COPASI's Use In Signaling

Anderl F, Salvadori G, Veletic M, Balasingham I (2024) Computational Modeling of Bacterial Sensor Dynamics. paper presented at the 8th Workshop on Molecular Communications. Oslo, Norway. Signaling Link
Khilwani R, Singh S (2024) Traversing through the Mechanistic Event Analysis in IL-6 and IL-17 Signaling for a New Therapeutic Paradigm in NSCLC. International Journal of Molecular Sciences 25:1216 Signaling Link
Lang PF, Penas DR, Banga JR, Weindl D, Novak B (2024) Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. PLOS Computational Biology 20:e1011151 Signaling Link
Yin F, Song T, Wang Z, Liu J, Zhang H, Tang Y, Zhang Z (2024) Hsp70-Bim incoherent feedforward loop contributes to cell-fate heterogeneity and fractional killing. British Journal of Pharmacology 181:659–669 Signaling Link

4 publications
Friedhoff VN (2023) Stochastic Modelling of Calcium Dynamics. Ph. D. thesis, Humboldt-Universität zu Berlin, Germany. Signaling 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
Mendes P (2023) Reproducibility and FAIR principles: the case of a segment polarity network model. Frontiers in Cell and Developmental Biology 11:1201673 Genetics Signaling Computational Method Link
Ramesh V, Krishnan J (2023) A unified approach to dissecting biphasic responses in cell signaling. eLife 12:e86520 Signaling Link
Ramesh V, Suwanmajo T, Krishnan J (2023) Network regulation meets substrate modification chemistry. Journal of the Royal Society Interface 20:20220510 Signaling Link
Schaumburger N, Pally J, Moraru II, Kositsawat J, Kuchel GA, Blinov ML (2023) Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes. Frontiers in Network Physiology 3:1079070 Signaling Physiology Link
Schuster M, Li C, Smith P, Kuttler C (2023) Parameters, architecture and emergent properties of the Pseudomonas aeruginosa LasI/LasR quorum-sensing circuit. Journal of the Royal Society Interface 20:20220825 Microbiology Signaling Link
Suárez H, Guerra A, Mansilla R, Nieto-Villar JM (2023) Ferroptosis as a biological Phase transition II: Chronotherapy of avascular and vascular tumor growth. Biological Rhythm Research 54:722–731 Biochemistry Signaling Link
Sumi T, Harada K (2023) Muscarinic acetylcholine receptor-dependent and NMDA receptor-dependent LTP and LTD share the common AMPAR trafficking pathway. iScience 26:106133 Signaling Link

9 publications
Bell M (2022) Mechanochemical modeling of structural plasticity in synapses. Ph.D. Thesis, University of California San Diego, USA. Signaling Link
Burger GA, Nesenberend DN, Lems CM, Hille SC, Beltman JB (2022) Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFNγ-induced PD-L1 expression promotes tumour progression. Royal Society Open Science 9:220186 Signaling Link
Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR (2022) A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications 13:3555 Computational Method Signaling Link
Großeholz R, Wanke F, Rohr L, Glöckner N, Rausch L, Scholl S, Scacchi E, Spazierer A-J, Shabala L, Shabala S, Schumacher K, Kummer U, Harter K (2022) Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root. eLife 11:e73031 Signaling Physiology Plant Biology Link
Guimera AM, Clark P, Wordsworth J, Anugula S, Rasmussen LJ, Shanley DP (2022) Systems modelling predicts chronic inflammation and genomic instability prevent effective mitochondrial regulation during biological ageing. Experimental Gerontology 166:111889 Signaling 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
Samarth NH, Singh S (2022) Chapter 37 - Methods to study systems biology of signaling networks: A case study of NSCLC. In: Tripathi T and Dubey VK (eds) Advances in Protein Molecular and Structural Biology Methods. Academic Press, 625–634. Signaling Link
