articles | essays | chapters | preprints
I Mirzaev, J Gunawardena, "Laplacian dynamics on general graphs", submitted, 2013.
N Hao, B A Budnik, J Gunawardena, E K O'Shea, "Tunable signal processing through modular control of transcription factor translocation", Science, 339:460-4 2013. PDF Sci Signal
J P Dexter, J Gunawardena, "Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli", J Biol Chem, 288:5770-8 2013. PDF.
T Dasgupta, D H Croll, J A Owen, M G Vander Heiden, J W Locasale, U Alon, L C Cantley, J Gunawardena, "A fundamental trade off in covalent switching and its circumvention in glucose homeostasis", submitted, 2012.
S L Field, T Dasgupta, H Bulsara, R S Savage, J Adebayo, M Cummings, J Gunawardena, N M Orsi, "IL-12 (p40), IL-13 and MCP-1 drive murine inflammatory networks in vivo", submitted, 2012.
Y Xu, J Gunawardena, "Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited", J Theor Biol, 311:139-52 2012. PDF.
R L Karp, M Peréz Millán, T Dasgupta, A Dickenstein, J Gunawardena, "Complex-linear invariants of biochemical reaction networks", J Theor Biol, 311:130-8 2012. PDF Supplementary information.
S Prabakaran, G Lippens, H Steen, J Gunawardena, "Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding", WIREs Systems Biology and Medicine, 4:565-83 2012. PDF.
J Gunawardena, "A linear framework for time-scale separation in nonlinear biochemical systems", PLoS ONE, 7:e36321 2012. Full text PDF Supplementary information.
F Gnad, J. Estrada, J Gunawardena, "Proteus: a web-based, context-specific modelling tool", Bioinformatics, 28:1284-6 2012. Full text PDF.
Y Xu, J Gunawardena, "Heterogeneity, bimodality and the dose-time trade off in EGF signalling", submitted, 2011.
S L Harvey, G Enciso, N E Dephoure, S P Gygi, J Gunawardena, D R Kellogg, "Protein phosphatase 2A functions at a systems level to modulate the activities of Wee1 and Cdk1 in early mitosis", Mol Biol Cell, 22:3595-608 2011. Full text PDF.
S Prabakaran, R A Everley, I Landrieu, J-M Wieruszeski, G Lippens, H Steen, J Gunawardena, "Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions", Mol Sys Biol, 7:482 2011. Full text PDF. This was a featured paper in Molecular Systems Biology.
F Gnad, J Gunawardena, M Mann, "PHOSIDA 2011: the posttranslational modification database", Nucleic Acids Res, 39:253-60 2010. PDF. This was a featured article in Nucleic Acids Research.
F Gnad, F Forner, D F Zielinska, E Birney, J Gunawardena, M Mann, "Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes and mitochondria", Mol Cell Proteomics, 9:2642-53 2010. PDF
M. Thomson, J Gunawardena, "The rational parameterisation theorem for multisite post-translational modification systems", J Theor Biol, 261:626-36 2009. PDF
M Thomson, J Gunawardena, "Unlimited multistability in multisite phosphorylation systems", Nature, 460:274-7 2009. doi:10.1038/nature08102. PDF Supplementary Information
A Mallavarapu, M Thomson, B Ullian, J Gunawardena, "Programming with models: modularity and abstraction provide powerful capabilities for systems biology", J Roy Soc Interface, 6:257-70 2009. PDF
2008 and earlier
A Manrai, J Gunawardena, "The geometry of multisite phosphorylation", Biophys J, 95:5533-43 2008. PDF Supplementary Mathematica notebook
N Andrew, D Craig, J P Urbanski, J Gunawardena, T Thorsen, "Microfluidic temporal cell stimulation", Proceedings of the 12th International Conference on Miniaturized Systems for the Life Sciences, μTAS 2008. PDF
J Gunawardena, "Signals and systems: towards a systems biology of signal transduction", invited paper for the Special Issue on Computational Systems Biology, Proc IEEE, 96:1386-97 2008. PDF
J Gunawardena, "Distributivity and processivity in multisite phosphorylation can be distinguished through steady-state invariants", Biophys J, 93:3828-34 2007. PDF
J Gunawardena, "Multisite protein phosphorylation makes a good threshold but can be a poor switch", PNAS 102:14617-22 2005. PDF
J Gunawardena, "Biology is more theoretical than physics", Mol Biol Cell, invited perspective, to appear, 2013.
J Gunawardena, "Silicon dreams of cells into symbols", Nat Biotech 30:838-40 2012. PDF. News & Views on Karr et al, "A whole-cell computational model predicts phenotype from genotype", Cell 150:389-401 2012.
J Gunawardena, "Some lessons about models from Michaelis and Menten", Mol Biol Cell 23:517-9 2012. Invited perspective. PDF
J Gunawardena, "Biological systems theory", Science 328:581-2 2010. PDF. News & Views on G Shinar, M Feinberg, "Structural sources of robustness in biochemical reaction networks", Science 327:1389-91 2010.
J Gunawardena, "Models in systems biology: minimalist versus exhaustive strategies". In B Engquist (editor), Encyclopedia of Applied and Computational Methods, Springer, Berlin, Heidleberg, New York. To appear, 2012.
J Gunawardena, "Modeling of interaction networks in the cell: theory and mathematical methods". In H Weinstein (editor), Simulation and Modeling, Volume 9 of E Egelman (editor), Comprehensive Biophysics, Academic Press, Elsevier, Amsterdam. 2012. Elsevier
J Gunawardena, "Models in systems biology: the parameter problem and the meanings of robustness". In H. Lodhi, S. Muggleton (editors), Elements of Computational Systems Biology, John Wiley and Sons, New York, 2009. PDF
J Gunawardena, "A linear elimination framework", 2011. q-bio.MN:1109.6231
M Thomson, J Gunawardena, "Multi-bit information storage by multisite phosphorylation", 2007. q-bio.MN:0706.3735
A Mallavarapu, M Thomson, B Ullian, J Gunawardena, "Modular model building", 2007. q-bio.MN:0710.3421
M Lipson, "Differential and graphical approaches to multistability for chemical reaction networks", Senior Honours Thesis, Hoopes Prize, 2007. q-bio.MN:0709.0125
J Gunawardena, "Chemical Reaction Network Theory for in-silico biologists", 2003. PDF
J Gunawardena, "Notes on Metabolic Control Analysis", 2002. PDF