Models: Difference between revisions
From Laboratory of Modeling in Biology and Medicine
mNo edit summary |
mNo edit summary |
||
| Line 11: | Line 11: | ||
* <span class="pmbm">Lipniacki T</span>, <span class="pmbm">Puszyński K</span>, <span class="nopmbm">Paszek P</span>, <span class="nopmbm">Brasier AR</span>, <span class="nopmbm">Kimmel M</span>. '''Single TNFα trimers mediating NF-κB activation: Stochastic robustness of NF-κB signaling''', ''BMC Bioinformatics'' <u>8</u>:376 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17925009 PubMed] [http://dx.doi.org/10.1186/1471-2105-8-376 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Lipniacki-2007-BMCBioinformatics.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-Supp1.pdf PDF-supp1] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-Supp2.pdf PDF-supp2] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-Supp3.pdf PDF-supp3] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-SourceCode.zip Code] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-SourceCodeSupp.zip Code-supp] | * <span class="pmbm">Lipniacki T</span>, <span class="pmbm">Puszyński K</span>, <span class="nopmbm">Paszek P</span>, <span class="nopmbm">Brasier AR</span>, <span class="nopmbm">Kimmel M</span>. '''Single TNFα trimers mediating NF-κB activation: Stochastic robustness of NF-κB signaling''', ''BMC Bioinformatics'' <u>8</u>:376 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17925009 PubMed] [http://dx.doi.org/10.1186/1471-2105-8-376 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Lipniacki-2007-BMCBioinformatics.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-Supp1.pdf PDF-supp1] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-Supp2.pdf PDF-supp2] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-Supp3.pdf PDF-supp3] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-SourceCode.zip Code] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2007-BMCBioinformatics-SourceCodeSupp.zip Code-supp] | ||
===Early immune response: TCR, BCR=== | ===Early immune response: TCR, BCR=== | ||
| Line 19: | Line 20: | ||
* <span class="pmbm">Lipniacki T</span>, <span class="nopmbm">Paszek P</span>, <span class="nopmbm">Brasier AR</span>, <span class="nopmbm">Luxon B</span>, <span class="nopmbm">Kimmel M</span>. '''Stochastic regulation in early immune response''', ''Biophys J'' <u>90</u>:725-742 (2006) [http://www.ncbi.nlm.nih.gov/pubmed/16284261 PubMed] [http://dx.doi.org/10.1529/biophysj.104.056754 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Lipniacki-2006-BiophysJ.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2006-BiophysJ-SourceCode.zip Code] | * <span class="pmbm">Lipniacki T</span>, <span class="nopmbm">Paszek P</span>, <span class="nopmbm">Brasier AR</span>, <span class="nopmbm">Luxon B</span>, <span class="nopmbm">Kimmel M</span>. '''Stochastic regulation in early immune response''', ''Biophys J'' <u>90</u>:725-742 (2006) [http://www.ncbi.nlm.nih.gov/pubmed/16284261 PubMed] [http://dx.doi.org/10.1529/biophysj.104.056754 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Lipniacki-2006-BiophysJ.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Lipniacki-2006-BiophysJ-SourceCode.zip Code] | ||
===p53 network=== | ===p53 network=== | ||
| Line 29: | Line 31: | ||
* <span class="pmbm">Puszyński K</span>, <span class="pmbm">Hat B</span>, <span class="pmbm">Lipniacki T</span>. '''Oscillations and bistability in the stochastic model of p53''', ''J Theor Biol'' <u>254</u>(2):452-465 (2008) [http://www.ncbi.nlm.nih.gov/pubmed/18577387 PubMed] [http://dx.doi.org/10.1016/j.jtbi.2008.05.039 CrossRef] | [http://pmbm.ippt.pan.pl/publications/supplementary/Puszynski-2008-JTheorBiol-SourceCode.zip Code] | * <span class="pmbm">Puszyński K</span>, <span class="pmbm">Hat B</span>, <span class="pmbm">Lipniacki T</span>. '''Oscillations and bistability in the stochastic model of p53''', ''J Theor Biol'' <u>254</u>(2):452-465 (2008) [http://www.ncbi.nlm.nih.gov/pubmed/18577387 PubMed] [http://dx.doi.org/10.1016/j.jtbi.2008.05.039 CrossRef] | [http://pmbm.ippt.pan.pl/publications/supplementary/Puszynski-2008-JTheorBiol-SourceCode.zip Code] | ||
===MAPK signaling=== | ===MAPK signaling=== | ||
| Line 37: | Line 40: | ||
* <span class="pmbm">Kocieniewski P</span>, <span class="pmbm">Lipniacki T</span>. '''MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response''', ''Phys Biol'' <u>10</u>(3):035006 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23735655 PubMed] [http://dx.doi.org/10.1088/1478-3975/10/3/035006 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Kocieniewski-2013-PhysBiol-MS.pdf PDF-ms] [http://pmbm.ippt.pan.pl/publications/supplementary/Kocieniewski-2013-PhysBiol-SourceCode.zip Code-BioNetGen] | * <span class="pmbm">Kocieniewski P</span>, <span class="pmbm">Lipniacki T</span>. '''MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response''', ''Phys Biol'' <u>10</u>(3):035006 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23735655 PubMed] [http://dx.doi.org/10.1088/1478-3975/10/3/035006 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Kocieniewski-2013-PhysBiol-MS.pdf PDF-ms] [http://pmbm.ippt.pan.pl/publications/supplementary/Kocieniewski-2013-PhysBiol-SourceCode.zip Code-BioNetGen] | ||
===Autophagy=== | ===Autophagy=== | ||
| Line 43: | Line 47: | ||
<br /> | <br /> | ||
<br /> | <br /> | ||
Revision as of 16:21, 16 June 2017
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