Shelton MG, Kerns KA, Castora FJ, Coleman RA (2022) Incorporating Mitochondrial Gene Expression Changes Within a Testable Mathematical Model for Alzheimer’s Disease: Stress Response Modulation Predicts Potential Therapeutic Targets. Journal of Alzheimer’s Disease 90:109–117 Signaling Metabolism Link
Trošanová Z, Louša P, Kozeleková A, Brom T, Gašparik N, Tungli J, Weisová V, Župa E, Žoldák G, Hritz J (2022) Quantitation of Human 14-3-3ζ Dimerization and the Effect of Phosphorylation on Dimer-monomer Equilibria. Journal of Molecular Biology 434:167479 Signaling Macromolecular Biochemistry Link
White C, Rottschäfer V, Bridge LJ (2022) Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis. Journal of Theoretical Biology 538:110996 Signaling Biochemistry Link

10 publications
Dalle Pezze P, Karanasios E, Kandia V, Manifava M, Walker SA, Le Novère NG, Ktistakis NT (2021) ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling. Autophagy 17:1131–1141 Cell Biology Signaling Link
Friedhoff VN, Antunes G, Falcke M, Simões de Souza FM (2021) Stochastic reaction-diffusion modeling of calcium dynamics in 3D dendritic spines of Purkinje cells. Biophysical Journal 120:2112–2123 Signaling Link
Guhe V, Soni B, Ingale P, Singh S (2021) Autophagy proteins and its homeostasis in cellular environment. Advances in Protein Chemistry and Structural Biology 123:73–93 Cell Biology Signaling Link
Hetmanski JHR, Jones MC, Chunara F, Schwartz J-M, Caswell PT (2021) Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration. PLoS Computational Biology 17:e1008213 Cell Biology Signaling Link
Ibáňez Gaspar V, Catozzi S, Ternet C, Luthert PJ, Kiel C (2021) Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context. Small GTPases 12:209–225 Signaling Link
Koch D, Alexandrovich A, Funk F, Kho AL, Schmitt JP, Gautel M (2021) Molecular noise filtering in the β-adrenergic signaling network by phospholamban pentamers. Cell Reports 36:109448 Signaling Link
Korobkin JD, Balabin FA, Yakovenko SA, Simonenko EY, Sveshnikova AN (2021) Occurrence of Calcium Oscillations in Human Spermatozoa Is Based on Spatial Signaling Enzymes Distribution. International Journal of Molecular Sciences 22:8018 Signaling Link
Quiros-Fernandez I, Figueroa-Protti L, Arias-Arias JL, Brenes-Cordero N, Siles-Canales F, Mora J, Mora-Rodríguez R (2021) Perturbation-Based Modeling Unveils the Autophagic Modulation of Chemosensitivity and Immunogenicity in Breast Cancer Cells. Metabolites 11:637 Signaling Link
Ramesh V, Krishnan J (2021) Symmetry breaking meets multisite modification. eLife 10:e65358 Signaling Link
Scott KE, Fraley SI, Rangamani P (2021) A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes. Proceedings of the National Academy of Sciences USA 118:e2021571118 Signaling 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
Teilum K, Olsen JG, Kragelund BB (2021) On the specificity of protein-protein interactions in the context of disorder. Biochemical Journal 478:2035–2050 Signaling Macromolecular Biochemistry Link
Tisi R, Spinelli M, Palmioli A, Airoldi C, Cazzaniga P, Besozzi D, Nobile MS, Mazzoleni E, Arnhold S, De Gioia L, Grandori R, Peri F, Vanoni M, Sacco E (2021) The Multi-Level Mechanism of Action of a Pan-Ras Inhibitor Explains its Antiproliferative Activity on Cetuximab-Resistant Cancer Cells. Frontiers in Molecular Biosciences 8:625979 Signaling Cell Biology Link
Yahya G, Pérez AP, Mendoza MB, Parisi E, Moreno DF, Artés MH, Gallego C, Aldea M (2021) Stress granules display bistable dynamics modulated by Cdk. Journal of Cell Biology 220:jcb202005102 Cell Biology Signaling Link
Yang Y, Filipovic D, Bhattacharya S (2021) A Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8-Tetrachlorodibenzo-p-Dioxin in the Mouse Liver. Hepatology Communications 6:750-764 Signaling Physiology Toxicology Link
