2024
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
Bálint D, Póti ÁL, Alexa A, Sok P, Albert K, Torda L, Földesi-Nagy D, Csókás D, Turczel G, Imre T, Szarka E, Fekete F, Bento I, Bojtár M, Palkó R, Szabó P, Monostory K, Pápai I, Soós T, Reményi A (2024) Reversible covalent c-Jun N-terminal kinase inhibitors targeting a specific cysteine by precision-guided Michael-acceptor warheads. Nature Communications 15:8606
Signaling
Link
Chakrabarti KS, Bakhtiari D, Rezaei-Ghaleh N (2024) Bifurcations in coupled amyloid-β aggregation-inflammation systems. npj Systems Biology and Applications 10:80
Signaling
Macromolecular Biochemistry
Link
Goglia I, Węglarz-Tomczak E, Gioia C, Liu Y, Virtuoso A, Bonanomi M, Gaglio D, Salmistraro N, De Luca C, Papa M, Alberghina L, Westerhoff HV, Colangelo AM (2024) Fusion–fission–mitophagy cycling and metabolic reprogramming coordinate nerve growth factor (NGF)-dependent neuronal differentiation. FEBS Journal 291:2811–2835
Signaling
Link
Kampourakis T, Ponnam S, Campbell KS, Wellette-Hunsucker A, Koch D (2024) Cardiac myosin binding protein-C phosphorylation as a function of multiple protein kinase and phosphatase activities. Nature Communications 15:5111
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
Kolokotroni E, Abler D, Ghosh A, Tzamali E, Grogan J, Georgiadi E, Büchler P, Radhakrishnan R, Byrne H, Sakkalis V, Nikiforaki K, Karatzanis I, McFarlane NJB, Kaba D, Dong F, Bohle RM, Meese E, Graf N, Stamatakos G (2024) A Multidisciplinary Hyper-Modeling Scheme in Personalized In Silico Oncology: Coupling Cell Kinetics with Metabolism, Signaling Networks, and Biomechanics as Plug-In Component Models of a Cancer Digital Twin. Journal of Personalized Medicine 14:475
Physiology
Signaling
Link
Korobkina JD, Panteleev MA, Sveshnikova AN (2024) Comparative Investigation of the Mechanisms of Calcium Response in Human and Murine Spermatozoa. Biochemistry (Moscow) 18:110–126
Signaling
Cell Biology
Biophysics
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
Pontisso I, Ornelas-Guevara R, Chevet E, Combettes L, Dupont G (2024) Gradual ER calcium depletion induces a progressive and reversible UPR signaling. PNAS Nexus 3:pgae229
Signaling
Link
Poprawa SM, Stasi M, Kriebisch BAK, Wenisch M, Sastre J, Boekhoven J (2024) Active droplets through enzyme-free, dynamic phosphorylation. Nature Communications 15:4204
Chemistry
Synthetic Biology
Signaling
Link
Ramsey K, Britt M, Maramba J, Ushijima B, Moller E, Anishkin A, Häse C, Sukharev S (2024) The dynamic hypoosmotic response of Vibrio cholerae relies on the mechanosensitive channel MscS. iScience 27:110001
Signaling
Microbiology
Link
Sveshnikova AN, Shibeko AM, Kovalenko TA, Panteleev MA (2024) Kinetics and regulation of coagulation factor X activation by intrinsic tenase on phospholipid membranes. Journal of Theoretical Biology 582:111757
Signaling
Biophysics
Link
Tseng Y-Y (2024) Comparative mathematical modeling reveals the differential effects of high-fat diet and ketogenic diet on the PI3K-Akt signaling pathway in heart. Nutrition & Metabolism 21:65
Metabolism
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
15 publications
2022
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
2021
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
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
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
2019
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
