Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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Systems biology of responses of human cells to stress. Generation of heterogeneity, paracrine regulation and evolutionary analysis.

2012/04/A/ST7/00353

Keywords:

transcription regulation cell cycle regulation regulatory networks,carcinogenesis mathematical models heteogeneity

Descriptors:

  • ST7_4: Micro- and nanosystems engineering
  • ST7_11: Electronic, optoelectronic and photonic components and systems for applications (e.g. in biomedical engineering)
  • NZ2_9: Systems biology

Panel:

ST7 - Systems and communication engineering: electronics, communication, optoelectronics

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. Marek Kimmel 

Number of co-investigators in the project: 10

Call: MAESTRO 2 - announced on 2011-12-15

Amount awarded: 2 258 517 PLN

Project start date (Y-m-d): 2012-09-26

Project end date (Y-m-d): 2017-09-25

Project duration:: 60 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. komputer przenośny (6 szt.) (36 000 PLN)

Information in the final report

  • Publication in academic press/journals (26)
  • Articles in post-conference publications (13)
  • Book publications / chapters in book publications (7)
  1. Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia.
    Authors:
    T. Wojdyla, H. Mehta, T. Glaubach, R. Bertolusso, M. Iwanaszko, R. Braun, S.J. Corey , M. Kimmel
    Academic press:
    PLoS Computational Biology (rok: 2019, tom: 15(1), strony: e1006664), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1006664 - link to the publication
  2. Sensitivity of signaling pathway dynamics to plasmid transfection and its consequences
    Authors:
    Śmieja J., Dołbniak M.
    Academic press:
    Mathematical Biosciences and Engineering (rok: 2016, tom: 13(6), strony: 1207-1222), Wydawca: AIMS
    Status:
    Published
    DOI:
    10.3934/mbe.2016039 - link to the publication
  3. Stochastic Hypothesis of Transition from Inborn Neutropenia to AML: Interactions of Cell Population Dynamics and Population Genetics
    Authors:
    Marek Kimmel, Seth Corey
    Academic press:
    Frontiers in Oncology (rok: 2013, tom: 3, strony: 45298), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fonc.2013.00089 - link to the publication
  4. Microarray experiments and factors which affect their reliability
    Authors:
    Roman Jaksik, Marta Iwanaszko, Joanna Rzeszowska, Marek Kimmel
    Academic press:
    BMC Genomics (rok: 2015, tom: 10, strony: 45319), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s13062-015-0077-2 - link to the publication
  5. Multitype infinite-allele branching processes in continuous time
    Authors:
    Thomas O. McDonald, Marek Kimmel
    Academic press:
    Journal of Applied Probability (rok: 2017, tom: 54, strony: 550-568), Wydawca: Applied Probability Trust
    Status:
    Published
    DOI:
    10.1017/jpr.2017.17 - link to the publication
  6. Radionuclides in radiation-induced bystander effect; may it share in radionuclide therapy?
    Authors:
    M. Wideł
    Academic press:
    Neoplasma (rok: 2017, tom: 64 (5), strony: 641-654), Wydawca: AEPress
    Status:
    Published
    DOI:
    10.4149/neo_2017_501 - link to the publication
  7. Stable feature selection and classification algorithms for multiclass microarray data
    Authors:
    Sebastian Student, Krzysztof Fujarewicz
    Academic press:
    Biology Direct (rok: 2012, tom: 7, strony: 45311), Wydawca: Biomed Central
    Status:
    Published
    DOI:
    10.1186/1745-6150-7-33 - link to the publication
  8. The meaning of sensitivity functions in signaling pathways analysis
    Authors:
    Jarosław Śmieja, Małgorzata Kardyńska, Arkadiusz Jamróz
    Academic press:
    Discrete and Continuous Dynamical Systems - Series B (rok: 2014, tom: 10 (8), strony: 2697-2707), Wydawca: AIMS
    Status:
    Published
    DOI:
    10.3934/dcdsb.2014.19.2697 - link to the publication
  9. Cancer heterogeneity and multilayer spatial evolutionary games
    Authors:
    A. Świerniak, M. Krześlak
    Academic press:
    Biology Direct (rok: 2016, tom: 11, strony: 53 (1-16)), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s13062-016-0156-z - link to the publication
