Models: Difference between revisions
From Laboratory of Modeling in Biology and Medicine
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* <span class="pmbm">Tudelska K</span>, <span class="pmbm">Markiewicz J</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Korwek Z</span>, <span class="nopmbm">Abdi A</span>, <span class="pmbm">Błoński S</span>, <span class="pmbm">Kaźmierczak B</span>, <span class="pmbm">Lipniacki T</span>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef] | [http://www.nature.com/articles/s41598-017-16166-y.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppDataset1.zip SuppCode-BNGL] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppDataset2.zip SuppCode-Py] | * <span class="pmbm">Tudelska K</span>, <span class="pmbm">Markiewicz J</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Korwek Z</span>, <span class="nopmbm">Abdi A</span>, <span class="pmbm">Błoński S</span>, <span class="pmbm">Kaźmierczak B</span>, <span class="pmbm">Lipniacki T</span>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef] | [http://www.nature.com/articles/s41598-017-16166-y.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppDataset1.zip SuppCode-BNGL] [http://pmbm.ippt.pan.pl/publications/supplementary/Tudelska-2017-SciRep-SuppDataset2.zip SuppCode-Py] | ||
* <span class="pmbm">Korwek Z</span>, <span class="pmbm">Tudelska K</span>, <span class="nopmbm">Nałęcz-Jawecki P</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Markiewicz J</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Importins promote high-frequency NF-κB oscillations increasing information channel capacity''', '' | * <span class="pmbm">Korwek Z</span>, <span class="pmbm">Tudelska K</span>, <span class="nopmbm">Nałęcz-Jawecki P</span>, <span class="pmbm">Czerkies M</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Markiewicz J</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Importins promote high-frequency NF-κB oscillations increasing information channel capacity''', ''Biology Direct'' <u>11</u>:61 (2016) [http://dx.doi.org/10.1186/s13062-016-0164-z CrossRef] | [{{SERVER}}/publications/Korwek-2016-BiolDirect.pdf PDF] [{{SERVER}}/publications/supplementary/Korwek-2016-BiolDirect-Fig1d-HiRes.pdf Scheme-PDF] [{{SERVER}}/publications/supplementary/Korwek-2016-BiolDirect-AddFile1-ModelDescription.pdf Supp-ModelInfo-PDF] [{{SERVER}}/publications/supplementary/Korwek-2016-BiolDirect-AddFile2-NFkBImportinsModel.bngl Supp-ModelCode-BNGL] [{{SERVER}}/publications/supplementary/Korwek-2016-BiolDirect-AddFile3-SuppFigs-S1-to-S7.pdf Supp-Figs] [{{SERVER}}/publications/supplementary/Korwek-2016-BiolDirect-AddFiles4567-SuppImages.zip Supp-Images] | ||
* <span class="pmbm">Pękalski J</span>, <span class="pmbm">Zuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="nopmbm">Junkin M</span>, <span class="nopmbm">Kellog R</span>, <span class="nopmbm">Tay S</span>, <span class="pmbm">Lipniacki T</span>. '''Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis''', ''PLOS One'' <u>8</u>(11):e78887 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/24324544 PubMed] [http://dx.doi.org/10.1371/journal.pone.0078887 CrossRef] | [http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0078887&representation=PDF PDF] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppText-S1.pdf Supp-PDF] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S1.zip Code-Matlab] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S2.zip Code-BioNetGen] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S3.zip Code-MatCont] | * <span class="pmbm">Pękalski J</span>, <span class="pmbm">Zuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="nopmbm">Junkin M</span>, <span class="nopmbm">Kellog R</span>, <span class="nopmbm">Tay S</span>, <span class="pmbm">Lipniacki T</span>. '''Spontaneous NF-κB activation by autocrine TNFα signaling: A computational analysis''', ''PLOS One'' <u>8</u>(11):e78887 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/24324544 PubMed] [http://dx.doi.org/10.1371/journal.pone.0078887 CrossRef] | [http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0078887&representation=PDF PDF] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppText-S1.pdf Supp-PDF] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S1.zip Code-Matlab] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S2.zip Code-BioNetGen] [{{SERVER}}/publications/supplementary/Pekalski-2013-PLOSOne-SuppMaterial-S3.zip Code-MatCont] | ||