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
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
2017
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
Galochkina T, Chelushkin M, Sveshnikova A (2017) Activation of Contact Pathway of Blood Coagulation on the Lipopolysaccharide Aggregates. Mathematical Modelling of Natural Phenomena 12:196–207
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
17 publications
2016
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
Gallimore AR, Aricescu AR, Yuzaki M, Calinescu R (2016) A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression. PLoS Computational Biology 12:e1004664
Signaling
Link
Obydennyy SI, Sveshnikova AN, Ataullakhanov FI, Panteleev MA (2016) Dynamics of calcium spiking, mitochondrial collapse and phosphatidylserine exposure in platelet subpopulations during activation. Journal of Thrombosis and Haemostasis 14:1867–1881
Signaling
Link
Panchal C, Azimi S, Petre I (2016) Generating the Logicome of a Biological Network. International Conference on Algorithms for Computational Biology. Springer, 38–49
Computational Method
Signaling
Link
Pappalardo F, Russo G, Candido S, Pennisi M, Cavalieri S, Motta S, McCubrey JA, Nicoletti F, Libra M (2016) Computational Modeling of PI3K/AKT and MAPK Signaling Pathways in Melanoma Cancer. PLoS One 11:e0152104
Signaling
Link
Proctor CJ, Gartland A (2016) Simulated interventions to ameliorate age-related bone loss indicate the importance of timing. Frontiers in Endocrinology 7:61
Physiology
Signaling
Link
Sano T, Kawata K, Ohno S, Yugi K, Kakuda H, Kubota H, Uda S, Fujii M, Kunida K, Hoshino D, Hatano A, Ito Y, Sato M, Suzuki Y, Kuroda S (2016) Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin. Science Signaling 9:ra112–ra112
Signaling
Physiology
Link
Sveshnikova AN, Balatskiy AV, Demianova AS, Shepelyuk TO, Shakhidzhanov SS, Balatskaya MN, Pichugin AV, Ataullakhanov FI, Panteleev MA (2016) Systems biology insights into the meaning of the platelet’s dual-receptor thrombin signaling. Journal of Thrombosis and Haemostasis 14:2045–2057
Physiology
Signaling
Link
Talemi SR, Tiger C-F, Andersson M, Babazadeh R, Welkenhuysen N, Klipp E, Hohmann S, Schaber J (2016) Systems Level Analysis of the Yeast Osmo-Stat. Scientific Reports 6:30950
Signaling
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
Woller A, Duez H, Staels B, Lefranc M (2016) A mathematical model of the liver circadian clock linking feeding and fasting cycles to clock function. Cell Reports 17:1087–1097
Metabolism
Physiology
Signaling
Link
Xie Y (2016) Multi-scale modelling of the cellular and molecular mechanisms of hyperpolarisation mediated synaptic plasticity in the vestibular nuclei. MSc Thesis, The University of Edinburgh, UK
Signaling
Physiology
Link
19 publications
2015
Amemiya T, Honma M, Kariya Y, Ghosh S, Kitano H, Kurachi Y, Fujita K, Sasaki Y, Homma Y, Abernethy DR, Kume H, Suzuki H (2015) Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology. npj Systems Biology and Applications 1:15005
Toxicology
Signaling
Link
Everetts NJ (2015) Computational Analysis of the Control of Cell Cycle Entry. Bachelor's Thesis, Department of Molecular and Cellular Biology, University of Arizona, USA
Cell Biology
Signaling
Link
Hamacher-Brady A, Brady NR (2015) Bax/Bak-Dependent, Drp1-Independent Targeting of XIAP into Inner-Mitochondrial Compartments Counteracts Smac-Dependent Effector Caspase Activation. Journal of Biological Chemistry 290:22005-18.
