Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Efficient simulation algorithms for models of stochastic processes in computational biology and synthesis of the signaling pathways models.

2016/23/B/ST6/03455

Keywords:

computational biology signaling pathways modelling and simulation

Descriptors:

  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • ST6_12: Scientific computing, simulation and modelling tools
  • ST7_4: Micro- and nanosystems engineering

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):

dr Krzysztof Puszyński 

Number of co-investigators in the project: 6

Call: OPUS 12 - announced on 2016-09-15

Amount awarded: 895 400 PLN

Project start date (Y-m-d): 2017-08-24

Project end date (Y-m-d): 2021-08-23

Project duration:: 48 months (the same as in the proposal)

Project status: Project settled

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Equipment purchased [PL]

  1. Komputer przenośny (7 000 PLN)

Information in the final report

  • Publication in academic press/journals (10)
  • Articles in post-conference publications (3)
  • Book publications / chapters in book publications (3)
  1. Computational determination of the optimal dose of the cis-platinum to maximize the life time of patients diagnosed with cancer
    Authors:
    Emilia Kozłowska, Krzysztof Puszynski
    Academic press:
    Mathematica Applicanda (Matematyka Stosowana) (rok: 2019, tom: 47 (2), strony: 187-196), Wydawca: Polskie Towarzystwo Matematyczne
    Status:
    Published
    DOI:
    10.14708/ma.v47i2.6485 - link to the publication
  2. Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level.
    Authors:
    Kardyńska M, Paszek A, Smieja J, Spiller D, Widlak W, White MR, Paszek P, Kimmel M
    Academic press:
    Plos Computational Biology (rok: 2018, tom: 14, strony: 25), Wydawca: Plos Computational Biology
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1006130 - link to the publication
  3. Sensitivity Analysis Aimed at Finding Potential Molecular Drug Targets
    Authors:
    Jaroslaw Smieja, Małgorzata Kardyńska, Marta Pudlo
    Academic press:
    Mathematica Applicanda (Matematyka Stosowana) (rok: 2019, tom: 47 (2), strony: 197-205), Wydawca: Polskie Towarzystwo Matematyczne
    Status:
    Published
    DOI:
    10.14708/ma.v47i2.6488 - link to the publication
  4. Piece-wise linear models of biological systems - Application, analysis, and comparison with nonlinear models using the example of the p53 regulatory module
    Authors:
    Magdalena Ochab, Krzysztof Puszynski
    Academic press:
    Plos One (rok: 2020, tom: 1, strony: 20), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0243823 - link to the publication
  5. Activation of the atypical NF-κB pathway induced by ionizing radiation is not affected by a p53 status.
    Authors:
    Gracjana Zając, Marek Rusin, Barbara Łasut-Szyszka, Krzysztof Puszyński, Piotr Widłak
    Academic press:
    Acta Biochimica Polonica (rok: 2021, tom: N.A., strony: N.A.), Wydawca: Polish Biochemical Society
    Status:
    Published
    DOI:
    10.18388/abp.2020_5942 - link to the publication
  6. Application of Sensitivity Analysis for Molecular Drug Targets Searching with Regard to the NF-κB Signaling Pathway
    Authors:
    Kardyńska M, Smieja J, Puszynski K
    Academic press:
    International Journal of Pharma Medicine and Biological Sciences (rok: 2021, tom: 1, strony: 82-87), Wydawca: IJPMBS
    Status:
    Published
    DOI:
    10.2.82-87 - link to the publication
  7. Single stranded-DNA detection: the role of Wip1 in ATR-dependent pathway.
    Authors:
    Kurpas M, Jonak K, Puszynski K
    Academic press:
    Mathematica Applicanda (Matematyka Stosowana) (rok: 2018, tom: 46, strony: 10), Wydawca: Polskie Towarzystwo Matematyczne
    Status:
    Published
    DOI:
    10.14708/ma.v46i1.6375 - link to the publication
  8. Application of sensitivity analysis to discover potential molecular drug targets
    Authors:
    Malgorzata Kardynska, Jaroslaw Smieja, Pawel Paszek, Krzysztof Puszynski
    Academic press:
    European Journal of Pharmacology (rok: 2020, tom: n.d., strony: n.d.), Wydawca: Elsevier
    Status:
    Submitted
    DOI:
    brak - link to the publication
  9. Heat shock response regulates stimulus-specificity and sensitivity of the pro-inflammatory NF-κB signalling
    Authors:
    Paszek A, Kardyńska M, Begnall J, Smieja J, Spiller D, Widlak P, Kimmel M, Widlak W, Paszek P
    Academic press:
    Cell Communication and Signaling (rok: 2020, tom: 18, strony: 45312), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12964-020-00583-0 - link to the publication
  10. Petri nets and ODEs as complementary methods for comprehensive analysis on an example of the ATM–p53–NF-κB signaling pathways
    Authors:
    Gutowska K, Kogut D, Kardynska M, Formanowicz P, Smieja J, Puszynski K
    Academic press:
    Scientific Reports (rok: 2021, tom: N.A., strony: N.A.), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-022-04849-0 - link to the publication
  1. Correction of the genes expression measurements based on the probes design features.
    Authors:
    Krzysztof Puszynski ; Anna Lalik ; Roman Jaksik
    Conference:
    The 13th International Conference on Signal Processing and Communication Systems, ICSPCS'2019 (rok: 2019, ), Wydawca: IEEE
    Data:
    konferencja 43815
    Status:
    Published
  2. Influence of the Stochasticity in the Model on the Certain Drugs Pharmacodynamics
    Authors:
    Krzysztof Puszynski
    Conference:
    7th International Work-Conference, IWBBIO 2019 (rok: 2019, ), Wydawca: Springer Nature Switzerland AG 2019
    Data:
    konferencja 43593
    Status:
    Published
  3. Apoptotic Regulatory Module as Switched Control System - Analysis of Asymptotic Properties
    Authors:
    Ochab M , Swierniak Andrzej , Klamka Jerzy , Puszynski Krzysztof
    Conference:
    the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018) (rok: 2018, ), Wydawca: SCITEPRESS – Science and Technology Publications, Lda.
    Data:
    konferencja 19-21.01.2018
    Status:
    Published
  1. System with switchings as models of regulatory modules in genomic cell systems
    Authors:
    Andrzej Swierniak, Magdalena Ochab, Krzysztof Puszynski
    Book:
    Studies in Systems, Decision and Control (rok: 2020, tom: 1, strony: 29), Wydawca: Springer
    Status:
    Published
  2. Układy sterowania z przełaczeniami jako modele modułów regulacyjnych w sieciach genowo-komórkowych
    Authors:
    Andrzej Swierniak, Magdalena Ochab, Krzysztof Puszynski
    Book:
    Automatyka, robotyka i przetwarzanie informacji (rok: 2019, tom: 1, strony: 31), Wydawca: PWN
    Status:
    Published
  3. Influence of the Number of Thresholds on the Dynamics of Models with Switchings of the Biological Systems
    Authors:
    Magdalena Ochab, Krzysztof Puszynski
    Book:
    Advanced, Contemporary Control (rok: 2020, tom: 1, strony: 587-598), Wydawca: Springer, Cham
    Status:
    Published

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