Zang J, Gesemann M, Keim J, Samardzija M, Grimm C, Neuhauss SC (2021) Circadian regulation of vertebrate cone photoreceptor function. eLife 10:e68903 Signaling Link

16 publications
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
Dhasmana A, Uniyal S, Anukriti, Kashyap VK, Somvanshi P, Gupta M, Bhardwaj U, Jaggi M, Yallapu MM, Haque S, Chauhan SC (2020) Topological and system-level protein interaction network (PIN) analyses to deduce molecular mechanism of curcumin. Scientific Reports 10:12045 Signaling Link
Erlendsson S, Teilum K (2020) Binding Revisited-Avidity in Cellular Function and Signaling. Frontiers in Molecular Biosciences 7:615565 Signaling Theory Link
Ghorbani S, Szigetvari PD, Haavik J, Kleppe R (2020) Serine 19 phosphorylation and 14-3-3 binding regulate phosphorylation and dephosphorylation of tyrosine hydroxylase on serine 31 and serine 40. Journal of Neurochemistry 152:29–47 Signaling Link
Iwasaki T, Takiguchi R, Hiraiwa T, Yamada TG, Yamazaki K, Hiroi NF, Funahashi A (2020) Neural Differentiation Dynamics Controlled by Multiple Feedback Loops in a Comprehensive Molecular Interaction Network. Processes 8:166 Signaling Link
Li L, Lai M, Cole S, Le Novère N, Edelstein SJ (2020) Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies. PLoS Computational Biology 16:e1006991 Signaling 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
Mazet F, Tindall MJ, Gibbins JM, Fry MJ (2020) A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data. Scientific Reports 10:13244 Signaling Link
Meyer K, Morales-Navarrete H, Seifert S, Wilsch-Braeuninger M, Dahmen U, Tanaka EM, Brusch L, Kalaidzidis Y, Zerial M (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985 Signaling Cell Biology Link
Rana P (2020) Mathematical models of cellular signaling and supramolecular self-assembly. Ph.D. Thesis, Virginia Commonwealth University, USA. Signaling Macromolecular Biochemistry Link
Song X, Yu Y, Shen C, Wang Y, Wang N (2020) Dimerization/oligomerization of the extracellular domain of the GLP-1 receptor and the negative cooperativity in its ligand binding revealed by the improved NanoBiT. FASEB Journal 34:4348–4368 Macromolecular Biochemistry Signaling Link
Sumi T, Harada K (2020) Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors. Scientific Reports 10:14711 Signaling Cell Biology Link
Suwanmajo T, Ramesh V, Krishnan J (2020) Exploring cyclic networks of multisite modification reveals origins of information processing characteristics. Scientific Reports 10:16542 Signaling Link
Tenner B, Getz M, Ross B, Ohadi D, Bohrer CH, Greenwald E, Mehta S, Xiao J, Rangamani P, Zhang J (2020) Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit. eLife 9:e55013 Signaling Link

14 publications
Aguilera LU, Bergmann FT, Dalmasso G, Elmas S, Elsässer T, Großeholz R, Holzheu P, Kalra P, Kummer U, Sahle S, Veith N (2019) Robustness of frequency vs. amplitude coding of calcium oscillations during changing temperatures. Biophysical Chemistry 245:17–24 Signaling Biophysics 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
Bell M, Bartol T, Sejnowski T, Rangamani P (2019) Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. Journal of General Physiology 151:1017–1034 Cell Biology Biophysics Signaling Link
Bockwoldt M, Houry D, Niere M, Gossmann TI, Reinartz I, Schug A, Ziegler M, Heiland I (2019) Identification of evolutionary and kinetic drivers of NAD-dependent signaling. Proceedings of the National Academy of Sciences USA 116:15957–15966 Signaling Metabolism Link
Getz M, Swanson L, Sahoo D, Ghosh P, Rangamani P (2019) A predictive computational model reveals that GIV/girdin serves as a tunable valve for EGFR-stimulated cyclic AMP signals. Molecular Biology of the Cell 30:1621–1633 Signaling Cell Biology Link