  10. Cell fate in antiviral response is decided in the crosstalk of the IRF, NF-kBa;B and JAK/STAT pathways
    Authors:
    M. Czerkies, Z. Korwek, W. Prus, M. Kochańczyk, J. Jaruszewicz-Błońska, K. Tudelska, S. Błoński, M. Kimmel, AR. Brasier, T. Lipniacki
    Academic press:
    Nature Communications (rok: 2018, tom: 9(1), strony: 493), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41467-017-02640-8 - link to the publication
  11. Coalescence computations for large samples drawn from populations of time-varying sizes
    Authors:
    A. Polanski, A. Szczesna, M. Garbulowski, M. Kimmel
    Academic press:
    PLOS One (rok: 2017, tom: 12(2), strony: e0170701), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0170701 - link to the publication
  12. Genetic demographic networks: Mathematical model and applications
    Authors:
    M. Kimmel, T. Wojdyła
    Academic press:
    Theoretical Population Biology (rok: 2016, tom: 111, strony: 75-86), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.tpb.2016.06.004 - link to the publication
  13. Multidimensional Extended Spatial Evolutionary Games
    Authors:
    Michał Krześlak, Andrzej Świerniak
    Academic press:
    Computers in Biology and Medicine (rok: 2016, tom: 69, strony: 315-327), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.compbiomed.2015.08.003 - link to the publication
  14. A multitype infinite-allele branching process with applications to cancer evolution
    Authors:
    Thomas O. McDonald, Marek Kimmel
    Academic press:
    Journal of Applied Probability (rok: 2015, tom: 52, strony: 864–876), Wydawca: Applied Probability Trust
    Status:
    Published
    DOI:
    brak - link to the publication
  15. EMQIT: a machine learning approach for energy based PWM matrix quality improvement
    Authors:
    K. Smolińska, M. Pacholczyk
    Academic press:
    Biology Direct (rok: 2017, tom: 0,511805555555556, strony: 45299), Wydawca: BMC
    Status:
    Published
    DOI:
    10.1186/s13062-017-0189-y - link to the publication
  16. Klasyfikacja, budowa i funkcjonowanie białek Ago u Eukariontów
    Authors:
    A. Poterała, J. Rzeszowska-Wolny
    Academic press:
    Postępy Higieny i Medycyny Doświadczalnej (rok: 2016, tom: 70, strony: 1005-1016), Wydawca: Index Copernicus International S.A.
    Status:
    Published
    DOI:
    brak - link to the publication
  17. Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells
    Authors:
    M. Mura, C. Feillet, F. Delauney, R, Bertolusso, M. Kimmel
    Academic press:
    PLOS Computational Biology (rok: 2019, tom: 15(6), strony: e1007054), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1007054 - link to the publication
  18. Modeling epigenetic regulation of PRC1 protein accumulation in the cell cycle
    Authors:
    Dołbniak M., Kimmel M., Śmieja J.
    Academic press:
    Biology Direct (rok: 2015, tom: 10, strony: 45306), Wydawca: Biomed Central
    Status:
    Published
    DOI:
    10.1186/s13062-015-0078-1 - link to the publication
  19. Comparison of Simple Models of Periodic Protocols for Combined Anticancer Therapy
    Authors:
    Marzena Dołbniak, Andrzej Świerniak
    Academic press:
    Computational and Mathematical Methods in Medicine (rok: 2013, tom: 2013, strony: 45302), Wydawca: Hindawi Publishing Corporation
    Status:
    Published
    DOI:
    10.1155/2013/567213 - link to the publication
  20. Crosstalk between cytokine and hyperthermia induced pathways: identification of different subsets of NFkappaB-dependent genes regulated by TNF-alfa and heat shock
    Authors:
    Janus P, Stokowy T, Jaksik R, Szoltysek K, Handschuh L, Podkowinski J, Widlak W, Kimmel M, Widlak P
    Academic press:
    Molecular Genetics and Genomics (rok: 2015, tom: 290(5), strony: 1979-1990), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00438-015-1055-1 - link to the publication
  21. Development of a population of cancer cells: Observation and modeling by a Mixed Spatial Evolutionary Games approach
    Authors:
    A. Świerniak, M. Krzeslak, S. Student, J. Rzeszowska-Wolny
    Academic press:
    Journal of Theoretical Biology (rok: 2016, tom: 405, strony: 94-103), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jtbi.2016.05.027 - link to the publication
