Dr inż. Joanna Żyła, Adiunkt
pokój: 333
telefon: +48 32 2371166
Ten adres pocztowy jest chroniony przed spamowaniem. Aby go zobaczyć, konieczne jest włączenie w przeglądarce obsługi JavaScript.
Plan zajęć

Computer Hope         Computer Hope

Computer Hope




Nota biograficzna:

lipiec 2019 - - adiunkt w Zakładzie Analizy Eksploracyjnej Danych Politechniki Śląskiej w Gliwicach.

luty 2019 - czerwiec 2019 - asystent naukowo-dydaktyczny w Zakładzie Analizy Eksploracyjnej Danych Politechniki Śląskiej w Gliwicach.

luty 2018 - styczeń 2019 - asystent naukowy, Max-Planck Institute for Infection Biology, Department of Immunology.



Stopnie naukowe:

16.04.2019 - Uzyskanie stopnia doktora nauk technicznych w dziedzinie Biocybernetyka i Inżynieria Biomedyczna, specjalizacja Bioinformatyka. Temat rozprawy "Zastosowanie modelowania matematycznego oddziaływań genetycznych oraz metod integratywnej analizy danych w badaniach typu GWAS o mało licznych próbach". Recenzenci: prof. dr hab. inż. Małgorzata Kotulska, prof. dr hab. n med. Rafał Dziadziuszko.

2012 - uzyskanie tytułu magistra na kierunku Biotechnologia, specjalizacja Bioinformatyka.

2011 - uzyskanie tytułu inżyniera na kierunku Biotechnologia, specjalizacja Bioinformatyka.



staże naukowe:

luty - kwiecień 2012 - trzymiesięczny staż naukowy w Health Protection Agency, Wielka Brytania (obecnie Public Health England).



stypendia:

październik 2015 - wrzesień 2016 - Stypendium "Naukowcy Przyszłości" przyznawane przez Dziekana Wydziału Automatyki, Elektroniki i Informatyki.

2012/2013 - 2013/2014 - Stypendium "DoktoRis" Program stypendialny na rzecz innowacyjnego Śląska. Stypendium przyznawane z funduszy Unijnych przez Marszałka woj. Śląskiego.



kursy naukowe:

lipiec 2019 Warwick University, UK; Introduction to Immunology

lipiec 2016 University of Washington, Seattle, USA; Population genetic data analysis, Network and pathway analysis of omic data, Bayesian statistics for genetics. (stypendium University of Washington)

lipiec 2016 CREAL research center, Barcelona, Spain; "Uncertainty Analysis for Low Dose Research"

lipiec 2014 University of Washington, Seattle, USA; Quantitative genetics, Statistical & quantitative genetics of disease (stypendium University of Washington)

grudzień 2012 University Paris-Sud, Instytut Curie, France; "Inter-individual variability of radiation-sensitivity: Mechanisms and Biomarkers".

Rozwiń/Zwiń



Zainteresowania naukowe:

Genome Wide Association Study - quantitative, case-control studies

Statystyka w genetyce populacyjnej

Analiza statystyczna danych omicznych

Aspekty integracji p-wartości oraz integracji danych

Multiomiczna analiza funkcjonalna in silico z szczególnym uwzględnieniem metod typu enrichment.

Modele liniowe w danych wysokoprzepustowej biologii molekularnej.

