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Items: 49

1.

A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin.

Zalewska-Piątek B, Olszewski M, Lipniacki T, Błoński S, Wieczór M, Bruździak P, Skwarska A, Nowicki B, Nowicki S, Piątek R.

PLoS Pathog. 2020 Jan 9;16(1):e1008247. doi: 10.1371/journal.ppat.1008247. eCollection 2020 Jan.

2.

Limits to the rate of information transmission through the MAPK pathway.

Grabowski F, Czyż P, Kochańczyk M, Lipniacki T.

J R Soc Interface. 2019 Mar 29;16(152):20180792. doi: 10.1098/rsif.2018.0792.

3.

Sampling rare events in stochastic reaction-diffusion systems within trajectory looping.

Zuk PJ, Kochańczyk M, Lipniacki T.

Phys Rev E. 2018 Aug;98(2-1):022401. doi: 10.1103/PhysRevE.98.022401.

PMID:
30253540
4.

Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways.

Czerkies M, Korwek Z, Prus W, Kochańczyk M, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T.

Nat Commun. 2018 Feb 5;9(1):493. doi: 10.1038/s41467-017-02640-8.

5.

Polarization of concave domains by traveling wave pinning.

Bialecki S, Kazmierczak B, Lipniacki T.

PLoS One. 2017 Dec 28;12(12):e0190372. doi: 10.1371/journal.pone.0190372. eCollection 2017.

6.

Genetic toggle switch controlled by bacterial growth rate.

Jaruszewicz-Błońska J, Lipniacki T.

BMC Syst Biol. 2017 Dec 2;11(1):117. doi: 10.1186/s12918-017-0483-4.

7.

Information processing in the NF-κB pathway.

Tudelska K, Markiewicz J, Kochańczyk M, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T.

Sci Rep. 2017 Nov 21;7(1):15926. doi: 10.1038/s41598-017-16166-y.

8.

SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

Kochanczyk M, Hlavacek WS, Lipniacki T.

Bioinformatics. 2017 Nov 15;33(22):3667-3669. doi: 10.1093/bioinformatics/btx456.

9.

Computation and measurement of cell decision making errors using single cell data.

Habibi I, Cheong R, Lipniacki T, Levchenko A, Emamian ES, Abdi A.

PLoS Comput Biol. 2017 Apr 5;13(4):e1005436. doi: 10.1371/journal.pcbi.1005436. eCollection 2017 Apr.

10.

RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα.

Varga A, Ehrenreiter K, Aschenbrenner B, Kocieniewski P, Kochanczyk M, Lipniacki T, Baccarini M.

Sci Signal. 2017 Mar 7;10(469). pii: eaai8482. doi: 10.1126/scisignal.aai8482.

PMID:
28270557
11.

Relaxation oscillations and hierarchy of feedbacks in MAPK signaling.

Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błońska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T.

Sci Rep. 2017 Jan 3;7:38244. doi: 10.1038/srep38244.

12.

Importins promote high-frequency NF-κB oscillations increasing information channel capacity.

Korwek Z, Tudelska K, Nałęcz-Jawecki P, Czerkies M, Prus W, Markiewicz J, Kochańczyk M, Lipniacki T.

Biol Direct. 2016 Nov 11;11(1):61.

13.

Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System.

Hat B, Kochańczyk M, Bogdał MN, Lipniacki T.

PLoS Comput Biol. 2016 Feb 29;12(2):e1004787. doi: 10.1371/journal.pcbi.1004787. eCollection 2016 Feb.

14.

Effective reaction rates for diffusion-limited reaction cycles.

Nałęcz-Jawecki P, Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T.

J Chem Phys. 2015 Dec 7;143(21):215102. doi: 10.1063/1.4936131.

PMID:
26646890
15.

Digital signaling decouples activation probability and population heterogeneity.

Kellogg RA, Tian C, Lipniacki T, Quake SR, Tay S.

Elife. 2015 Oct 21;4:e08931. doi: 10.7554/eLife.08931.

16.

Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics.

Nienałtowski K, Włodarczyk M, Lipniacki T, Komorowski M.

