Institute of Fundamental Technological Research

Polish Academy of Sciences

NEW!

Mechanistic aspects and spatial effects in cell signalling

within Team Program financed by Fundation for Polish Science

Positions available!

Ph.D Students:

Paweł Paszek, Ph.D (2006)

Modelling stochasticity in gene regulation

Current research:

• Stochastic modeling of immune response and gene expression

• Anisotropic Superfluid Turbulence

Stochastic modeling of immune response and gene expression

Left: Two feedback loop stochastic model, and Right: NF-κB and IκB co-oscillations of single cells (red lines) and of population average (blue line), full story: Biophys. J. 2006 and pdf presentation

Protein-Protein probability distribution functions in repressor-repressor system, full story: J. Theor. Biol. 2006

Anisotropic Superfluid Turbulence

Superfluid vortex configuration during formation of plane Cuette flow, full story: Eur. J. Mech, B-Fluids 2006

Programs for Single TNFalpha trimers mediating NF-kappaB activation: Stochastic robustness of NF-kappaB signaling, BMC Bioinformatics 8: 376 (2007): programs, programsSupp

Programs for Stochasticity in early immune response, Biophysical Journal 90: 725-742 (2006): programs

Programs for Oscillations and bistability in the stochastic model of p53, J. Theor. Biol. doi:10.1016/j.jtbi.2008.05.039 programs.ZIP

Programs for Stochastic effects and bistability in T cell receptor signaling, J. Theor. Biol. doi:10.1016/j.jtbi.2008.05.001 (2008) Gillespie_Code.zip ODE_Code.zip BioNetBen_Code

for BioNetGen software go to http://bionetgen.org

Publications:

1. B. Hat, K. Puszynski, T. Lipniacki, Exploring mechanisms of oscillations in p53 and NF-kappa B systems, IET Sys. Biol. 2009 pdf

2. K. Puszynski, R. Bertolusso, T. Lipniacki Crosstalk between p53 and NF-κB systems: pro- and anti-apoptotic functions of NF-κB IET Sys. Biol. 2009 pdf

3. B. Kazmierczak, T. Lipniacki, Regulation of kinase activity by diffusion and feedback J. Theor. Biol. (2009), doi:10.1016/j.jtbi.2009.03.016 pdf

4. K.Puszynski, B.Hat, T.Lipniacki Oscillations and bistability in the stochastic model of p53, J. Theor. Biol. (2008) doi:10.1016/j.jtbi.2008.05.039 pdf , programs.ZIP

5. T. Lipniacki, B. Hat, J. R. Faeder, W. S. Hlavacek, Stochastic effects and bistability in T cell receptor signaling, J. Theor. Biol. doi:10.1016/j.jtbi.2008.05.001 (2008) pdf , Gillespie_Code.zip ODE_Code.zip BioNetGen_Code

6. T. Lipniacki, K. Puszynski, P. Paszek, A. R. Brasier, M. Kimmel, Single TNFalpha trimers mediating NF-kappaB activation: Stochastic robustness of NF-kappaB signaling, BMC Bioinformatics 8: 376 (2007)  pdf , supp1 ,  supp2  , supp3 ,  programs , programsSupp

7. T. Lipniacki, M. Kimmel, Deterministic and stochastic models of NF-κB pathway, Cardiovascular Toxicology; 7:215-234, (2007) pdf.

8. Bobrowski, T. Lipniacki, K. Pichór, R. Rudnicki, Asymptotic behavior of distributions of mRNA and protein levels in a model of stochastic gene expression, Journal of Mathematical Analysis and Applications  333, 753-769 (2007), pdf.

9. B. Hat, P. Paszek, M. Kimmel, K. Piechór, T. Lipniacki, How the number of alleles influences gene expression, J. Stat. Phys. 128: 511-533 (2007) DOI: 10.1007/s10955-006-9218-4 pdf.

10. K. Fujarewicz, M. Kimmel, T. Lipniacki A. Świerniak, Adjoint systems for models of cell
    signalling pathways and their application to parameter fitting, IEEE/ACM Transactions on
    Computational Biology and Bioinformatics 4, 322-335 (2007), pdf

11. T. Lipniacki, Dynamics of superfluid He: Two-scale approach, European Journal of Mechanics, B/Fluids, 25: 435-458 (2006), pdf.

12. T. Lipniacki, P. Paszek, A. R. Brasier, B. Luxon, M. Kimmel, Stochasticity in early immune response, Biophysical Journal 90: 725-742 (2006), pdf, programs

13. T. Lipniacki, P. Paszek, A. Marciniak-Czochra, A. R. Brasier, M. Kimmel, Transcriptional stochasticity in gene expression, J. Theor. Biol.  238: 348-367 (2006), pdf.

14. P. Paszek, T. Lipniacki, A. R. Brasier, B. Tian, D. E. Nowak, M. Kimmel, Stochastic effects of multiple regulators on expression profiles in eukaryotes, J. Theor. Biol.  233: 423-433 (2005), pdf.

15. T. Lipniacki, P. Paszek, A. R. Brasier, B. Luxon, M. Kimmel, Mathematical model of NF-κB regulatory module, J. Theor. Biol. 228: 195-215, (2004), pdf.

16. T. Lipniacki, Shape-preserving solutions for quantum vortex motion under localized induction approximation, Physics of Fluids 15 (6): 1381-1395, (2003), pdf.

17. T. Lipniacki, Quasi-static solution for quantum vortex motion under the localized induction approximation, J. Fluid Mech. 477: 321-337, (2002), pdf.

18. B. Kaźmierczak, T. Lipniacki, Homoclinic solutions in mechanical systems with small dissipation. Application to DNA dynamics,  J. Math. Biol. 44: 309-329 (2002), pdf

19. T. Lipniacki, Evolution of line-length density and anisotropy of quantum tangle, Phys. Rev B 64: 214516-1-9 (2001), pdf

20. T. Lipniacki, Thermodynamics of local DNA openings, Phys. Rev. E 64: 051919-1-5 (2001), pdf.

21. T. Lipniacki, On quantum turbulence in superfluid Helium, Arch. Mech. 53 (1): 23-43 (2001).

22. T. Lipniacki, Torsional travelling waves in DNA, J. Non-linear Math. Phys. 8: 188-194 (2001).

23. T. Lipniacki, Statics of rigid units chain, International Journal of Bifurcation and Chaos 11, (3): 845-854 (2001), pdf

24. T. Lipniacki, Evolution of quantum vortices following reconnection, European Journal of
    Mechanics, B/Fluids 19: 361-378 (2000), pdf

25. T. Lipniacki, Chemically driven traveling waves in DNA, Phys. Rev. E, 60: 7253-7561 (1999), pdf.

26. T. Lipniacki, Non linear mechanical model of DNA dynamics, Nuovo Cimento D 20 (6): 831-843 (1998), pdf.

27. T. Lipniacki, Dynamics of quantum vortices in superfluid He, Arch. Mech. 50 (3): 439-454 (1998).

28. T. Lipniacki, Dynamics of superfluid Helium - Limits of the Vinen model, Arch. Mech. 49 (4): 615-633 (1997).

29. T. Lipniacki, Can the system of discrete vortices imitate boundary layer, Arch. Mech. 49 (1): 103-109 (1997).