Signaling
Link
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
Li L, Gervasi N, Girault J-A (2015) Dendritic geometry shapes neuronal cAMP signalling to the nucleus. Nature Communications 6:6319
Cell Biology
Signaling
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
Subramanian A, Sarkar RR (2015) Dynamics Of GLI Regulation And A Strategy To Control Cancerous Situation: Hedgehog Signaling Pathway Revisited. Journal of Biological Systems 23:681-719
Signaling
Link
Suwanmajo T, Krishnan J (2015) Mixed mechanisms of multi-site phosphorylation. Journal of the Royal Society Interface 12:20141405
Signaling
Link
Sveshnikova AN, Ataullakhanov FI, Panteleev MA (2015) Compartmentalized calcium signaling triggers subpopulation formation upon platelet activation through PAR1. Molecular BioSystems 11:1052-60
Signaling
Link
Wang H-Y, Huang Y-X, Zheng L-H, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Sun Y, Wang G-N, Ma Z-Q, Li Y-X (2015) Modelling Coupled Oscillations in the Notch, Wnt, and FGF Signaling Pathways during Somitogenesis: A Comprehensive Mathematical Model. Computational Intelligence and Neuroscience 2015:387409
Signaling
Link
Willems PH, Pahle J, Stalpers XL, Mugahid D, Nikolaew A, Koopman WJ, Kummer U (2015) PKC-mediated inhibitory feedback of the cholecystokinin 1 receptor controls the shape of oscillatory Ca2+ signals. FEBS Journal 282:2187-201
Signaling
Link
11 publications
2014
Antunes G, Sebastião AM, de Souza FMS (2014) Mechanisms of regulation of olfactory transduction and adaptation in the olfactory cilium. PLoS One 9:e105531
Signaling
Pharmacology
Link
Dalle Pezze P, Nelson G, Otten EG, Korolchuk VI, Kirkwood TBL, von Zglinicki T, Shanley DP (2014) Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions. PLoS Computational Biology 10:e1003728.
Signaling
Link
Graybill C, Prehoda KE (2014) Ordered multisite phosphorylation of lethal giant larvae by atypical protein kinase C. Biochemistry 53:4931-7
Signaling
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
Kleppe R, Ghorbani S, Martinez A, Haavik J (2014) Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins. FEBS Letters 588:92–98
Signaling
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
McAuley MT, Khalil R, Stockton DJ, Schilstra MJ (2014) Modelling the flagellar motor assembly process to help improve industrial operations systems design. Preprint
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
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S (2014) A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. BioSystems 124:26–38
Metabolism
Signaling
Genetics
Link
Schaber J, Lapytsko A, Flockerzi D (2014) Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. Journal of the Royal Society Interface 11:20130971
Signaling
Link
Ventura AC, Bush A, Vasen G, Goldín MA, Burkinshaw B, Bhattacharjee N, Folch A, Brent R, Chernomoretz A, Colman-Lerner A (2014) Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range. Proceedings of the National Academy of Sciences USA 111:E3860–E3869
Signaling
Link
Wang CCN, Chang P-C, Ng K-L, Chang C-M, Sheu PCY, Tsai JJP (2014) A model comparison study of the flowering time regulatory network in Arabidopsis. BMC Systems Biology 8:15
Signaling
Link
12 publications
2013
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
Gow C-H (2013) Novel mechanisms of transcriptional regulation by leukemia fusion proteins. Ph.D. Thesis, University of Cincinnati, Ohio, USA.
Signaling
Link
Hayashi K, Piras V, Tabata S, Tomita M, Selvarajoo K (2013) A systems biology approach to suppress TNF-induced proinflammatory gene expressions. Cell Communication and Signaling 11:84
Signaling
Link
Helgeson LA, Nolen BJ (2013) Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP. eLife 2:e00884
Macromolecular Biochemistry
Signaling
Link
Kolodkin AN, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant NJ (2013) Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications 4:1792
Signaling
Link
Qi Y-F, Huang Y-X, Wang H-Y, Zhang Y, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Zheng L-H, Sun Y, Wang G-N, Li Y-X (2013) Elucidating the crosstalk mechanism between IFN-gamma and IL-6 via mathematical modelling. BMC Bioinformatics 14:41
Signaling
Link
Ravichandran S, Rao KVS, Jain S (2013) Bistability in a model of early B cell receptor activation and its role in tonic signaling and system tunability. Molecular BioSystems 9:2498-2511
Signaling
Link
Sahaboglu A, Paquet-Durand O, Dietter J, Dengler K, Bernhard-Kurz S, Ekström PAR, Hitzmann B, Ueffing M, Paquet-Durand F (2013) Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms. Cell Death & Disease 4:e488
Cell Biology
Signaling
Link
Sharma V, Compagnoni A (2013) Computational and mathematical models of the JAK-STAT signal transduction pathway. Proceedings of the 2013 Summer Computer Simulation Conference 15
Computational Method
Signaling
Link
Sharp GC (2013) Comprehensive data analysis to study parturition. Ph.D. Thesis, University of Edinburgh, UK.
