COPASI

COPASI's Use In Immunology

2024
King CR, Berezin C-T, Peccoud J (2024) Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. PLOS Computational Biology 20:e1011373 Immunology Link
Sumi T, Harada K (2024) Vaccine and antiviral drug promise for preventing post-acute sequelae of COVID-19, and their combination for its treatment. Frontiers in Immunology 15:1329162 Immunology Link
Uttley M, Horne G, Tsigkinopoulou A, Del Carratore F, Hawari A, Kiezel-Tsugunova M, Kendall AC, Jones J, Messenger D, Bhogal RK, Breitling R, Nicolaou A (2024) An adaptable in silico ensemble model of the arachidonic acid cascade. Molecular Omics 20:453–468 Metabolism Immunology Link

3 publications
2023
Bartosh AV, Sotnikov DV, Zherdev AV, Dzantiev BB (2023) Handling Detection Limits of Multiplex Lateral Flow Immunoassay by Choosing the Order of Binding Zones. Micromachines 14:333 Laboratory Method Immunology Link
Jawale D, Khandibharad S, Singh S (2023) Decoding systems immunological model of sphingolipids with IL-6/IL-17/IL-23 axes in L. major infection. Biochimica et Biophysica Acta 1868:159261 Signaling Immunology Link
Lems CM, Burger GA, Beltman JB (2023) Tumor-mediated immunosuppression and cytokine spreading affects the relation between EMT and PD-L1 status. Frontiers in Immunology 14:1219669 Immunology Link
Martyanov AA, Stepanyan MG, Sveshnikova AN (2023) Theoretical Explanation for the Variability in Platelet Activation through the GPVI Receptor. Biochemistry (Moscow) 17:83–91 Immunology Link

4 publications
2022
Boldova AE, Korobkin JD, Nechipurenko YD, Sveshnikova AN (2022) Theoretical Explanation for the Rarity of Antibody-Dependent Enhancement of Infection (ADE) in COVID-19. International Journal of Molecular Sciences 23:11364 Immunology Link
Fueyo-González F, McGinty M, Ningoo M, Anderson L, Cantarelli C, Andrea Angeletti null, Demir M, Llaudó I, Purroy C, Marjanovic N, Heja D, Sealfon SC, Heeger PS, Cravedi P, Fribourg M (2022) Interferon-β acts directly on T cells to prolong allograft survival by enhancing regulatory T cell induction through Foxp3 acetylation. Immunity 55:459-474.e7 Immunology Link
Maier BD, Aguilera LU, Sahle S, Mutz P, Kalra P, Dächert C, Bartenschlager R, Binder M, Kummer U (2022) Stochastic dynamics of Type-I interferon responses. PLoS Computational Biology 18:e1010623 Immunology Signaling Link
Mokry RL, O’Brien BS, Adelman JW, Rosas S, Schumacher ML, Ebert AD, Terhune SS (2022) Nitric Oxide Attenuates Human Cytomegalovirus Infection yet Disrupts Neural Cell Differentiation and Tissue Organization. Journal of Virology 96:e0012622 Microbiology Immunology Link
Nieto F, Garrido F, Dinamarca S, Cebrian I, Mayorga LS (2022) Kinetics of antigen cross-presentation assessed experimentally and by a model of the complete endomembrane system. Cellular Immunology 382:104636 Immunology Link
Sumi T, Harada K (2022) Immune response to SARS-CoV-2 in severe disease and long COVID-19. iScience 25:104723 Immunology Link
Tokarev A, Mozokhina A, Volpert V (2022) Competition of SARS-CoV-2 Variants in Cell Culture and Tissue: Wins the Fastest Viral Autowave. Vaccines 10:995 Immunology Link

7 publications
2021
Erlendsson S, Teilum K (2021) Binding Revisited-Avidity in Cellular Function and Signaling. Frontiers in Molecular Biosciences 7:615565 Biochemistry Immunology Link
Soni B, Singh S (2021) COVID-19 co-infection mathematical model as guided through signaling structural framework. Computational and Structural Biotechnology Journal 19:1672–1683 Signaling Immunology Link
Vasilev GA, Filkova AA, Sveshnikova AN (2021) Study of Reversible Platelet Aggregation Model by Nonlinear Dynamics. Mathematics 9:759 Immunology Link