Lista publikacji:

1. Zyla J., Kabacik S., O'Brien G., Wakil S., Al-Harbi N., Kaprio J., Badie C., Polanska J. and Alsbeih G.: Combining CDKN1A gene expression and genome wide SNPs in a twin cohort to gain insight into heritability of individual radiosensitivity, Functional and Integrative Genomics, 2019, 19:575–585 doi:10.1007/s10142-019-00658-3

2. Joanna Zyla; Michal Marczyk; Teresa Domaszewska; Stefan H.E. Kaufmann; Joanna Polanska; January Weiner: Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. Bioinformatics, 2019, doi: 10.1093/bioinformatics/btz447

3. O'Brien G., Cruz-Garcia L., Zyla J., Brown N., Finnon R., Polanska J., Badie C.: Kras mutations and PU.1 promoter methylation are new pathways in murine radiation-induced AML, Carcinogenesis, 2019, doi: 10.1093/carcin/bgz175

4. Weiner J, Maertzdorf J, Sutherland J.S., Duffy F.J., Thompson E., Suliman S., McEwen G., Thiel B., Parida S.K., Zyla J., Hanekom W.A., Mohney R.P., Boom W.H., Mayanja-Kizza H., Howe R., Dockrell H.M., Ottenhoff T.H.M, Scriba T.J., Zak D.E., Walzl G., Kaufmann S.H.E & The GC6-74 consortium: Metabolite changes in blood predict the onset of tuberculosis. Nature Communications. 9(1): 5208 (2018)

5. G. O’Brien, L. Cruz Garcia, N. Brown, R. Finnon, J. Zyla, J. Polanska, C. Badie: Tracking Sfpi1/PU.1 and Kras mutations in murine acute myeloid leukaemia: role in radiation leukaemogenesis. European Radiation Research 2018, 44th Annual Meeting of the European Radiation Research Society, August 21-25, Pécs, Hungary

6. Zyla J, Marczyk M, Weiner J, Polanska J: Ranking metrics in Gene Set Enrichment Analysis: do they matter? BMC Bioinformatics, 2017, 18(1):256, doi:10.1186/s12859-017-1674-0

7. Zyla J., Marczyk M., Polanska J.: Reproducibility of Finding Enriched Gene Sets in Biological Data Analysis. In: Fdez-Riverola F., Mohamad M., Rocha M., De Paz J., Pinto T. (eds) 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. PACBB 2017. Advances in Intelligent Systems and Computing, vol 616. p. 146-154 (2017) Springer, Cham ISBN:978-3-319-60815-0

8. Zyla J., Danek A., Labaj P., Polanska J.: iK-means clustering in RNA-Seq data analysis of complex experiment design structure. Book of abstracts p.27, Computational Approached in Precision Medicine, 2017, 27-28 July, Vienna, Austria

9. Manning G, Cruz Garcia L., Manola K., Pagoni M., Brown N., Finnon R., Zyla J., Polanska J. and Badie C.: Tracking Kras mutations in human and murine acute myeloid leukaemia: role in radiation leukaemogenesis. Book of abstracts of 43rd Annual Meeting of the European Radiation Research Society, p.376, Essen, Gemany (17-21.09.2017)

10. Papiez A, Zyla J, Binczyk F, Polanska J: Drosophila melanogaster RNA-Seq analysis by k-means clustering with adaptive initial conditions, XXI Gliwickie Spotkania Naukowe 2017, 17-18.11.2017, Gliwice, Polska, Book of Abstracts, p.135.

11. Zyla J., Kabacik S., Manning G., Finnon P., Wakil S., Alsbeih G., Badie C., Polanska J.: Genetic factors in radiation-induced gamma-H2AX phosphorylation and in silico based identification of SNPs influencing its response level. 4th International Symposium on the System of Radiological Protection of International Commission on Radiological Protection and 2nd European Radiation Protection Research Week, ICRP-ERPW 2017, p.83, 10-12.10.2017, Paryż, France

12. Zyla J, Badie C, Albeih G, Polanska J: Heritability in radiation response investigation of H2AX and MDM2. In Proceedings of the XXIII National Conference on Applications of Mathematics in Biology and Medicine, 2017, p. 155-160. Eds. U. Forys, J. Smieja, ISBN: 978-83-932893-3-2