BMC Syst Biol. 2015 Sep 29;9:65. doi: 10.1186/s12918-015-0205-8.

17.

Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles.

Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Feb;91(2):022702. Epub 2015 Feb 3.

PMID:
25768526
18.

Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1.

Szymańska P, Martin KR, MacKeigan JP, Hlavacek WS, Lipniacki T.

PLoS One. 2015 Mar 11;10(3):e0116550. doi: 10.1371/journal.pone.0116550. eCollection 2015.

19.

Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude.

Jaruszewicz J, Kimmel M, Lipniacki T.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Feb;89(2):022710. Epub 2014 Feb 11.

PMID:
25353512
20.

Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise.

Bertolusso R, Tian B, Zhao Y, Vergara L, Sabree A, Iwanaszko M, Lipniacki T, Brasier AR, Kimmel M.

PLoS One. 2014 Apr 7;9(4):e93396. doi: 10.1371/journal.pone.0093396. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e103019.

21.

Spontaneous NF-κB activation by autocrine TNFα signaling: a computational analysis.

Pękalski J, Zuk PJ, Kochańczyk M, Junkin M, Kellogg R, Tay S, Lipniacki T.

PLoS One. 2013 Nov 11;8(11):e78887. doi: 10.1371/journal.pone.0078887. eCollection 2013.

22.

Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate.

Bogdał MN, Hat B, Kochańczyk M, Lipniacki T.

BMC Syst Biol. 2013 Jul 24;7:67. doi: 10.1186/1752-0509-7-67.

23.

Toggle switch: noise determines the winning gene.

Jaruszewicz J, Lipniacki T.

Phys Biol. 2013 Jun;10(3):035007. doi: 10.1088/1478-3975/10/3/035007. Epub 2013 Jun 4.

24.

MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response.

Kocieniewski P, Lipniacki T.

Phys Biol. 2013 Jun;10(3):035006. doi: 10.1088/1478-3975/10/3/035006. Epub 2013 Jun 4.

PMID:
23735655
25.

Stochastic transitions in a bistable reaction system on the membrane.

Kochanczyk M, Jaruszewicz J, Lipniacki T.

J R Soc Interface. 2013 May 1;10(84):20130151. doi: 10.1098/rsif.2013.0151. Print 2013 Jul 6.

26.

Type of noise defines global attractors in bistable molecular regulatory systems.

Jaruszewicz J, Zuk PJ, Lipniacki T.

J Theor Biol. 2013 Jan 21;317:140-51. doi: 10.1016/j.jtbi.2012.10.004. Epub 2012 Oct 11.

27.

Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth-death process.

Zuk PJ, Kochańczyk M, Jaruszewicz J, Bednorz W, Lipniacki T.

Phys Biol. 2012 Oct;9(5):055002. doi: 10.1088/1478-3975/9/5/055002. Epub 2012 Sep 25.

PMID:
23011381
28.

A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn.

Barua D, Hlavacek WS, Lipniacki T.

J Immunol. 2012 Jul 15;189(2):646-58. doi: 10.4049/jimmunol.1102003. Epub 2012 Jun 18.

29.

The interplay of double phosphorylation and scaffolding in MAPK pathways.

Kocieniewski P, Faeder JR, Lipniacki T.

J Theor Biol. 2012 Feb 21;295:116-24. doi: 10.1016/j.jtbi.2011.11.014. Epub 2011 Nov 25.

30.

B cell activation triggered by the formation of the small receptor cluster: a computational study.

Hat B, Kazmierczak B, Lipniacki T.

PLoS Comput Biol. 2011 Oct;7(10):e1002197. doi: 10.1371/journal.pcbi.1002197. Epub 2011 Oct 6.

31.

Exact solutions to a spatially extended model of kinase-receptor interaction.

Szopa P, Lipniacki T, Kazmierczak B.

Phys Biol. 2011 Oct;8(5):055005. doi: 10.1088/1478-3975/8/5/055005. Epub 2011 Aug 10.

PMID:
21832804
32.

Guidelines for visualizing and annotating rule-based models.

Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS.

Mol Biosyst. 2011 Oct;7(10):2779-95. doi: 10.1039/c1mb05077j. Epub 2011 Jun 7.