3 publications
2020
Abudukelimu A, Barberis M, Redegeld FA, Sahin N, Sharma RP, Westerhoff HV (2020) Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity. Frontiers in Immunology 10:3091 Immunology Signaling Link
Fribourg M (2020) A case for the reuse and adaptation of mechanistic computational models to study transplant immunology. American Journal of Transplantation 20:355–361 Immunology Link
Martyanov AA, Balabin FA, Dunster JL, Panteleev MA, Gibbins JM, Sveshnikova AN (2020) Control of Platelet CLEC-2-Mediated Activation by Receptor Clustering and Tyrosine Kinase Signaling. Biophysical Journal 118:2641–2655 Immunology Signaling Link
Martyanov AA, Morozova DS, Sorokina MA, Filkova AA, Fedorova DV, Uzueva SS, Suntsova EV, Novichkova GA, Zharkov PA, Panteleev MA, Sveshnikova AN (2020) Heterogeneity of Integrin αIIbβ3 Function in Pediatric Immune Thrombocytopenia Revealed by Continuous Flow Cytometry Analysis. International Journal of Molecular Sciences 21:3035 Immunology Link
Merk LN, Shur AS, Pandey A, Murray RM, Green LN (2020) Engineering Logical Inflammation Sensing Circuit for Gut Modulation. bioRxiv 2020.11.10.377085 Immunology Link
Mokry RL, Schumacher ML, Hogg N, Terhune SS (2020) Nitric Oxide Circumvents Virus-Mediated Metabolic Regulation during Human Cytomegalovirus Infection. mBio 11:e02630-20 Immunology Link
Pappalardo F, Russo G, Pennisi M, Parasiliti Palumbo GA, Sgroi G, Motta S, Maimone D (2020) The Potential of Computational Modeling to Predict Disease Course and Treatment Response in Patients with Relapsing Multiple Sclerosis. Cells 9:586 Immunology Link

7 publications
2019
Aguilera LU, Rodríguez-González J (2019) Modeling the effect of tat inhibitors on HIV latency. Journal of Theoretical Biology 473:20–27 Immunology Link
Bagaev AV, Garaeva AY, Lebedeva ES, Pichugin AV, Ataullakhanov RI, Ataullakhanov FI (2019) Elevated pre-activation basal level of nuclear NF-κB in native macrophages accelerates LPS-induced translocation of cytosolic NF-κB into the cell nucleus. Scientific Reports 9:4563 Signaling Immunology Link
Houston MT, Gutierrez JB (2019) The FRiND Model: A Mathematical Model for Representing Macrophage Plasticity in Muscular Dystrophy Pathogenesis. Bulletin of Mathematical Biology 81:3976–3997 Immunology Link
Lang SN, Germerodt S, Glock C, Skerka C, Zipfel PF, Schuster S (2019) Molecular crypsis by pathogenic fungi using human factor H. A numerical model. PLoS One 14:e0212187 Immunology Microbiology Link
Mohapatra SR, Sadik A, Tykocinski L-O, Dietze J, Poschet G, Heiland I, Opitz CA (2019) Hypoxia Inducible Factor 1α Inhibits the Expression of Immunosuppressive Tryptophan-2,3-Dioxygenase in Glioblastoma. Frontiers in Immunology 10:2762 Immunology Signaling Link
Shockey WA (2019) Proteolytic network dynamics in breast cancer and tumor associated macrophages. Ph.D. Thesis, Georgia Tech, Atlanta, USA Signaling Immunology Link
Verma M, Bassaganya-Riera J, Leber A, Tubau-Juni N, Hoops S, Abedi V, Chen X, Hontecillas R (2019) High-resolution computational modeling of immune responses in the gut. GigaScience 8:giz062 Immunology Link