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===Early immune response: TCR, BCR=== | ===Early immune response: TCR, BCR=== | ||
* <span class="nopmbm">Barua D</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn''', '' | * <span class="nopmbm">Barua D</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn''', ''Journal of Immunology'' <u>189</u>:646-658 (2012) [http://www.ncbi.nlm.nih.gov/pubmed/22711887 PubMed] [http://dx.doi.org/10.4049/jimmunol.1102003 CrossRef] | [{{SERVER}}/publications/supplementary/Barua-2012-JImmunol-SourceCode.bngl Code-BioNetGen] | ||
* <span class="pmbm">Lipniacki T</span>, <span class="pmbm">Hat B</span>, <span class="nopmbm">Faeder JR</span>, <span class="nopmbm">Hlavacek WS</span>. '''Stochastic effects and bistability in T cell receptor signaling''', '' | * <span class="pmbm">Lipniacki T</span>, <span class="pmbm">Hat B</span>, <span class="nopmbm">Faeder JR</span>, <span class="nopmbm">Hlavacek WS</span>. '''Stochastic effects and bistability in T cell receptor signaling''', ''Journal of Theoretical Biology'' <u>254</u>(1):110-122 (2008) [http://www.ncbi.nlm.nih.gov/pubmed/18556025 PubMed] [http://dx.doi.org/10.1016/j.jtbi.2008.05.001 CrossRef] | [{{SERVER}}/publications/Lipniacki-2008-JTheorBiol-MS.pdf PDF-ms] [{{SERVER}}/publications/supplementary/Lipniacki-2008-JTheorBiol-ODE.zip Code-ODE] [{{SERVER}}/publications/supplementary/Lipniacki-2008-JTheorBiol-Gillespie.zip Code-Gillespie] [{{SERVER}}/publications/supplementary/Lipniacki-2008-JTheorBiol.bngl Code-BioNetGen] | ||
* <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''', '' | * <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''', ''Biophysical Journal'' <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] | [{{SERVER}}/publications/Lipniacki-2006-BiophysJ.pdf PDF] [{{SERVER}}/publications/supplementary/Lipniacki-2006-BiophysJ-SourceCode.zip Code] | ||
===p53 network=== | ===p53 network=== | ||
* <span class="pmbm">Hat B</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Bogdał M</span>, <span class="pmbm">Lipniacki T</span>. '''Feedbacks, bifurcations, and cell fate decision-making in the p53 system''', ''PLOS | * <span class="pmbm">Hat B</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Bogdał M</span>, <span class="pmbm">Lipniacki T</span>. '''Feedbacks, bifurcations, and cell fate decision-making in the p53 system''', ''PLOS Computational Biology'' <u>12</u>(2):e1004787 (2016) [http://www.ncbi.nlm.nih.gov/pubmed/26928575 PubMed] [http://dx.doi.org/10.1371/journal.pcbi.1004787 CrossRef] | [{{SERVER}}/publications/Hat-2016-PLOSComputBiol.pdf PDF] [{{SERVER}}/publications/supplementary/Hat-2016-PLOSComputBiol-SuppText.pdf SuppText] [{{SERVER}}/publications/supplementary/Hat-2016-PLOSComputBiol-SuppFigures.zip SuppFigs] [{{SERVER}}/publications/supplementary/Hat-2016-PLOSComputBiol-SuppCode.zip SuppCode] | ||
* <span class="pmbm">Bogdał MN</span>, <span class="pmbm">Hat B</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate''', ''BMC | * <span class="pmbm">Bogdał MN</span>, <span class="pmbm">Hat B</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate''', ''BMC Systems Biology'' <u>7</u>:67 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23883471 PubMed] [http://dx.doi.org/10.1186/1752-0509-7-67 CrossRef] | [http://www.biomedcentral.com/content/pdf/1752-0509-7-67.pdf PDF] [{{SERVER}}/publications/supplementary/Bogdal-2013-BMCSystBiol-SourceCode.zip Code-Matlab] | ||
* <span class="pmbm">Puszyński K</span>, <span class="nopmbm">Bertolusso R</span>, <span class="pmbm">Lipniacki T</span>. '''Crosstalk between p53 and NF-κB systems: pro- and anti-apoptotic functions of NF-κB''', ''IET | * <span class="pmbm">Puszyński K</span>, <span class="nopmbm">Bertolusso R</span>, <span class="pmbm">Lipniacki T</span>. '''Crosstalk between p53 and NF-κB systems: pro- and anti-apoptotic functions of NF-κB''', ''IET Systems Biology'' <u>3</u>(5):356-367 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/21028926 PubMed] [http://dx.doi.org/10.1049/iet-syb.2008.0172 CrossRef] | [{{SERVER}}/publications/Puszynski-2009-IETSystBiol-MS.pdf PDF-ms] [{{SERVER}}/publications/supplementary/Puszynski-2009-IETSystBiol-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''', '' | * <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''', ''Journal of Theoretical Biology'' <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] | [{{SERVER}}/publications/supplementary/Puszynski-2008-JTheorBiol-SourceCode.zip Code] | ||
