
    DOI:
    link to the publication
  7. Modelling of Genetic Interactions in GWAS Reveals More Complex Relations between Genotype and Phenotype
    Authors:
    Zyla J., Badie C., Alsbeih G., Polanska J.
    Conference:
    5th International Conference on Bioinformatics Models, Methods and Algorithms - BIOSTEC/Bioinformatics 2014 (rok: 2014, ), Wydawca: SCITEPRESS – Science and Technology Publications, ISBN: 978-989-758-012-3
    Data:
    konferencja 3-7.03.2014 Angers, FRANCE
    Status:
    Published
    DOI:
    link to the publication
  8. Searching for radiosensitivity biomarkers by Monte Carlo feature selection and rought sets approach
    Authors:
    Zyla J., Marczyk M., Polanska J.
    Conference:
    8th Symposium of the Polish Bioinformatics Society (rok: 2015, ), Wydawca: Polskie Towarzystwo Chemii Medycznej, Polskie Towarzystwo Bioinformatyczne, ISBN 978-83-63657-38-3
    Data:
    konferencja 17-19.09.2015, Lublin, Poland
    Status:
    Published
  9. Comparison of black box implementations of two algorithms of processing of NMR spectra, Gaussian Mixture Model and Singular Value Decomposition
    Authors:
    Staniszewski M., Binczyk F., Skorupa A., Boguszewicz L., Sokol M., Polanska J., Polanski A.
    Conference:
    8th International Conference on Bio-inspired Systems and Signal Processing BIOSIGNALS 2015 (rok: 2015, ), Wydawca: SCITEPRESS – Science and Technology Publications, ISBN: 978-989-758-069-7
    Data:
    konferencja 12-15.01.2015, Lisbon, Portugal
    Status:
    Published
    DOI:
    link to the publication
  10. Do the dose and the time post irradiation affect functional V genes frequencies in murine TCR?
    Authors:
    Kotas J., Badie C., Candéias S., Polanska J.
    Conference:
    XIXth Gliwice Scientific Meetings (rok: 2015, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 20-21.11.2015, Gliwice, Poland
    Status:
    Published
    DOI:
    link to the publication
  11. Functionality status of murice TCR sequences – comparative analysis of diversity indices and effect size statistics
    Authors:
    Mika J., Candeias S., Badie C.,Polanska J.
    Conference:
    2nd Congress of Polish Biochemistry, Cell biology, Biotechnology and Bioinformatics (rok: 2016, ), Wydawca: Polish Biochemical Society
    Data:
    konferencja 13-16.09.2016
    Status:
    Published
    DOI:
    link to the publication
  12. Gene - cell-cycle correlation in response to ionizing radiation (preliminary analysis)
    Authors:
    Zyla J., Badie C., Alsbeih G., Polanska J.
    Conference:
    XVII Gliwice Scientific Meetings (rok: 2013, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 15-16.11.2013
    Status:
    Published
    DOI:
    link to the publication
  13. Impact of the selection of statistical test on the quality of gene signatures in an integrative analysis approach
    Authors:
    Papiez A, Badie C, Polanska J.
    Conference:
    XVIII Gliwice Scientific Meetings (rok: 2014, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 21-22.11.2014 Gliwice, Poland
    Status:
    Published
    DOI:
    link to the publication
  14. Improvement in the accuracy of Nuclear Magnetic Resonance spectrum analysis by automatic tuning of phase correction algorithms.
    Authors:
    Binczyk F., Tarnawski R., Polanska J.
    Conference:
    International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) (rok: 2014, ), Wydawca: Copicentro Granada S.L, ISBN: 978-84-15814-84-9
    Data:
    konferencja 7-9.04.2014, Granada, Spain
    Status:
    Published
    DOI:
    link to the publication
  15. Integrative data analysis for DNA damage repair genes related to p53.
    Authors:
    Zyla J., Badie C., Alsbeih G., Polanska J.
    Conference:
    1st Congress of Biochemistry, Cell Biology, Biophysics and Bioinformatics (rok: 2014, ), Wydawca: Polish Biochemical Society
    Data:
    konferencja 9-12.09.2014 Warszawa, Poland
    Status:
    Published
    DOI:
    link to the publication
  16. Methods for meta-analysis of expression data from different microarray platforms
    Authors:
    Papiez A., Finnon P., Bouffler S., Badie C., Polanska J.
    Conference:
    XVII Gliwice Scientific Meetings (rok: 2013, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 15-16.11.2013 Gliwice, Poland
    Status:
    Published
    DOI:
    link to the publication
  17. Novel algorithm for highly efficient Gaussian mixture modeling in mass spectrometry
    Authors:
    Polanski A., Marczyk M., Pietrowska M., Widlak P., Polanska J.