  22. Dynamic cross talk model of the epithelial innate immune response to double-stranded rna stimulation: coordinated dynamics emerging from cell-level noise
    Authors:
    R. Bertolusso, B. Tian, Y. Zhao, L. Vergara, A. Sabree, M. Iwanaszko, T. Lipniacki, A.R Brasier, M. Kimmel
    Academic press:
    PLOS One (rok: 2014, tom: 9(4), strony: 45312), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0093396 - link to the publication
  23. Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis
    Authors:
    Li B, Sierra A, Deudero J, Semerci F, Laitman A, Kimmel M, Maletic-Savatic M
    Academic press:
    BMC Systems Biology (rok: 2017, tom: 11(Suppl 5), strony: 90), Wydawca: Biomed Central
    Status:
    Published
    DOI:
    10.1186/s12918-017-0468-3 - link to the publication
  24. NF-κB and IRF pathways: cross-regulation on target genes promoter level.
    Authors:
    Iwanaszko M, Kimmel M
    Academic press:
    BMC Genomics (rok: 2015, tom: 16, strony: 307), Wydawca: Biomed Central
    Status:
    Published
    DOI:
    10.1186/s12864-015-1511-7 - link to the publication
  25. Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude
    Authors:
    Joanna Jaruszewicz, Marek Kimmel, Tomasz Lipniacki
    Academic press:
    Physical Review E (rok: 2014, tom: 89 (2), strony: 22710), Wydawca: American Physical Society
    Status:
    Published
    DOI:
    10.1103/PhysRevE.89.022710 - link to the publication
  26. Detection of DNA replication origins based on somatic mutation patterns
    Authors:
    R. Jaksik, M. Kimmel
    Academic press:
    Genome Research (rok: 2017, tom: brak, strony: 45314), Wydawca: COLD SPRING HARBOR LAB PRESS
    Status:
    Submitted
    DOI:
    brak - link to the publication
  1. Chaos versus randomness in cell cycle dynamics: correlation dimension analysis
    Authors:
    M. Dołbniak, M. Kimmel
    Conference:
    XXII Krajowa Konferencja Zastosowań Matematyki w Biologii i Medycynie (rok: 2016, ), Wydawca: Politechnika Świętokrzyska
    Data:
    konferencja 5-9.09.2016
    Status:
    Published
  2. Deterministic modeling of stochastic gene transcription processes
    Authors:
    Jarosław Śmieja
    Conference:
    IASTED International Conference Modelling, Identification and Control (MIC 2014) (rok: 2014, ), Wydawca: ACTA Press
    Data:
    konferencja 17-19.02.2014
    Status:
    Published
  3. Distribution of PRC1 protein in a cell population originated by a single ancestor
    Authors:
    Marzena Dołbniak, Jarosław Śmieja
    Conference:
    Krajowa Konferencja Zastosowań Matematyki w Biologii i Medycynie (rok: 2013, ), Wydawca: Gdański Uniwersytet Medyczny
    Data:
    konferencja 16 – 20.09.2013
    Status:
    Published
  4. Experimental Data In Modeling Of Intracellular Processes
    Authors:
    Jarosław Śmieja, Marzena Dołbniak
    Conference:
    34th IASTED International Conference on Modelling, Identification and Control (rok: 2015, ), Wydawca: ACTA Press
    Data:
    konferencja 16-17.02.2015
    Status:
    Published
  5. Finite absorbing Markov chain as a model of small ligand binding process
    Authors:
    Marcin Pacholczyk, Damian Borys, Marek Kimmel
    Conference:
    International Work-Conference on Bioinformatics and Biomedical Engineering (rok: 2013, ), Wydawca: IWBBIO 2013. Proceedings
    Data:
    konferencja 18-20 March
    Status:
    Published
  6. Control properties of two- and three-compartmental models of combined anticancer therapy
    Authors:
    Andrzej Świerniak, Marzena Dołbniak
    Conference:
    IASTED International Conference Modelling, Identification and Control (rok: 2014, ), Wydawca: ACTA Press
    Data:
    konferencja 17-19.02.2014
    Status:
    Published
  7. Four phenotype model of interaction between tumour cells
    Authors:
    Andrzej Świerniak, Michał Krześlak, Jarosław Śmieja
    Conference:
    IASTED International Conference Biomedical Engineering (rok: 2013, ), Wydawca: ACTA Press
    Data:
    konferencja 13-15.02.2013
    Status:
    Published
  8. Application of the stochastic Moran Model of population genetics to understanding the timing of a driver mutation in Myelodysplastic Syndrome (MDS)
    Authors:
    Tomasz Wojdyła, Taly Glaubach, Steh J. Corey, Marek Kimmel
    Conference:
    19th World Congress The International Federation of Automatic Control (rok: 2014, ), Wydawca: International Federation of Automatic Control
