Models: Difference between revisions

Latest revision as of 11:58, 24 December 2023

Articles featured by executable codes (usually implemented in Matlab and/or BioNetGen):

Innate immunity

Korwek Z, Czerkies M, Jaruszewicz-Błońska J, Prus W, Kosiuk I, Kochańczyk M, Lipniacki T. Nonself RNA rewires IFN-β signaling: A mathematical model of the innate immune response, Science Signaling 16(815):eabq1173 (2023) PubMed CrossRef | FullText bioRxiv

Grabowski F, Kochańczyk M, Korwek Z, Czerkies M, Prus W, Lipniacki T. Antagonism between viral infection and innate immunity at the single-cell level, PLOS Pathogens 19(9):e1011597 (2023) PubMed CrossRef | bioRxiv Code Data

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

NF-κB network

Jaruszewicz-Błońska J, Kosiuk I, Prus W, Lipniacki T. A plausible identifiable model of the canonical NF-κB signaling pathway, PLOS One 8(6):e0286416 (2023) PubMed CrossRef bioRxiv

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

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-Articles featured by executable codes (implemented in Matlab and/or BioNetGen):
+Articles featured by executable codes (usually implemented in Matlab and/or BioNetGen):
+===Innate immunity===
+* <span class="pmbm">Korwek&nbsp;Z</span>, <span class="pmbm">Czerkies&nbsp;M</span>, <span class="pmbm">Jaruszewicz-Błońska&nbsp;J</span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Kosiuk&nbsp;I</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="pmbm">Lipniacki&nbsp;T</span>. '''Nonself RNA rewires IFN-β signaling: A mathematical model of the innate immune response''', ''Science&nbsp;Signaling'' <u>16</u>(815):eabq1173 (2023) [https://pubmed.ncbi.nlm.nih.gov/38085817 PubMed] [https://doi.org/10.1126/scisignal.abq1173 CrossRef] | [{{SERVER}}/publications/Korwek-2023-SciSignal.pdf FullText] [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]
+* <span class="pmbm">Grabowski&nbsp;F</span>, <span class="pmbm">Kochańczyk&nbsp;M</span>, <span class="pmbm">Korwek&nbsp;Z</span>, <span class="pmbm">Czerkies&nbsp;M</span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Lipniacki&nbsp;T</span>. '''Antagonism between viral infection and innate immunity at the single-cell level''', ''PLOS&nbsp;Pathogens'' <u>19</u>(9):e1011597 (2023) [https://pubmed.ncbi.nlm.nih.gov/37669278 PubMed] [https://doi.org/10.1371/journal.ppat.1011597 CrossRef] | [https://doi.org/10.1101/2022.11.18.517110 bioRxiv] [https://github.com/grfrederic/visavis Code] [https://doi.org/10.5281/zenodo.7428925 Data]
+* <span class="pmbm">Czerkies M</span>, <span class="pmbm">Korwek Z</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Jaruszewicz-Błońska J</span>, <span class="pmbm">Tudelska K</span>, <span class="pmbm">Błoński S</span>, <span class="nopmbm">Kimmel M</span>, <span class="nopmbm">Brasier AR</span>, <span class="pmbm">Lipniacki T</span>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Czerkies-2018-NatCommun.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-AllSuppData.zip SuppData] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-AllMovies.zip SuppMovies] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-ModelCode.zip SuppCode]
 ===NF-κB network===
-* <span class="pmbm">Czerkies M</span>, <span class="pmbm">Korwek Z</span>, <span class="pmbm">Prus W</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Jaruszewicz-Błońska J</span>, <span class="pmbm">Tudelska K</span>, <span class="pmbm">Błoński S</span>, <span class="nopmbm">Kimmel M</span>, <span class="nopmbm">Brasier AR</span>, <span class="pmbm">Lipniacki T</span>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef] | [http://pmbm.ippt.pan.pl/publications/Czerkies-2018-NatCommun.pdf PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-SuppInfo.pdf SuppInfo-PDF] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-AllSuppData.zip SuppData] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-AllMovies.zip SuppMovies] [http://pmbm.ippt.pan.pl/publications/supplementary/Czerkies-2018-NatCommun-ModelCode.zip SuppCode]
+* <span class="pmbm">Jaruszewicz-Błońska&nbsp;J</span>, <span class="pmbm">Kosiuk&nbsp;I</span>, <span class="pmbm">Prus&nbsp;W</span>, <span class="pmbm">Lipniacki&nbsp;T</span>. '''A plausible identifiable model of the canonical NF-κB signaling pathway''', ''PLOS One'' <u>8</u>(6):e0286416 (2023) [https://pubmed.ncbi.nlm.nih.gov/37267242 PubMed] [https://doi.org/10.1371/journal.pone.0286416 CrossRef] [https://doi.org/10.1101/2022.06.09.495460 bioRxiv]
-* <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&nbsp;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&nbsp;S</span>, <span class="pmbm">Kaźmierczak B</span>, <span class="pmbm">Lipniacki T</span>. '''Information processing in the NF-κB pathway''', ''Scientific&nbsp;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&nbsp;M</span>, <span class="pmbm">Lipniacki T</span>. '''Importins promote high-frequency NF-&kappa;B 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]
@@ Line 49: / Line 57: @@
 ===Autophagy===
-* <span class="pmbm">Szymańska P</span>,  <span class="nopmbm">Martin KR</span>, <span class="nopmbm">MacKeigan JP</span>,  <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''Computational analysis of an autophagy/translation switch based on mutual inhibition of mTORC1 and ULK1''', ''PLOS One'' <u>10</u>(3):e0116550 (2015) [http://www.ncbi.nlm.nih.gov/pubmed/25761126 PubMed] [http://dx.doi.org/10.1371/journal.pone.0116550 CrossRef] | [{{SERVER}}/publications/Szymanska-2015-PLOSOne.pdf PDF] [{{SERVER}}/publications/supplementary/Szymanska-2015-PLOSOne-SuppFileS1.bngl.txt supp-BNGL] [{{SERVER}}/publications/supplementary/Szymanska-2015-PLOSOne-SuppFileS2.pdf supp-PDF]
+* <span class="pmbm">Szymańska P</span>,  <span class="nopmbm">Martin KR</span>, <span class="nopmbm">MacKeigan JP</span>,  <span class="nopmbm">Hlavacek WS</span>, <span class="pmbm">Lipniacki T</span>. '''Computational analysis of an autophagy/translation switch based on mutual inhibition of mTORC1 and ULK1''', ''PLOS&nbsp;One'' <u>10</u>(3):e0116550 (2015) [http://www.ncbi.nlm.nih.gov/pubmed/25761126 PubMed] [http://dx.doi.org/10.1371/journal.pone.0116550 CrossRef] | [{{SERVER}}/publications/Szymanska-2015-PLOSOne.pdf PDF] [{{SERVER}}/publications/supplementary/Szymanska-2015-PLOSOne-SuppFileS1.bngl.txt supp-BNGL] [{{SERVER}}/publications/supplementary/Szymanska-2015-PLOSOne-SuppFileS2.pdf supp-PDF]
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