7 publications
2018
Abudukelimu A, Barberis M, Redegeld FA, Sahin N, Westerhoff HV (2018) Predictable Irreversible Switching Between Acute and Chronic Inflammation. Frontiers in Immunology 9:1596 Signaling Immunology Link
Das A, Grosser R, Velazquez Albino A, Saha K, Capitani CM (2018) Mathematical modeling of CAR T cell therapy outcomes to develop design specifications for CAR T cell engineering. Journal for ImmunoTherapy of Cancer 6:434 Immunology Link
Hodgson D (2018) Using systems biology to investigate how age-related changes in TGFβ signalling alter pro-inflammatory stimuli. Ph.D. Thesis, Newcastle University, UK. Signaling Immunology Link
Kaliamurthi S, Selvaraj G, Kaushik AC, Gu K-R, Wei D-Q (2018) Designing of cD8+ and cD8+-overlapped cD4+ epitope vaccine by targeting late and early proteins of human papillomavirus. Biologics: Targets & Therapy 12:107–125 Immunology Link
Kosey D, Soni B, Nimsarkar P, Singh S (2018) Infection dynamics in L. major autophagic machinery is regulated by ATG9-PI3P negative feedback loop. bioRxiv Preprint bioRxiv:398545 Cell Biology Immunology Link
Maiorov AS, Shepelyuk TO, Balabin FA, Martyanov AA, Nechipurenko DY, Sveshnikova AN (2018) Modeling of Granule Secretion upon Platelet Activation through the TLR4-Receptor. Biophysics 63:357–364 Signaling Immunology Link
Soni B, Saha B, Singh S (2018) Systems cues governing IL6 signaling in leishmaniasis. Cytokine 106:169–175 Signaling Immunology Link

7 publications
2017
Aguilera LU, Zimmer C, Kummer U (2017) A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study. BMC Systems Biology 11:26 Computational Method Immunology Link
Barry JK (2017) Mathematical Modelling of the HIV Life Cycle: Identifying Optimal Treatment Strategies. Ph.D. Thesis, Universitätsmedizin der Ernst-Moritz-Arndt-Universität Greifswald, Germany. Microbiology Immunology Link
Beuke K, Schildberg FA, Pinna F, Albrecht U, Liebe R, Bissinger M, Schirmacher P, Dooley S, Bode JG, Knolle PA, Kummer U, Breuhahn K, Sahle S (2017) Quantitative and integrative analysis of paracrine hepatocyte activation by non-parenchymal cells upon lipopolysaccharide induction. FEBS Journal 284:796–813 Immunology Link
Kale SD, Ayubi T, Chung D, Tubau-Juni N, Leber A, Dang HX, Karyala S, Hontecillas R, Lawrence CB, Cramer RA, Bassaganya-Riera J (2017) Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis. Scientific Reports 7:17096 Immunology Link
Leber A, Hontecillas R, Abedi V, Tubau-Juni N, Zoccoli-Rodriguez V, Stewart C, Bassaganya-Riera J (2017) Modeling new immunoregulatory therapeutics as antimicrobial alternatives for treating Clostridium difficile infection. Artificial Intelligence in Medicine 78:1–13 Immunology Link
Oroszlán G, Dani R, Szilágyi A, Závodszky P, Thiel S, Gál P, Dobó J (2017) Extensive basal level activation of complement mannose-binding lectin-associated serine protease (MASP)-3: kinetic modeling of lectin pathway activation provides possible mechanism. Frontiers in Immunology 8:1821 Immunology Signaling Link