Ghorbani S, Szigetvari PD, Haavik J, Kleppe R (2020) Serine 19 phosphorylation and 14-3-3 binding regulate phosphorylation and dephosphorylation of tyrosine hydroxylase on serine 31 and serine 40. Journal of Neurochemistry 152:29–47 Signaling Link
Ghosh A, Radhakrishnan R (2019) Time-dependent antagonist-agonist switching in receptor tyrosine kinase-mediated signaling. BMC Bioinformatics 20:242 Signaling Link
Gianì F, Russo G, Pennisi M, Sciacca L, Frasca F, Pappalardo F (2019) Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells. Bioinformatics 35:2267–2275 Signaling Pharmacology Link
Hodgson D, Rowan AD, Falciani F, Proctor CJ (2019) Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. PLoS Computational Biology 15:e1006685 Signaling Link
Iancu B, Sanwal U, Gratie C, Petre I (2019) Refinement-based modeling of the ErbB signaling pathway. Computers in Biology and Medicine 106:91–96 Signaling Computational Method Link
Jayanthi BEK, Zhao W, Segatori L (2019) Input-dependent post-translational control of the reporter output enhances dynamic resolution of mammalian signaling systems. Methods in Enzymology 622:1–27 Signaling Synthetic Biology Link
Kalra P, Brandl J, Gaub T, Niederalt C, Lippert J, Sahle S, Küpfer L, Kummer U (2019) Quantitative systems pharmacology of interferon alpha administration: A multi-scale approach. PLoS One 14:e0209587 Pharmacology Signaling Link
Kaspar S (2019) The role of promoter architecture in transduction, integration and multiplexing of environmental signals in bacteria. Ph.D. Thesis, University of Heidelberg, Germany Signaling Microbiology Link
Kaushik AC, Mao X, Li C-D, Li Y, Wei D-Q, Sahi S (2019) G-protein-coupled receptors function as logic gates for nanoparticle binding using systems and synthetic biology approach. Journal of Materials Research 34:1854–1867 Signaling Synthetic Biology Link
Knight-Schrijver V (2019) Towards systems pharmacology models of druggable targets and disease mechanisms. Thesis, University of Cambridge, UK Pharmacology Physiology Signaling Link
Kühn C, Checa S (2019) Computational Modeling to Quantify the Contributions of VEGFR1, VEGFR2, and Lateral Inhibition in Sprouting Angiogenesis. Frontiers in Physiology 10:288 Signaling Physiology Link
Lombardo SD, Presti M, Mangano K, Petralia MC, Basile MS, Libra M, Candido S, Fagone P, Mazzon E, Nicoletti F, Bramanti A (2019) Prediction of PD-L1 Expression in Neuroblastoma via Computational Modeling. Brain Sciences 9:E221 Signaling Link
Macikova L, Sinica V, Kadkova A, Villette S, Ciaccafava A, Faherty J, Lecomte S, Alves ID, Vlachova V (2019) Putative interaction site for membrane phospholipids controls activation of TRPA1 channel at physiological membrane potentials. FEBS Journal 286:3664–3683 Signaling Biochemistry Link
Miller DSJ, Schmierer B, Hill CS (2019) TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation. Journal of Cell Science 132:jcs234039 Signaling Link
Mitchell S, Hoffmann A (2019) Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB. Proceedings of the National Academy of Sciences USA 116:10592–10597 Signaling Link
Mitchell S, Mercado E, Ho J, Cheng Q, Ghosh G, Hoffmann A (2019) An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. Frontiers in Immunology 10:1425 Signaling 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
Moreno DF, Jenkins K, Morlot S, Charvin G, Csikász-Nagy A, Aldea M (2019) Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1. eLife 8:e48240 Signaling Cell Biology Link
Moreno DF, Parisi E, Yahya G, Vaggi F, Csikász-Nagy A, Aldea M (2019) Competition in the chaperone-client network subordinates cell-cycle entry to growth and stress. Life Science Alliance 2:e201800277 Signaling Cell Biology Link
Ohadi D, Schmitt DL, Calabrese B, Halpain S, Zhang J, Rangamani P (2019) Computational modeling reveals frequency modulation of calcium-cAMP/PKA pathway in dendritic spines. bioRxiv Preprint bioRxiv:521740 Signaling Link