Signaling
Link
Sharp GC, Ma H, Saunders PTK, Norman JE (2013) A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour. PLoS One 8:e70180
Signaling
Link
Smith GR, Shanley DP (2013) Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Systems Biology 7:41
Signaling
Link
Wang H-Y, Huang Y-X, Qi Y-F, Zhang Y, Bao Y-L, Sun L-G, Zheng L-H, Zhang Y-W, Ma Z-Q, Li Y-X (2013) Mathematical models for the Notch and Wnt signaling pathways and the crosstalk between them during somitogenesis. Theoretical Biology & Medical Modelling 10:27
Signaling
Link
13 publications
2012
Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I (2012) Regulation of release factor expression using a translational negative feedback loop: A systems analysis. RNA 18:2320-2334
Signaling
Link
Dalle Pezze P, Sonntag AG, Thien A, Prentzell MT, Godel M, Fischer S, Neumann-Haefelin E, Huber TB, Baumeister R, Shanley DP, Thedieck K (2012) A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation. Science Signaling 5:ra25-ra25
Signaling
Link
Heiland I, Bodenstein C, Hinze T, Weisheit O, Ebenhoeh O, Mittag M, Schuster S (2012) Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii. Journal of Biological Physics 38:449-464
Signaling
Link
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
Li Y, Wang M, Carra C, Cucinotta FA (2012) Modularized Smad-regulated TGFβ signaling pathway. Mathematical Biosciences 240:187-200
Signaling
Link
Maiwald T (2012) Computational Analysis of The Interferon Alpha Signalling Using a Systems Biology Modelling Approach Pathway. Ph.D. Thesis, Heidelberg University, Germany.
Signaling
Link
Mazemondet O, John M, Leye S, Rolfs A, Uhrmacher AM (2012) Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells. PLoS One 7:e42792
Signaling
Link
Phelix CF, Rahimi O, Colom L, Perry G, Ginsberg S (2012) Transcriptome-to-reactome biosimulation: Basal forebrain cholinergic neuron neurotrophin signaling. Alzheimer’s & Dementia 8:P467–P468
Signaling
Link
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
Piras V, Hayashi K, Tomita M, Selvarajoo K (2012) Investigation of stochasticity in TRAIL signaling cancer model. Proceedings of the 2012 ICME International Conference on Complex Medical Engineering (CME) 609-614.
Signaling
Link
Rahimi O, Phelix CF, Perry G (2012) Transcriptome-To-Reactome Biosimulation: Oxidative Pathways to Apoptotic Cell Death. Alzheimer’s & Dementia 8:P478–P479
Signaling
Cell Biology
Link
Salvado B, Vilaprinyo E, Karathia H, Sorribas A, Alves R (2012) Two Component Systems: Physiological Effect of a Third Component. PLoS One 7:e31095
Signaling
Link
Sarma U, Ghosh I (2012) Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. BMC Systems Biology 6:82
Signaling
Link
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
Sarma U, Sareen A, Maiti M, Kamat V, Sudan R, Pahari S, Srivastava N, Roy S, Sinha S, Ghosh I, Chande AG, Mukhopadhyaya R, Saha B (2012) Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases. PLoS One 7:e39898
Signaling
Link
Schaber J, Baltanas R, Bush A, Klipp E, Colman-Lerner A (2012) Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast. Molecular Systems Biology 8:622
Signaling
Link
Schimek C, Vlaic S, Wöstemeyer J, Werner S, Schuster S, Schroeter A (2012) Model of the synthesis of trisporic acid in Mucorales showing bistability. IET Systems Biology 6:207-214
Signaling
Link
Tiedemann MT, Heinrichs DE, Stillman MJ (2012) Multiprotein Heme Shuttle Pathway in Staphylococcus aureus : Iron-Regulated Surface Determinant Cog-Wheel Kinetics. Journal of the American Chemical Society 134:16578-16585
