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Articles featured by executable codes (implemented in Matlab and/or BioNetGen):

NF-κB network

  • Tay S, Hughey J, Lee T, Lipniacki T, Covert M, Quake S. Single-cell NF-κB dynamics reveal digital activation and analogue information processing, Nature 466:267-271 (2010) PubMed CrossRef | PDF Code

Early immune response: TCR, BCR

  • Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn, J Immunol 189:646-658 (2012) PubMed CrossRef | Code-BioNetGen
  • Lipniacki T, Paszek P, Brasier AR, Luxon B, Kimmel M. Stochastic regulation in early immune response, Biophys J 90:725-742 (2006) PubMed CrossRef | PDF Code

p53 network

  • Hat B, Kochańczyk M, Bogdał M, Lipniacki T. Feedbacks, bifurcations, and cell fate decision-making in the p53 system, PLOS Comput Biol 12(2):e1004787 (2016) PubMed CrossRef | PDF SuppText SuppFigs SuppCode
  • Bogdał MN, Hat B, Kochańczyk M, Lipniacki T. Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate, BMC Syst Biol 7:67 (2013) PubMed CrossRef | PDF Code-Matlab
  • Puszyński K, Bertolusso R, Lipniacki T. Crosstalk between p53 and NF-κB systems: pro- and anti-apoptotic functions of NF-κB, IET Syst Biol 3(5):356-367 (2009) PubMed CrossRef | PDF-ms Code
  • Puszyński K, Hat B, Lipniacki T. Oscillations and bistability in the stochastic model of p53, J Theor Biol 254(2):452-465 (2008) PubMed CrossRef | Code

MAPK signaling

  • Varga A, Ehrenreiter K, Aschenbrenner B, Kocieniewski P, Kochanczyk M, Lipniacki T, Baccarini M. RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα, Sci Signal 10(469):eaai8482 (2017) PubMed CrossRef | SuppCode-BioNetGen
  • Kocieniewski P, Lipniacki T. MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response, Phys Biol 10(3):035006 (2013) PubMed CrossRef | PDF-ms Code-BioNetGen


  • Szymańska P, Martin KR, MacKeigan JP, Hlavacek WS, Lipniacki T. Computational analysis of an autophagy/translation switch based on mutual inhibition of mTORC1 and ULK1, PLOS One 10(3):e0116550 (2015) PubMed CrossRef | PDF supp-BNGL supp-PDF