Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Bioinformatics and biophysical models of NF-kappaB binding sites in DNA: genome-wide prediction of binding sites, experimental confirmation and co-evolution with the NF-kappaB family

2012/05/B/NZ2/01618

Keywords:

NF-kappaB binding sites biophysical modeling

Descriptors:

  • NZ2_7: Bioinformatics
  • NZ2_10: Biological systems analysis, modelling and simulation
  • NZ2_2: Genomics, transcriptomics, epigenomics

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

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: 9

Call: OPUS 3 - announced on 2012-03-15

Amount awarded: 716 325 PLN

Project start date (Y-m-d): 2013-03-06

Project end date (Y-m-d): 2016-09-05

Project duration:: 42 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Macierz dyskowa RAID (NAS) wraz z dyskami (15 000 PLN)
  2. Stacje robocze (2 szt.) (2 765 PLN)
  3. Sonikator.

Information in the final report

  • Publication in academic press/journals (6)
  • Articles in post-conference publications (8)
  • Book publications / chapters in book publications (3)
  1. Different Rates of DNA Replication at Early Versus Late S-phase Sections: Multiscale Modeling of Stochastic Events Related to DNA Content/EdU (5-ethynyl-20deoxyuridine) Incorporation Distributions
    Authors:
    Li B, Zhao H, Rybak P, Dobrucki JW, Darzynkiewicz Z, Kimmel M
    Academic press:
    Cytometry Part A (rok: 2014, tom: 85 (9), strony: 785-797), Wydawca: International Society for Advancement of Cytometry
    Status:
    Published
    DOI:
    10.1002/cyto.22484 - link to the publication
  2. EMQIT: A machine learning approach for energy based PWM matrix quality improvement
    Authors:
    Smolińska K, Pacholczyk M
    Academic press:
    Biology Direct (rok: 2017, tom: 0,511805555555556, strony: 45299), Wydawca: BioMed Cetral
    Status:
    Published
    DOI:
    10.1186/s13062-017-0189-y - link to the publication
  3. Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-kB signaling at the single cell level
    Authors:
    Kardyńska M, Paszek A, Śmieja J, Spiller D, Widłak W, White MR, Paszek P, Kimmel M
    Academic press:
    PLOS Computational Biology (rok: 2018, tom: 14(4): e1006130, strony: 45316), Wydawca: International Society for Computational Biology
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1006130 - link to the publication
  4. A novel mathematical model of ATM/p53/NF-κB pathways points to the importance of the DDR switch-off mechanisms
    Authors:
    Jonak K, Kurpas M, Szoltysek K, Janus P, Abramowicz A, Puszynski K
    Academic press:
    BMC Systems Biology (rok: 2016, tom: 10, strony: 75), Wydawca: Springer (Biomed Central)
    Status:
    Published
    DOI:
    10.1186/s12918-016-0293-0 - link to the publication
  5. Induction of reactive oxygen and nitrogen species at different stages of the cell cycle and after exposure of human K562 and HL60 cells to ionizing radiation
    Authors:
    K. Gajda, M. Skonieczna, A. Cieslar–Pobuda, Y. Saenko and J. Rzeszowska-Wolny,
    Academic press:
    FEBS Journal (rok: 2013, tom: 280, Suppl. s1, strony: 244), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1111/febs.12340 - link to the publication
  6. 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
  1. Changes of reactive oxygen species and nucleic acid modifications during cell cycle progression
    Authors:
    K. Gajda, M. Skonieczna, S. Student, D. Hudy, K. Biernacki, A. Krzywoń, I. Ślęzak-Prochazka, J. Rzeszowska-Wolny,
    Conference:
    48th Congress of the Polish Biochemical Society (rok: 2013, ), Wydawca: Acta Biochimica Polonica