===MAPK signaling=== | ===MAPK signaling=== | ||
* <span class="nopmbm">Varga A</span>, <span class="nopmbm">Ehrenreiter K</span>, <span class="nopmbm">Aschenbrenner B</span>, <span class="pmbm">Kocieniewski P</span>, <span class="pmbm">Kochanczyk M</span>, <span class="pmbm">Lipniacki T</span>, <span class="nopmbm">Baccarini M</span>. '''RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα''', '' | * <span class="nopmbm">Varga A</span>, <span class="nopmbm">Ehrenreiter K</span>, <span class="nopmbm">Aschenbrenner B</span>, <span class="pmbm">Kocieniewski P</span>, <span class="pmbm">Kochanczyk M</span>, <span class="pmbm">Lipniacki T</span>, <span class="nopmbm">Baccarini M</span>. '''RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα''', ''Science Signaling'' <u>10</u>(469):eaai8482 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/28270557 PubMed] [http://dx.doi.org/10.1126/scisignal.aai8482 CrossRef] | [{{SERVER}}/publications/supplementary/Varga-2017-SciSignal-SuppCode.bngl SuppCode-BioNetGen] | ||
* <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Kocieniewski P</span>, <span class="nopmbm">Kozłowska E</span>, <span class="pmbm">Jaruszewicz-Błońska J</span>, <span class="nopmbm">Sparta B</span>, <span class="nopmbm">Pargett M</span>, <span class="nopmbm">Albeck JG</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''Relaxation oscillations and hierarchy of feedbacks in MAPK signaling''', '' | * <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Kocieniewski P</span>, <span class="nopmbm">Kozłowska E</span>, <span class="pmbm">Jaruszewicz-Błońska J</span>, <span class="nopmbm">Sparta B</span>, <span class="nopmbm">Pargett M</span>, <span class="nopmbm">Albeck JG</span>, <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''Relaxation oscillations and hierarchy of feedbacks in MAPK signaling''', ''Scientific Reports'' <u>6</u>:38244 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/28045041 PubMed] [http://dx.doi.org/10.1038/srep38244 CrossRef] | [http://www.nature.com/articles/srep38244.pdf PDF] [{{SERVER}}/publications/supplementary/Kochanczyk-2017-SciRep-SuppInfo.pdf SuppInfo-PDF] [{{SERVER}}/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeBionetgen-UPDATED.zip SuppCode-BNG] [{{SERVER}}/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeMatlabMatcont.zip SuppCode-MatCont] [{{SERVER}}/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeBionetgenNoisyEGFR.zip SuppCode-BNG-noisy] [{{SERVER}}/publications/supplementary/Kochanczyk-2017-SciRep-SuppCodeComsol.zip SuppCode-Comsol] [{{SERVER}}/publications/supplementary/Kochanczyk-2017-SciRep-Movie.mp4 SuppMovie] | ||
* <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''', '' | * <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''', ''Physical Biology'' <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] | [{{SERVER}}/publications/Kocieniewski-2013-PhysBiol-MS.pdf PDF-ms] [{{SERVER}}/publications/supplementary/Kocieniewski-2013-PhysBiol-SourceCode.zip Code-BioNetGen] | ||
Revision as of 19:22, 14 February 2018
Articles featured by executable codes (implemented in Matlab and/or BioNetGen):
NF-κB network
- Czerkies M, Korwek Z, Prus W, Kochańczyk M, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nature Communications 9:493 (2018) PubMed CrossRef | PDF SuppInfo-PDF SuppData SuppMovies SuppCode
- Tudelska K, Markiewicz J, Kochańczyk M, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T. Information processing in the NF-κB pathway, Scientific Reports 7:15926 (2017) PubMed CrossRef | PDF SuppInfo-PDF SuppCode-BNGL SuppCode-Py
- 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, Biology 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, Journal of Immunology 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, Journal of Theoretical Biology 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, Biophysical Journal 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 Computational Biology 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 Systems Biology 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 Systems Biology 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, Journal of Theoretical Biology 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, Science Signaling 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, Scientific Reports 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, Physical Biology 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
