COPASI's Use In Immunology

2021
Vasilev GA, Filkova AA, Sveshnikova AN (2021) Study of Reversible Platelet Aggregation Model by Nonlinear Dynamics. Mathematics 9:759 Immunology Link

1 publication
2020
Abudukelimu A, Barberis M, Redegeld F, 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, 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
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

4 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
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. PhD Thesis 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

6 publications
2018
Abudukelimu A, Barberis M, Redegeld FA, Sahin N, Westerhoff HV (2018) Predictable Irreversible Switching Between Acute and Chronic Inflammation. Frontiers in Immunology. Frontiers 9:1596 Signaling Immunology Link
Barry JK (2018) Mathematical Modelling of the HIV Life Cycle: Identifying Optimal Treatment Strategies. Doctoral Thesis, University of Greifswald Immunology Link
Hodgson D (2018) Using systems biology to investigate how age-related changes in TGFβ signalling alter pro-inflammatory stimuli. PhD Thesis, Newcastle University. 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

6 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 Methods Immunology Link
Barry JK (2017) Mathematical Modelling of the HIV Life Cycle: Identifying Optimal Treatment Strategies. PhD Thesis, Universitätsmedizin der Ernst-Moritz-Arndt-Universität Greifswald. 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
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

4 publications
2016
Beuke K (2016) TNF-induced NF-κB Signal Transduction in the Liver. PhD Thesis, Heidelberg University. 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
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

5 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 C, 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. PhD Thesis, University of Cincinnati Immunology Signaling Link
Mei Y, Abedi V, Carbo A, Zhang X, Lu P, Philipson C, 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. PhD Thesis, Virginia Tech 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
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

6 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
Philipson CW, Bassaganya-Riera J, Hontecillas R (2013) Animal models of enteroaggregative Escherichia coli infection. Gut Microbes 4:281-291 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

3 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
Wendelsdorf KV (2011) Models of the Mucosal Inflammatory and Regulatory Immune Pathways: The Role of Host Response in Microbial Persistence and Pathogenesis. PhD Thesis, Virginia Tech, Blacksburg, Virginia, USA. Immunology Link

3 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
Sun T, Adra S, Smallwood R, Holcombe M, MacNeil S (2009) Exploring Hypotheses of the Actions of TGF-β1 in Epidermal Wound Healing Using a 3D Computational Multiscale Model of the Human Epidermis. PLOS One 4:e8515 Immunology Computational Method Software Link

1 publication
2008
Jordão L, Bleck CKE, Mayorga L, Griffiths G, Anes E (2008) On the killing of mycobacteria by macrophages. Cellular Microbiology 10:529-48 Immunology Link

1 publication
2007
Kummer U, Zobeley J, Brasen JC, Fahmy R, Kindzelskii AL, Petty AR, Clark AJ, Petty HR (2007) Elevated Glucose Concentrations Promote Receptor-Independent Activation of Adherent Human Neutrophils: An Experimental and Computational Approach. Biophysical Journal 92:2597-2607 Immunology Link

1 publication
2006

0 publication