Schoch A (2019) Quantitative Analysis of Information Transfer in Signal Transduction. Ph.D. Thesis, University of Heidelberg, Germany Signaling Link
Shaw WM, Yamauchi H, Mead J, Gowers G-OF, Bell DJ, Öling D, Larsson N, Wigglesworth M, Ladds G, Ellis T (2019) Engineering a Model Cell for Rational Tuning of GPCR Signaling. Cell 177:782-796.e27 Synthetic Biology Signaling Link
Sheppard S, Dikicioglu D (2019) Dynamic modelling of the killing mechanism of action by virus-infected yeasts. Journal of the Royal Society Interface 16:20190064 Biochemistry 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
Silva E, Martin RR, Pomuceno JP, Mansilla R, Betancourt-Mar JA, Cocho G, Nieto-Villar JM (2019) Dose and frequency in cancer therapy. Theoretical non-autonomous model of p53 network. Biological Rhythm Research 50:483–489 Signaling Link
Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, Aittokallio T (2019) Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer. npj Systems Biology and Applications 5:20 Pharmacology Signaling Link
Yvinec R, Ayoub MA, De Pascali F, Crépieux P, Reiter E, Poupon A (2019) Workflow Description to Dynamically Model β-Arrestin Signaling Networks. Methods in Molecular Biology 1957:195–215 Signaling Computational Method Link
Zhang X, Nagai T, Ahammad RU, Kuroda K, Nakamuta S, Nakano T, Yukinawa N, Funahashi Y, Yamahashi Y, Amano M, Yoshimoto J, Yamada K, Kaibuchi K (2019) Balance between dopamine and adenosine signals regulates the PKA/Rap1 pathway in striatal medium spiny neurons. Neurochemistry International 122:8–18 Signaling Link

33 publications
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
Arora D, Singh A (2018) Systems biology approach deciphering the biochemical signaling pathway and pharmacokinetic study of PI3K/mTOR/p53-Mdm2 module involved in neoplastic transformation. Network Modeling Analysis in Health Informatics and Bioinformatics 7:2 Signaling Link
Behinaein B, Rudie K, Sangrar W (2018) Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15:231–243 Signaling Link
Diedrichs DR, Gomez JA, Huang C-S, Rutkowski DT, Curtu R (2018) A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded protein response. Molecular Biology of the Cell 29:1502–1517 Signaling Link
Getz M, Swanson L, Sahoo D, Ghosh P, Rangamani P (2018) Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals. bioRxiv Preprint bioRxiv:149781 Signaling Link
Guimera AM (2018) Investigating homeostatic disruption by constitutive signals during biological ageing. Thesis, Newcastle University Signaling Physiology 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
Kleppe R, Jonassen I, Døskeland SO, Selheim F (2018) Mathematical Modelling of Nitric Oxide/Cyclic GMP/Cyclic AMP Signalling in Platelets. International Journal of Molecular Sciences 19:612 Signaling Link
Li X, Holmes WR (2018) Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach. PLoS Computational Biology 14:e1005946 Biophysics Signaling 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
McDonald NW (2018) Exploring the mechanistic effects of life extending treatments on the mTOR network : a combined computational and experimental approach. Ph.D. Thesis, Newcastle University Signaling Link
Mishra M, Jayal P, Karande AA, Chandra N (2018) Identification of a co-target for enhancing efficacy of sorafenib in HCC through a quantitative modeling approach. FEBS Journal 285:3977–3992 Metabolism Signaling Link
Rossi F, Torbensen K, Ristori S, Abou-Hassan A (2018) Signal Transduction and Communication Through Model Membranes in Networks of Coupled Chemical Oscillators. In: Pelillo M, Poli I, Roli A, Serra R, Slanzi D, Villani M (eds.) Artificial Life and Evolutionary Computation. WIVACE 2017. Communications in Computer and Information Science, vol 830. Springer Biochemistry Signaling Link