33.

Spatial gradients in kinase cascade regulation.

Kazmierczak B, Lipniacki T.

IET Syst Biol. 2010 Nov;4(6):348-55. doi: 10.1049/iet-syb.2010.0002.

PMID:
21073234
34.

Crosstalk between p53 and nuclear factor-B systems: pro- and anti-apoptotic functions of NF-B.

Puszynski K, Bertolusso R, Lipniacki T.

IET Syst Biol. 2009 Sep;3(5):356-67. doi: 10.1049/iet-syb.2008.0172.

PMID:
21028926
35.

Exploring mechanisms of oscillations in p53 and nuclear factor-B systems.

Hat B, Puszynski K, Lipniacki T.

IET Syst Biol. 2009 Sep;3(5):342-55. doi: 10.1049/iet-syb.2008.0156.

PMID:
21028925
36.

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.

Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW.

Nature. 2010 Jul 8;466(7303):267-71. doi: 10.1038/nature09145. Epub 2010 Jun 27.

37.

Regulation of kinase activity by diffusion and feedback.

Kazmierczak B, Lipniacki T.

J Theor Biol. 2009 Jul 21;259(2):291-6. doi: 10.1016/j.jtbi.2009.03.016. Epub 2009 Mar 21.

PMID:
19306885
38.

Oscillations and bistability in the stochastic model of p53 regulation.

Puszyński K, Hat B, Lipniacki T.

J Theor Biol. 2008 Sep 21;254(2):452-65. doi: 10.1016/j.jtbi.2008.05.039. Epub 2008 Jun 4.

PMID:
18577387
39.

Stochastic effects and bistability in T cell receptor signaling.

Lipniacki T, Hat B, Faeder JR, Hlavacek WS.

J Theor Biol. 2008 Sep 7;254(1):110-22. doi: 10.1016/j.jtbi.2008.05.001. Epub 2008 May 10.

40.

Deterministic and stochastic models of NFkappaB pathway.

Lipniacki T, Kimmel M.

Cardiovasc Toxicol. 2007;7(4):215-34. Epub 2007 Oct 18.

PMID:
17943462
41.

Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling.

Lipniacki T, Puszynski K, Paszek P, Brasier AR, Kimmel M.

BMC Bioinformatics. 2007 Oct 9;8:376.

42.

Adjoint systems for models of cell signaling pathways and their application to parameter fitting.

Fujarewicz K, Kimmel M, Lipniacki T, Swierniak A.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):322-35.

PMID:
17666754
43.

Stochastic regulation in early immune response.

Lipniacki T, Paszek P, Brasier AR, Luxon BA, Kimmel M.

Biophys J. 2006 Feb 1;90(3):725-42. Epub 2005 Nov 11.

44.

Transcriptional stochasticity in gene expression.

Lipniacki T, Paszek P, Marciniak-Czochra A, Brasier AR, Kimmel M.

J Theor Biol. 2006 Jan 21;238(2):348-67. Epub 2005 Jul 21.

PMID:
16039671
45.

Stochastic effects of multiple regulators on expression profiles in eukaryotes.

Paszek P, Lipniacki T, Brasier AR, Tian B, Nowak DE, Kimmel M.

J Theor Biol. 2005 Apr 7;233(3):423-33. Epub 2004 Dec 8.

PMID:
15652150
46.

Mathematical model of NF-kappaB regulatory module.

Lipniacki T, Paszek P, Brasier AR, Luxon B, Kimmel M.

J Theor Biol. 2004 May 21;228(2):195-215.

PMID:
15094015
47.

Homoclinic solutions in mechanical systems with small dissipation. Application to DNA dynamics.

Kazmierczak B, Lipniacki T.

J Math Biol. 2002 Apr;44(4):309-29.

PMID:
11984642
48.

Chemically driven traveling waves in DNA.

Lipniacki T.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Dec;60(6 Pt B):7253-61.

PMID:
11970669
49.

Thermodynamics of local DNA openings.

Lipniacki T.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Nov;64(5 Pt 1):051919. Epub 2001 Oct 29.

PMID:
11735980

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