    Data:
    konferencja 2-5.09.2013
    Status:
    Published
    DOI:
    link to the publication
  2. Induction of reactive oxygen species in normal human fibroblasts co-cultivated with irradiated melanoma cells
    Authors:
    K. Biernacki, D. Hudy, M. Skonieczna, K. Gajda, A. Krzywoń, M. Wideł, J. Rzeszowska-Wolny
    Conference:
    48th Congress of the Polish Biochemical Society (rok: 2013, ), Wydawca: Acta Biochimica Polonica
    Data:
    konferencja 2-5.09.2013
    Status:
    Published
    DOI:
    link to the publication
  3. Nitric oxide in control and irradiated K562 cells
    Authors:
    M. Skonieczna, A. Cieślar-Pobuda, M. Ochab, R. Buldak, J. Rzeszowska-Wolny,
    Conference:
    48th Congress of the Polish Biochemical Society (rok: 2013, ), Wydawca: Acta Biochimica Polonica
    Data:
    konferencja 2-5.09.2013
    Status:
    Published
    DOI:
    link to the publication
  4. Computational approach for modelinga and testing NF-kappaB binding sites
    Authors:
    Pacholczyk M, Smolinska K, Iwanaszko M, Kimmel M
    Conference:
    IWBBIO 2014:International Work-Conference on Bioinformatics and Biomedical Engineering (rok: 2014, ), Wydawca: brak
    Data:
    konferencja 7-9.04.2014
    Status:
    Published
  5. Crosstalk between stress-induced NF-κB, p53 and HSF1 signaling pathways – review.
    Authors:
    Widłak P, Gramatyka M, Kimmel M
    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
  6. In Silico Analysis of Interactions Between NFkB and HSF Pathways
    Authors:
    Smieja J, Kardynska M, Naumowicz A, Janus P, Widlak P, Kimmel M
    Conference:
    6th International Conference on Bioinformatics Models, Methods and Algorithms (rok: 2015, ), Wydawca: SCITEPRESS – Science and Technology Publications
    Data:
    konferencja 12-15.01.2015
    Status:
    Published
  7. Sloppy/Stiff Parameters Rankings in Sensitivity Analysis of Signaling Pathways
    Authors:
    Kardynska M, Smieja J, Naumowicz A, Janus P, Widlak P, Kimmel M
    Conference:
    9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) (rok: 2016, ), Wydawca: SCITEPRESS – Science and Technology Publications
    Data:
    konferencja 21-23.02.2016
    Status:
    Published
  8. Improved computational technique for modeling and testing transcription factor binding sites
    Authors:
    Pacholczyk M, Smolińska K, Kimmel M
    Conference:
    Recent Researches in Applied Informatics (rok: 2015, ), Wydawca: WSEAS Press
    Data:
    konferencja 27-29.06.2015
    Status:
    Published
  1. Uniwersalny kalibrator dla potrzeb estymacji ilości molekuł transkryptu
    Authors:
    Biernacki K, Hudy D, Jaksik R, Skonieczna M
    Book:
    Automatyzacja procesów dyskretnych. Teoria i zastosowania (rok: 2014, tom: II, strony: 41-49), Wydawca: Wydawnictwo Pracowni Komputerowej Jacka Skalmierskiego
    Status:
    Published
  2. Activation and inactiwation of DNA repair genes after irradiation
    Authors:
    Skonieczna M, Bensz W, Student S, Biernacki K, Widel M
    Book:
    Automatyzacja procesów dyskretnych. Teoria i zastosowania (rok: 2014, tom: II, strony: 207-215), Wydawca: Wydawnictwo Pracowni Komputerowej Jacka Skalmierskiego
    Status:
    Published
  3. Modeling protein-ligand interaction with finite absorbing Markov chain
    Authors:
    Marcin Pacholczyk, Damian Borys, Marek Kimmel
    Book:
    Computational Electrostatics for Biological Applications (rok: 2015, tom: nie dotyczy, strony: 297-306), Wydawca: Springer
    Status:
    Published

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