Silva E, Martin R, Pomuceno JP, Mansilla R, Betancourt-Mar JA, Cocho G, Nieto-Villar JM (2018) Dose and frequency in cancer therapy. Theoretical non-autonomous model of p53 network. Biological Rhythm Research 50:483-489 Signaling Link
Soni B, Saha B, Singh S (2018) Systems cues governing IL6 signaling in leishmaniasis. Cytokine 106:169–175 Signaling Immunology Link
Suwanmajo T, Krishnan J (2018) Exploring the intrinsic behaviour of multisite phosphorylation systems as part of signalling pathways. Journal of the Royal Society Interface 15:1520180109 Signaling Link
Ximing L (2018) Insights into Delivery of Somatic Calcium Signals to the Nucleus During LTP Revealed by Computational Modeling. Ph.D. Thesis, Ohio University, USA Signaling Biochemistry Link

17 publications
Agrawal R, Kalmady SV, Venkatasubramanian G (2017) In Silico Model-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology. Clinical Psychopharmacology and Neuroscience 15:115 Physiology Signaling Link
Bleicken S, Hantusch A, Das KK, Frickey T, García-Sáez AJ (2017) Quantitative interactome of a membrane Bcl-2 network identifies a hierarchy of complexes for apoptosis regulation. Nature Communications 8:73 Signaling Link
Hagen SJ, Son M (2017) Origins of heterogeneity in Streptococcus mutans competence: interpreting an environment-sensitive signaling pathway. Physical Biology 14:015001 Signaling Microbiology Link
Haurat MF, Figueiredo AS, Hoffmann L, Li L, Herr K, Wilson AJ, Beeby M, Schaber J, Albers S-V (2017) ArnS, a kinase involved in starvation-induced archaellum expression. Molecular Microbiology 103:181–194 Microbiology Signaling Link
Jiang Y, AkhavanAghdam Z, Tsimring LS, Hao N (2017) Coupled feedback loops control the stimulus-dependent dynamics of the yeast transcription factor Msn2. Journal of Biological Chemistry 292:12366–12372 Signaling Link
Jordão G, Tavares JN (2017) Mathematical models in cancer therapy. BioSystems 162:12–23 Signaling Link
Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, St Croix C, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H (2017) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology 13:81–90 Signaling Cell Biology Link
Kwon JS, Everetts NJ, Wang X, Wang W, Della Croce K, Xing J, Yao G (2017) Controlling Depth of Cellular Quiescence by an Rb-E2F Network Switch. Cell Reports 20:3223–3235 Signaling Link
Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VY, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Clark J, Hawkins PT, Stephens LR (2017) PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K. Molecular Cell 68:566-580.e10 Signaling Link
Musante V, Li L, Kanyo J, Lam TT, Colangelo CM, Cheng SK, Brody AH, Greengard P, Le Novère N, Nairn AC (2017) Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition. eLife 6:e24998 Signaling 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
Pinna F, Bissinger M, Beuke K, Huber N, Longerich T, Kummer U, Schirmacher P, Sahle S, Breuhahn K (2017) A20/TNFAIP3 Discriminates Tumor Necrosis Factor (TNF)-Induced NF-κB from JNK Pathway Activation in Hepatocytes. Frontiers in Physiology 8:610 Signaling Link
Proctor CJ, Goljanek-Whysall K (2017) Using computer simulation models to investigate the most promising microRNAs to improve muscle regeneration during ageing. Scientific Reports 7:12314 Genetics Signaling Link
Proctor CJ, Smith GR (2017) Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis. PLoS One 12:e0187568 Genetics Signaling Link
Rodesney CA, Roman B, Dehamani N, Cooley BJ, Katira P, Touhami A, Gordon VD (2017) Mechanosensing of shear by Pseudomonas aeruginosa leads to increased levels of the cyclic-di-GMP signal initiating biofilm development. Proceedings of the National Academy of Sciences USA 114:5906–5911 Microbiology Signaling Link