Signaling
Link
Usuyama M, Ushida C, Shingai R (2012) A model of the intracellular response of an olfactory neuron in Caenorhabditis elegans to odor stimulation. PLoS One 7:e42907
Signaling
Link
Wegner K, Bachmann A, Schad J-U, Lucarelli P, Sahle S, Nickel P, Meyer C, Klingmüller U, Dooley S, Kummer U (2012) Dynamics and feedback loops in the transforming growth factor β signaling pathway. Biophysical Chemistry 162:22-34
Signaling
Link
21 publications
2011
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
Danis J, Turányi T (2011) Sensitivity analysis of bacterial chemotaxis models. Procedia Computer Science 7:233–234
Signaling
Microbiology
Link
Hooshangi S, Bentley WE (2011) LsrR quorum sensing “switch” is revealed by a bottom-up approach. PLoS Computational Biology 7:e1002172
Microbiology
Signaling
Link
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
Kleppe R, Martinez A, Døskeland SO, Haavik J (2011) The 14-3-3 proteins in regulation of cellular metabolism. Seminars in Cell & Developmental Biology 22:713–719
Signaling
Metabolism
Link
Koh G, Lee D-Y (2011) Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators. Computers in Biology and Medicine 41:512–528
Signaling
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
Schaber J, Flöttmann M, Li J, Tiger C-F, Hohmann S, Klipp E (2011) Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PLoS One 6:e14791
Signaling
Computational Method
Software
Link
Schweizer N (2011) Calcium signaling in fish cells. Ph.D. Thesis, University of Heidelberg, Germany.
Signaling
Link
Schweizer N, Kummer U, Hercht H, Braunbeck T (2011) Amplitude-encoded calcium oscillations in fish cells. Biophysical Chemistry 159:294–302
Signaling
Link
10 publications
2009
Bauer-Mehren A, Furlong LI, Rautschka M, Sanz F (2009) From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. BMC Bioinformatics 10:S6
Signaling
Link
Figueiredo AS, Höfer T, Klotz C, Sers C, Hartmann S, Lucius R, Hammerstein P (2009) Modelling and simulating interleukin-10 production and regulation by macrophages after stimulation with an immunomodulator of parasitic nematodes: Modelling interleukin-10 production and regulation. FEBS Journal 276:3454-3469
Signaling
Link
Goyal M, Rizzo M, Schumacher F, Wong CF (2009) Beyond thermodynamics: drug binding kinetics could influence epidermal growth factor signaling. Journal of Medicinal Chemistry 52:5582-5585
Signaling
Link
Ibrahim B, Schmitt E, Dittrich P, Diekmann S (2009) In silico study of kinetochore control, amplification, and inhibition effects in MCC assembly. BioSystems 95:35-50
Signaling
Link
Jain P, Bhalla US (2009) Signaling Logic of Activity-Triggered Dendritic Protein Synthesis: An mTOR Gate But Not a Feedback Switch. PLoS Computational Biology 5:e1000287
Signaling
Link
Menolascina F, Bellomo D, Maiwald T, Bevilacqua V, Ciminelli C, Paradiso A, Tommasi S (2009) Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. BMC Bioinformatics 10:S4
Laboratory Method
Signaling
Link
Orton RJ, Adriaens ME, Gormand A, Sturm OE, Kolch W, Gilbert DR (2009) Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Systems Biology 3:100
Signaling
Link
Sun Y-C (2009) Examination of effects of GSK3β phosphorylation, β-catenin phosphorylation, and β-catenin degradation on kinetics of Wnt signaling pathway using computational method. Theoretical Biology & Medical Modelling 6:13
Signaling
Link
Williamson T, Schwartz J-M, Kell DB, Stateva L (2009) Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. BMC Systems Biology 3:70
Signaling
Metabolism
Link
9 publications