13. Zyla J, Marczyk M, Polanska J: Sensitivity, Specificity and Prioritization of Gene Set Analysis When Applying Different Ranking Metrics. In 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB'16, 1-3 June 2016, Sevilla, Spain. Advances in Intelligent Systems and Computing, vol. 477, p.61-69, Eds. M. Saberi Mohamad, P.M. Rocha, F. Fdez-Riverola, J.F. Domínguez Mayo, F.J. De Paz, Springer International Publishing 2016, ISBN: 978-3-319-40125-6

14. Zyla J, Badie C, Alsbeih G, Polanska J: Multigene P-value Integration Based on SNPs Investigation for Seeking Radiosensitivity Signatures, Bioinformatics and Biomedical Engineering, Lecture Notes in Computer Science, vol. 9656, pp. 125-134, 4th International Work-Conference on Bioinformatics and Biomedical Engineering IWBBIO 2016, Granada,Spain, 20-22.04.2016, (eds.): F. Ortuño and I. Rojas, ISBN 978-3-319-31743-4, DOI: 10.1007/978-3-319-31744-1_12

15. Szymanek A., Zyla J., Badie C., Alsbeih G, Polanska J.: Functional genomic data analysis of irradiation impact to ATF3 protein expression. Acta Biochim Polonica vol.63(Suppl.2):168 - 2nd Congress of the Polish Biochemistry, Cell Biology, Biophysics and Bioinformatics , Wrocław Sept. 13–16 2016

16. Zyla J, Marczyk M, Polanska J: Discovering new biologically relevant pathways by Gene Set Enrichment Analysis. Book of Abstracts, p.102, XX Gliwice Scientific Meetings, Gliwice, November 18-19, 2016

17. Zyla J., Badie C., Alsbeih G., Polanska J.: Integracja prawdopodobieństw dla analiz wyników eksperymentów wysokoprzepustowej biologii molekularnej, III Śląskie Spotkania Naukowe, str. 47, Dzierżno 3-4.06.2016

18. Zyla J., Bulman R., Badie C., Bouffler S.: Potential protein activity modifications of amino acid variants in the human transcriptome, Acta Biochimica Polonica, 64(1):57-61, 2015

19. Zyla J., M. Dolbniak, Badie C., Alsbeih G., Polanska J: Trend control focused integration in modeling genotype-phenotype interactions. 19th Annual International Conference on Research in Computational Molecular Biology RECOMB 2015, Book of abstracts, p. 84-85, 11.04-15.04.2015 Warsaw, POLAND

20. Zyla J, Marczyk M, Polanska J: Searching for radiosensitivity biomarkers by Monte Carlo feature selection and rought sets approach. 8th Symposium of the Polish Bioinformatics Society,PP'11, 17-19 September 2015, Lublin, Poland

21. Zyla J, Badie C, Alsbeih G and Polanska J: Comprehensive multiomics analysis of radiosensitivity phenomena, 2015. International Synthetic and Systems Biology Summer School (SSBSS 2015), 05/07/2015-09/07/2015, Taormina, pp. 34

22. Zyla J, Alsbeih G, Badie C: Comparision of gene set enrichment analysis methods in single nucleotide polymorphism investigation on radiosensitivity phenomena. XIXth Gliwice Scientific Meetings, Book of abstracts, p. 164. 20-21.11.2015, Gliwice, Poland

23. Dolbniak M, Zyla J, Kabacik S, Manning G, Badie C, Alsbeih G, Polanska J: Is the identification of SNP-miRNA interactions supporting the prediction of human lymphocyte transcriptional radiation responses? 6th International Conference on Bioinformatics Models, Methods and Algorithms. pp.243-250 Eds. Oscar Pastor, Christine Sinoquet, Ana Fred, Hugo Gamboa and Dirk Elias ISBN: 978-989-758-070-3 BIOSTEC/BIOINFORMATICS 2015, 12-15 January 2015, Lisbon, Portugal