6 publications
2016
Beuke K (2016) TNF-induced NF-κB Signal Transduction in the Liver. Ph.D. Thesis, Heidelberg University, Germany. Immunology Signaling Link
Leber A, Abedi V, Hontecillas R, Viladomiu M, Hoops S, Ciupe S, Caughman J, Andrew T, Bassaganya-Riera J (2016) Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection. Journal of Theoretical Biology 398:74–84 Immunology Link
Leber A, Bassaganya-Riera J, Tubau-Juni N, Zoccoli-Rodriguez V, Viladomiu M, Abedi V, Lu P, Hontecillas R (2016) Modeling the Role of Lanthionine Synthetase C-Like 2 (LANCL2) in the Modulation of Immune Responses to Helicobacter pylori Infection. PLoS One 11:e0167440 Immunology Link
Levenhagen MA, Ferreira GA, Pereira GM, Santos AR (2016) A computer simulation model for Strongyloides infection. PeerJ Preprints 4:e2399v1 Immunology Parasitology Link
Michalak P, Sobral BW, Abedi V, Kim YB, Deng X, Philipson CW, Viladomiu M, Lu P, Wendelsdorf K, Hontecillas R, Bassaganya-Riera J (2016) From Big Data Analytics and Network Inference to Systems Modeling. In: Bassaganya-Riera J (ed) Computational Immunology, Academic Press, 113–144. Computational Method Immunology Link
Podoplelova NA, Sveshnikova AN, Kurasawa JH, Sarafanov AG, Chambost H, Vasil’ev SA, Demina IA, Ataullakhanov FI, Alessi M-C, Panteleev MA (2016) Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization. Biochimica et Biophysica Acta 1858:1216–1227 Immunology Biochemistry Biophysics Link
Tyc KM, Herwald SE, Hogan JA, Pierce JV, Klipp E, Kumamoto CA (2016) The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. BMC Systems Biology 10:20 Microbiology Immunology Signaling Link

7 publications
2015
Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H (2015) Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. BMC Systems Biology 9:81. Immunology Cell Biology Signaling Link
Leber A, Viladomiu M, Hontecillas R, Abedi V, Philipson CW, Hoops S, Howard B, Bassaganya-Riera J (2015) Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PLoS One 10:e0134849 Immunology Link
Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J (2015) Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Mining 8:1-21 Computational Method Immunology Link
Marwaha S (2015) A Genomics and Mathematical Modeling Approach for the study of Helicobacter pylori associated Gastritis and Gastric Cancer. Ph.D. Thesis, University of Cincinnati, Ohio, USA Immunology Signaling Link
Mei Y, Abedi V, Carbo A, Zhang X, Lu P, Philipson CW, Hontecillas R, Hoops S, Liles N, Bassaganya-Riera J (2015) Multiscale modeling of mucosal immune responses. BMC Bioinformatics 16:Supp12:S2 Immunology Link
Philipson CW (2015) Systems analysis and characterization of mucosal immunity. Ph.D. Thesis, Virginia Tech, USA Immunology Link
Philipson CW, Bassaganya-Riera J, Viladomiu M, Kronsteiner B, Abedi V, Hoops S, Michalak P, Kang L, Girardin SE, Hontecillas R (2015) Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PLoS One 10:e0137839 Immunology Link

7 publications
2014
Carbo A, Olivares-Villagómez D, Hontecillas R, Bassaganya-Riera J, Chaturvedi R, Piazuelo MB, Delgado A, Washington MK, Wilson KT, Algood HMS (2014) Systems modeling of the role of IL-21 in the maintenance of effector CD4+ T cell responses during chronic Helicobacter pylori infection. mBio 5:e01243-14 Immunology Link
Hui W, Young DA, Rowan AD, Xu X, Cawston TE, Proctor CJ (2014) Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. Annals of the Rheumatic Diseases 75:449–458 Signaling Immunology Link
Jarrah AS, Castiglione F, Evans NP, Grange RW, Laubenbacher R (2014) A Mathematical Model of Skeletal Muscle Disease and Immune Response in the mdx Mouse. BioMed Research International 2014:871810 Immunology Link
Lutz A, Sanwald J, Thomas M, Feuer R, Sawodny O, Ederer M, Borner C, Humar M, Merfort I (2014) Interleukin-1beta Enhances FasL-Induced Caspase-3/-7 Activity without Increasing Apoptosis in Primary Mouse Hepatocytes. PLoS One 9:e115603. Immunology Link
Marwaha S, Schumacher MA, Zavros Y, Eghbalnia HR (2014) Crosstalks between Cytokines and Sonic Hedgehog in Helicobacter pylori Infection: A Mathematical Model. PLoS One 9:e111338. Immunology Signaling Link
Mol M, Patole MS, Singh S (2014) Immune signal transduction in leishmaniasis from natural to artificial systems: role of feedback loop insertion. Biochimica et Biophysica Acta 1840:71–79 Signaling Immunology Link
Proctor CJ, Macdonald C, Milner JM, Rowan AD, Cawston TE (2014) A Computer Simulation Approach to Assessing Therapeutic Intervention Points for the Prevention of Cytokine-Induced Cartilage Breakdown. Arthritis & Rheumatology 66:979-989 Immunology Link