    Conference:
    9th Central and Eastern European Proteomics Conference CEEPC 2015 (rok: 2015, ), Wydawca: Scientific Publishers OWN. Institute of Bioorganic Chemistry Polish Academy of Sciences
    Data:
    konferencja 15-18.06.2015, Poznań, Poland
    Status:
    Published
  18. P-value integration as a technique for validating high-throughput biomedical experiments
    Authors:
    Papiez A.
    Conference:
    International Synthetic & Systems Biology Summer School 2015 (rok: 2015, ), Wydawca: Taosciences Research Center
    Data:
    konferencja 05-09.07.2015, Taormina, Italy
    Status:
    Published
  19. An integrative approach vs restrictive thresholds for combining gene expression data sets on radiation response
    Authors:
    Papiez A., Badie C., Polanska J.
    Conference:
    2nd Congress of Polish Biochemistry, Cell biology, Biotechnology and Bioinformatics (rok: 2016, ), Wydawca: Polish Biochemical Society
    Data:
    konferencja 13-16.09.2016
    Status:
    Published
    DOI:
    link to the publication
  20. Calculation of nucleotide sequence occurrence probability in TCR sequencing data to examine effect of irradiation
    Authors:
    Mika J., Badie C., Candeias S., Polanska J.
    Conference:
    XXth Gliwice Scientific Meetings (rok: 2016, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 18-19.11.2016
    Status:
    Published
    DOI:
    link to the publication
  21. Discovering new biologically relevant pathways by Gene Set Enrichment Analysis
    Authors:
    Zyla J., Marczyk M., Polanska J.
    Conference:
    XXth Gliwice Scientific Meetings (rok: 2016, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 18-19.11.2016
    Status:
    Published
    DOI:
    link to the publication
  22. Functional genomic data analysis of irradiation impact to ATF3 protein expression
    Authors:
    Szymanek A., Zyla J., Badie C., Alsbeih G, Polanska J.
    Conference:
    2nd Congress of Polish Biochemistry, Cell biology, Biotechnology and Bioinformatics (rok: 2016, ), Wydawca: Polish Biochemical Society
    Data:
    konferencja 13-16.09.2016
    Status:
    Published
    DOI:
    link to the publication
  23. Long term alteration of mouse TCR repertoire following radiation exposure
    Authors:
    Candéias S., Mika J., Kabacik S, Olsen A., Polanska J., Bouffler S., Badie C.
    Conference:
    Radiation Protection Week 2016 (rok: 2016, ), Wydawca: University of Oxford
    Data:
    konferencja 19-23.09.2016
    Status:
    Published
    DOI:
    link to the publication
  24. Statistical integration of p-values for enhancing discovery of radiotoxicity gene signatures
    Authors:
    Papiez A., Kabacik S., Badie C., Bouffler S., Polanska J.
    Conference:
    Third International Work-Conference on Bioinformatics and Biomedical Engineering IWBBIO 2015 (rok: 2015, ), Wydawca: Springer, Series: Lecture Notes in Computer Science, vol.9043, ISBN: 978-3-319-16482-3
    Data:
    konferencja 15-17.04.2015, Granada, Spain
    Status:
    Published
  25. Statistical methods for integrating high-throughput biological data.
    Authors:
    Papiez A., Badie C., Polanska J.
    Conference:
    1st Congress of Biochemistry, Cell Biology, Biophysics and Bioinformatics (rok: 2014, ), Wydawca: Polish Biochemical Society
    Data:
    konferencja 9-12.09.2014 Warszawa, Poland
    Status:
    Published
    DOI:
    link to the publication
  26. The detection of neural progenitor cell signal in nuclear magnetic resonance spectroscopy data
    Authors:
    Binczyk F., Staniszewski M., Polnik A., Boguszewicz Ł., Sokół M., Polanski A., Polanska J.
    Conference:
    XVII Gliwice Scientific Meetings (rok: 2013, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 15-16.11.2013 Gliwice, Poland
    Status:
    Published
    DOI:
    link to the publication
  27. The differentation of head/neck tumors with use of information about the diffusion of water molecules obtained from nuclear magnetic resonance data
    Authors:
    Binczyk F., Bobek-Bilewicz B., Hebda A., Hejduk B., Polanska J.
    Conference:
    XVII Gliwice Scientific Meetings (rok: 2013, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 15-16.11.2013 Gliwice, Poland
    Status:
    Published
    DOI:
    link to the publication
  28. Analiza trendów zmian strukturanych w genomie w odpowiedzi na wybrane dawki promieniowania jonizującego
    Authors:
    Rolnik B., Al-Harbi N., Bin Judia S., Majid S., Alsbeih G., Polańska J.
    Conference:
    Śląskie Spotkania Naukowe (rok: 2017, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 24-25.03.2017
    Status:
    Published
    DOI:
    link to the publication
  29. Automatic detection of outlying microarrays using multiarray quality metrics
    Authors:
    Marczyk M., Krol L., Polanska J.
