Models

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

NF-κB network

• Korwek Z, Tudelska K, Nałęcz-Jawecki P, Czerkies M, Prus W, Markiewicz J, Kochańczyk M, Lipniacki T. Importins promote high-frequency NF-κB oscillations increasing information channel capacity, Biol Direct 11:61 (2016) CrossRef | PDF Scheme-PDF Supp-ModelInfo-PDF Supp-ModelCode-BNGL Supp-Figs Supp-Images

• Pękalski J, Zuk PJ, Kochańczyk M, Junkin M, Kellog R, Tay S, Lipniacki T. Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis, PLOS One 8(11):e78887 (2013) PubMed CrossRef | PDF Supp-PDF Code-Matlab Code-BioNetGen Code-MatCont

• 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

• Lipniacki T, Puszyński K, Paszek P, Brasier AR, Kimmel M. Single TNFα trimers mediating NF-κB activation: Stochastic robustness of NF-κB signaling, BMC Bioinformatics 8:376 (2007) PubMed CrossRef | PDF PDF-supp1 PDF-supp2 PDF-supp3 Code Code-supp

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, Hat B, Faeder JR, Hlavacek WS. Stochastic effects and bistability in T cell receptor signaling, J Theor Biol 254(1):110-122 (2008) PubMed CrossRef | PDF-ms Code-ODE Code-Gillespie 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

• Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błońska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T. Relaxation oscillations and hierarchy of feedbacks in MAPK signaling, Sci Rep 6:38244 (2017) PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNG SuppCode-MatCont SuppCode-BNG-noisy SuppCode-Comsol SuppMovie

• 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

Autophagy

• 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