7 publications
2013
Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe M, Eubank S, Wendelsdorf K, Bisset K, Hoops S, Deng X, Alam M, Kronsteiner B, Mei Y, Hontecillas R (2013) Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection. PLoS One 8:e73365 Immunology Link
Carbo A, Hontecillas R, Kronsteiner B, Viladomiu M, Pedragosa M, Lu P, Philipson CW, Hoops S, Marathe M, Eubank S, Bisset K, Wendelsdorf K, Jarrah AS, Mei Y, Bassaganya-Riera J (2013) Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity. PLoS Computational Biology 9:e1003027 Immunology Signaling Link
Philipson CW, Bassaganya-Riera J, Hontecillas R (2013) Animal models of enteroaggregative Escherichia coli infection. Gut Microbes 4:281-291 Immunology Link
Schokker D, Bannink A, Smits MA, Rebel JMJ (2013) A mathematical model representing cellular immune development and response to Salmonella of chicken intestinal tissue. Journal of Theoretical Biology 330:75–87 Immunology Link
Viladomiu M, Hontecillas R, Yuan L, Lu P, Bassaganya-Riera J (2013) Nutritional protective mechanisms against gut inflammation. Journal of Nutritional Biochemistry 24:929-939 Immunology Link

5 publications
2012
Kim B, Eggel A, Tarchevskaya SS, Vogel M, Prinz H, Jardetzky TS (2012) Accelerated disassembly of IgE-receptor complexes by a disruptive macromolecular inhibitor. Nature 491:613-617 Immunology Link
Viladomiu M, Hontecillas R, Pedragosa M, Carbo A, Hoops S, Michalak P, Michalak K, Guerrant RL, Roche JK, Warren CA, Bassaganya-Riera J (2012) Modeling the Role of Peroxisome Proliferator-Activated Receptor γ and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile. PLoS One 7:e47525 Genomics Immunology Link

2 publications
2011
Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Uehata T, Kuniyoshi K, Satoh T, Saitoh T, Matsushita M, Standley DM, Akira S (2011) The IkB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nature Immunology 12:1167-75 Immunology Signaling Link
Klotz C, Ziegler T, Figueiredo AS, Rausch S, Hepworth MR, Obsivac N, Sers C, Lang R, Hammerstein P, Lucius R, Hartmann S (2011) A Helminth Immunomodulator Exploits Host Signaling Events to Regulate Cytokine Production in Macrophages. PLoS Pathogens 7:e1001248 Immunology Link
Liu B, Zhang J, Tan PY, Hsu D, Blom AM, Leong B, Sethi S, Ho B, Ding JL, Thiagarajan PS (2011) A computational and experimental study of the regulatory mechanisms of the complement system. PLoS Computational Biology 7:e1001059 Immunology Signaling Link
Wendelsdorf K (2011) Models of the Mucosal Inflammatory and Regulatory Immune Pathways: The Role of Host Response in Microbial Persistence and Pathogenesis. Ph.D. Thesis, Virginia Tech, USA. Immunology Link

4 publications
2010
Wendelsdorf K, Bassaganya-Riera J, Hontecillas R, Eubank S (2010) Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease. Journal of Theoretical Biology 264:1225-1239 Immunology Link

1 publication
2009