    Conference:
    International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014) (rok: 2014, ), Wydawca: Copicentro Granada S.L, ISBN: 978-84-15814-84-9
    Data:
    konferencja 7-9.04.2014, Granada, Spain
    Status:
    Published
    DOI:
    link to the publication
  30. Heredity of the G1 and G2 cell cycle phase based on genes in p53 pathway.
    Authors:
    Zyla J., Alsbeih G., Kabacik S., Badie C., Polanska J.
    Conference:
    XVIII Gliwice Scientific Meetings (rok: 2014, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 21-22.11.2014, Gliwice, Poland
    Status:
    Published
    DOI:
    link to the publication
  31. Does the way of AML induction in mice influence protein signature of cells?
    Authors:
    Blachowicz A., Tapio S., Barjaktarovic Z., Benotmane R., Finnon R., Badie C., Bouffler S., Polanska J.
    Conference:
    9th Central and Eastern European Proteomics Conference CEEPC 2015 (rok: 2015, ), Wydawca: Scientific Publishers OWN. Institute of Bioorganic Chemistry Polish Academy of Sciences
    Data:
    konferencja 15-18.06.2015, Poznań, Poland
    Status:
    Published
  32. Effects of low dose radiation on the T lymphocyte repertoire in the mouse: analysis from a TCR point of view
    Authors:
    Candéias S., Kotas J., Kabacik S., Olsen A., Polanska J., Bouffler S., Badie C.
    Conference:
    XIXth Gliwice Scientific Meetings (rok: 2015, ), Wydawca: Association for the Support of Cancer Research
    Data:
    konferencja 20-21.11.2015, Gliwice, Poland
    Status:
    Published
    DOI:
    link to the publication
  33. Usage of bootstrap sampling in comparing biological diversity of differently sized data samples
    Authors:
    Kotas J., Badie C., Candéias S., Polanska J.
    Conference:
    19th Annual International Conference on Research in Computational Molecular Biology RECOMB 2015 (rok: 2015, ), Wydawca: Uniwersytet Warszawski
    Data:
    konferencja 11-15.04.2015, Warsaw, Poland
    Status:
    Published
    DOI:
    link to the publication
  1. Distributed Monte Carlo Feature Selection: extracting informative features out of multidimensional problems with linear speedup
    Authors:
    Krol L.
    Book:
    Communications in Computer and Information Science; ISBN: 978-3-319-34098-2 (rok: 2016, tom: 613, strony: 463-474), Wydawca: Springer
    Status:
    Published
  2. Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures
    Authors:
    Zyla J., Badie C., Ghazi A., Polanska J.
    Book:
    Lecture Notes in Bioninformatics; ISBN: 978-3-319-31743-4 (rok: 2016, tom: 9656, strony: 125-134), Wydawca: Springer
    Status:
    Published
  3. Sensitivity, specificity and prioritization of gene set analysis when applying different ranking metrics
    Authors:
    Zyla J., Marczyk M., Polanska J.
    Book:
    Advances in Intelligent Systems and Computing; ISBN: 978-3-319-40125-6 (rok: 2015, tom: 477, strony: 61-69), Wydawca: Springer
    Status:
    Published
  4. Comparative Analysis of microRNA-Target Gene Interaction Prediction Algorithms - The Attempt to Compare the Results of Three Algorithms
    Authors:
    Krawczyk A., Polanska J.
    Book:
    Bioinformatics and Biomedical Engineering, Lecture Notes in Computer Science; ISBN: 978-3-319-31743-4 (rok: 2016, tom: 9656, strony: 103-112), Wydawca: Springer
    Status:
    Published
  5. Deep data analysis of a large microarray collection for leukemia biomarker identification
    Authors:
    Labaj W., Papiez A., Polanska J., Polanski A.
    Book:
    Advances in Intelligent Systems and Computing; ISBN: 978-3-319-40125-6 (rok: 2016, tom: 477, strony: 71-79), Wydawca: Springer
    Status:
    Published
  6. Investigation for genetic signature of radiosensitivity - data analysis
    Authors:
    Zyla J., Finnon P., Bulman R., Bouffler S., Badie C., Polanska J
    Book:
    Advances in Intelligent Systems and Computing; ISBN: 978-3-319-02308-3 (rok: 2014, tom: 242, strony: 219-227), Wydawca: Springer
    Status:
    Published
    DOI:
    link to the publication
  7. A novel divisive iK-means algorithm with region-driven feature selection as a tool for automated detection of tumour heterogeneity in MALDI IMS experiments
    Authors:
    Mrukwa G., Drazek G., Pietrowska M., Widlak P., Polanska J.
    Book:
    Bioinformatics and Biomedical Engineering, Lecture Notes in Computer Science; ISBN: 978-3-319-31743-4 (rok: 2016, tom: 9656, strony: 113-124), Wydawca: Springer
    Status:
    Published

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