    Data:
    konferencja 24-29.02.2014
    Status:
    Published
  9. Development of Multi-Null-Hypotheses Method for Detection of Selective Forces at Molecular Level in Evolution of Human Genes involved in DNA-Repair Mechanism Impaired in Cancer Progression
    Authors:
    Krzysztof Cyran, Marek Kimmel
    Conference:
    19th World Congress The International Federation of Automatic Control (rok: 2014, ), Wydawca: International Federation of Automatic Control
    Data:
    konferencja 24-29.08.2014
    Status:
    Published
  10. ADFIT - narzędzie do estymacji parametrów modeli matematycznych przy użyciu sprzężonej analizy wrażliwości i środowiska Matlab
    Authors:
    Krzystof Łakomiec, Krzysztof Fujarewicz
    Conference:
    XV Jubileuszowe Sympozjum Podstawowe Problemy Energoelektroniki, Elektromechaniki i Mechatroniki PPEEm (rok: 2012, ), Wydawca: brak
    Data:
    konferencja 11-13.12.2012
    Status:
    Published
  11. Multilayer evolutionary games – a new tool for modelling cancer cell heterogeneity
    Authors:
    Swierniak A, Krzeslak M
    Conference:
    12th IASTED International Conference, Biomedical Engineering (BioMed 2016) (rok: 2016, ), Wydawca: IASTED
    Data:
    konferencja 15-16.02.2016
    Status:
    Published
  12. Changes in heat shock duration infuence regulatory schemes of HSF1 activity
    Authors:
    Marta Iwanaszko, Patryk Janus, Tomasz Stokowy, Piotr Widłak, Marek Kimmel
    Conference:
    IWBBIO 2014: International Work-Conference on Bioinformatics and Biomedical Engineering (rok: 2014, ), Wydawca: brak
    Data:
    konferencja 7-9.04.2014
    Status:
    Published
  13. Stem cell division strategies against cancerogenesis in colon crypts. A 2D cellular automaton model.
    Authors:
    M. Dolbniak
    Conference:
    XXI Krajowa Konferencja Zastosowań Matematyki w Biologii i Medycynie (rok: 2015, ), Wydawca: Politechnika Warszawska
    Data:
    konferencja 22-26.09.2015
    Status:
    Published
  1. Detection and repair of faults in cell cycle - Is it perfect?
    Authors:
    Smieja J, Jaksik R, Swierniak A
    Book:
    Advanced Systems for Automation and Diagnostics (rok: 2015, tom: n.d., strony: 63-72), Wydawca: Pomorskie Wydawnictwo Naukowo-Techniczne PWNT
    Status:
    Published
  2. Cancer – a Story on Fault Propagation in Gene-Cellular Networks
    Authors:
    Damian Borys, Roman Jaksik, Michał Krześlak, Jarosław Śmieja, Andrzej Świerniak
    Book:
    Propagation Phenomena in Real World Networks (rok: 2015, tom: 85, strony: 225-256), Wydawca: Springer Verlag
    Status:
    Published
  3. Searching for Cancer Signatures Using Data Mining Techniques
    Authors:
    Micek M, Pacholczyk M
    Book:
    Man-Machine Interactions 5. ICMMI 2017. Advances in Intelligent Systems and Computing (rok: 2018, tom: 659, strony: 154-162), Wydawca: Springer
    Status:
    Published
  4. An Operator Semigroup in Mathematical Genetics
    Authors:
    Bobrowski A, Kimmel M
    Book:
    An Operator Semigroup in Mathematical Genetics (rok: 2015, tom: n.d., strony: 32143), Wydawca: Springer
    Status:
    Published
  5. Reporterowy system FUCCI w przyżyciowej obserwacji proliferacji komórek nowotworowych
    Authors:
    P. Bil, S. Kała, K. Gajda, M. Skonieczna, J. Rzeszowska-Wolny
    Book:
    Automatyzacja Procesów Dyskretnych Teoria i Zastosowania (rok: 2016, tom: II, strony: 45487), Wydawca: Wydawnictwo Pracowni Komputerowej Jacka Skalmierskiego
    Status:
    Published
  6. System Engineering Approach to Planning Anticancer Therapies
    Authors:
    Swierniak A, Kimmel M, Smieja J, Puszynski K, Psiuk-Maksymowicz K
    Book:
    System Engineering Approach to Planning Anticancer Therapies (rok: 2016, tom: nie dotyczy, strony: 1-235), Wydawca: Springer
    Status:
    Published
    DOI:
    link to the publication
  7. Modelowanie matematyczne jako narzędzie planowania terapii antynowotworowych
    Authors:
    Andrzej Świerniak, Marek Kimmel, Jarosław Śmieja
    Book:
    Biocybernetyka i Inżynieria Biomedyczna - Podstawy i Zastosowania (rok: 2014, tom: 10 Bioinf., strony: 177-211), Wydawca: Akademicka Oficyna Wykładnicza Exit
    Status:
    Published

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