Tomasz
Lipniacki, Ph.D
head of
Division of Modelling in Biology and Medicine
Institute of Fundamental Technological Research
Warsaw, Poland.
Email: tlipnia@ippt.gov.pl or tomek@rice.edu
Ph.D Students:
Beata
Hat Gene copy number and
its role in regulatory pathways
Krzysztof
Puszyński Deterministic
and stochastic models of regulatory pathways related to apoptosis
Paweł Paszek, Ph.D (2006) Modelling stochasticity in gene regulation
CURRENT RESEARCH
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
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
PUBLICATIONS
K.Puszynski, B.Hat, T.Lipniacki Oscillations and bistability in the stochastic model of p53, J. Theor. Biol. doi:10.1016/j.jtbi.2008.05.039 pdf , programs.ZIP
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
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
T. Lipniacki, M. Kimmel, Deterministic and stochastic models of NF-κB pathway, Cardiovascular Toxicology; 7:215-234, (2007) pdf.
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.
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.
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
T. Lipniacki, Dynamics of superfluid He: Two-scale approach, European Journal of Mechanics, B/Fluids, 25: 435-458 (2006), pdf.
T. Lipniacki, P. Paszek, A. R. Brasier, B. Luxon, M. Kimmel, Stochasticity in early immune response, Biophysical Journal 90: 725-742 (2006), pdf, programs
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.
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.
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.
T. Lipniacki, Shape-preserving solutions for quantum vortex motion under localized induction approximation, Physics of Fluids 15 (6): 1381-1395, (2003), pdf.
T. Lipniacki, Quasi-static solution for quantum vortex motion under the localized induction approximation, J. Fluid Mech. 477: 321-337, (2002), pdf.
B. Kaźmierczak, T. Lipniacki, Homoclinic solutions in mechanical systems with small dissipation. Application to DNA dynamics, J. Math. Biol. 44: 309-329 (2002), pdf
T. Lipniacki, Evolution of line-length density and anisotropy of quantum tangle, Phys. Rev B 64: 214516-1-9 (2001), pdf
T. Lipniacki, Thermodynamics of local DNA openings, Phys. Rev. E 64: 051919-1-5 (2001), pdf.
T. Lipniacki, On quantum turbulence in superfluid Helium, Arch. Mech. 53 (1): 23-43 (2001).
T. Lipniacki, Torsional travelling waves in DNA, J. Non-linear Math. Phys. 8: 188-194 (2001).
T. Lipniacki, Statics of rigid units chain, International Journal of Bifurcation and Chaos 11, (3): 845-854 (2001), pdf
T. Lipniacki, Evolution of quantum vortices
following reconnection, European Journal
of
Mechanics,
B/Fluids 19:
361-378 (2000), pdf
T. Lipniacki, Chemically driven traveling waves in DNA, Phys. Rev. E, 60: 7253-7561 (1999), pdf.
T. Lipniacki, Non linear mechanical model of DNA dynamics, Nuovo Cimento D 20 (6): 831-843 (1998), pdf.
T. Lipniacki, Dynamics of quantum vortices in superfluid He, Arch. Mech. 50 (3): 439-454 (1998).
T. Lipniacki, Dynamics of superfluid Helium - Limits of the Vinen model, Arch. Mech. 49 (4): 615-633 (1997).
T. Lipniacki, Can the system of discrete vortices imitate boundary layer, Arch. Mech. 49 (1): 103-109 (1997).