Selvarajoo K (2017) A systems biology approach to overcome TRAIL resistance in cancer treatment. Progress in Biophysics and Molecular Biology 128:142–154 Signaling Link

16 publications
Andrews SS, Peria WJ, Richard CY, Colman-Lerner A, Brent R (2016) Push-pull and feedback mechanisms can align signaling system outputs with inputs. Cell Systems 3:444–455 Signaling Link
Balabin FA, Sveshnikova AN (2016) Computational biology analysis of platelet signaling reveals roles of feedbacks through phospholipase C and inositol 1,4,5-trisphosphate 3-kinase in controlling amplitude and duration of calcium oscillations. Mathematical Biosciences 276:67–74 Signaling Link
Beuke K (2016) TNF-induced NF-κB Signal Transduction in the Liver. Ph.D. Thesis, Heidelberg University, Germany. Immunology Signaling Link
Bush A, Vasen G, Constantinou A, Dunayevich P, Patop IL, Blaustein M, Colman-Lerner A (2016) Yeast GPCR signaling reflects the fraction of occupied receptors, not the number. Molecular Systems Biology 12:898 Signaling Link
Dalle Pezze P, Ruf S, Sonntag AG, Langelaar-Makkinje M, Hall P, Heberle AM, Navas PR, van Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B, Deitersen J, Stork B, Fäßler E, Schäuble S, Horvatovich P, Shanley DP, Thedieck K (2016) A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nature Communications 7:13254 Signaling Link
Di Camillo B, Carlon A, Eduati F, Toffolo GM (2016) A rule-based model of insulin signalling pathway. BMC Systems Biology 10:38 Signaling Link
Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances 2:e1600823 Biochemistry Signaling Link
Emiola A, Andrews SS, Heller C, George J (2016) Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli. Proceedings of the National Academy of Sciences USA 113:3108–3113 Signaling Cell Biology Link
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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
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19 publications
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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
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11 publications
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12 publications
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13 publications
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Koval OM, Snyder JS, Wolf RM, Pavlovicz RE, Glynn P, Curran J, Leymaster ND, Dun W, Wright PJ, Cardona N, Qian L, Mitchell CC, Boyden PA, Binkley PF, Li C, Anderson ME, Mohler PJ, Hund TJ (2012) Ca2+/calmodulin-dependent protein kinase II-based regulation of voltage-gated Na+ channel in cardiac disease. Circulation 126:2084–2094 Physiology Signaling Link
Leach MD, Tyc KM, Brown AJP, Klipp E (2012) Modelling the Regulation of Thermal Adaptation in Candida albicans, a Major Fungal Pathogen of Humans. PLoS One 7:e32467 Signaling Link
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Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D’Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, Breuhahn K (2012) A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes. Frontiers in Physiology 3:466 Signaling Link
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Sarma U, Ghosh I (2012) Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. BMC Research Notes 5:287 Signaling Link
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21 publications
Bairy S, Wong CF (2011) Influence of kinetics of drug binding on EGFR signaling: A comparative study of three EGFR signaling pathway models. Proteins: Structure, Function, and Bioinformatics 79:2491–2504 Signaling Link
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10 publications