24. Zyla J. Finnon P. Bulman R. Bouffler S. Badie C. Polanska J: Seeking genetic signature of radiosensitivity - a novel method for data analysis in case of small sample sizes, Theoretical Biology and Medical Modelling  2014, 11(S1), doi:10.1186/1742-4682-11-S1-S2

25. Zyla J. Badie C. Alsbeih G. Polanska J: Modelling of Genetic Interactions in GWAS Reveals More Complex Relations between Genotype and Phenotype. Proceedings of 5th International Conference on Bioinformatics Models, Methods and Algorithms, Eds. Oscar Pastor, Christine Sinoquet, Guy Plantier, Tanija Schultz, Ana Fred and Hugo Gamboa, pages: 204-208, ISBN:978-989-758-012-3. BIOSTEC/Bioinformatics 2014, 03-07.03.2014 Angers, FRANCE

26. Zyla J., Badie C., Alsbeih G., Polanska J.: Integrative data analysis for DNA damage repair genes related to p53. Acta Biochim Polonica vol.61(Suppl.1):101 - 1st Congress of Biochemistry, Cell Biology, Biophysics and Bioinformatics, Warszawa Sept. 9–12 2014

27. Zyla J. Alsbeih G. Kabacik S. Badie C. Polanska J: Heredity of the G1 and G2 cell cycle phase based on genes in p53 pathway. XVIII Gliwice Scientific Meetings, Book of abstracts, p. 160. 21-22.11.2014, Gliwice, Poland

28. Zyla J: Metody walidacji in silico polimorfizmów pojedynczego nukleotydu, I Seminarium Polskiego Towarzystwa Proteomicznego, Gliwice 4-5 czerwca 2014

29. Zyla J. Finnon P. Bulman R. Bouffler S. Badie C. Polanska J: Seeking for Genetic Signature of Radiosensitivity - Methods for data analysis. International Work-Conference on Bioinformatics and Biomedical Engineering IWBBIO 2013, p.79-86. Eds. F. Ortuno, I. Rojas ISBN: 978-84-15814-13-9, 18-20.03.2013 Granada, SPAIN

30. Zyla J. Finnon P. Bulman R. Bouffler S. Badie C. Polanska J: Investigation for genetic signature of radiosensitivity - data analysis. In Advances in Intelligent Systems and Computing, vol. 242 "Man-Machine Interactions 3", Eds. Gruca A, Czachorski T, Kozielski S, p: 219-227. Springer Berlin Heidelberg 2014. ISBN: 978-3-319-02308-3. ICMMI 2013, 22-25.10.2013 Brenna, Poland

31. Zyla J. Badie C. Alsbeih G. Polanska J: Discovery of polymorphisms responsible for radiosensitivity - preliminary analysis. Acta Biochim Polonica vol.60(Suppl.1):114. 48th Annual Meeting of the Polish Biochemical Society. 2-5.09.2013. Toruń, POLAND

32. Zyla J: Genome-Wide Association study as a tool in common disease research. XI International PhD Workshop OWD 2013. Conference Archives PTETiS. vol. 33. p.438-441. 2013. ISBN: 978-83-935427-2-7

33. Zyla J. Badie C. Alsbeih G. Polanska J: Gene - cell-cycle correlation in response to ionizing radiation (preliminary analysis). XVII Gliwice Scientific Meetings, Book of abstracts, p. 177. 15-16.11.2013, Gliwice, Poland

34. Zyla J. Finnon P. Bulman R. Bouffler S. Badie C. Polanska J: Novel Strategies for the Discovery of Genetic Signature of Radiosensitivity - Methods for data analysis. XVI Gliwice Scientific Meetings, Book of abstracts, p.55. 16-17.11.2012. Gliwice, Poland

35. Polanska J. Zyla J. Finnon P. Badie C: Novel strategies for the discovery of genes affecting individual cancer risk – data acquisition. XV Gliwice Scientific Meetings, Book of abstracts, p.100. 18-19.11.2011, Gliwice, Poland