M. Thomson, J Gunawardena, "The rationality theorem for multisite post-translational modification systems", submitted, 2009.
F Gnad, J Gunawardena, F Forner, E Birney, M Mann, "Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes and mitochondria", submitted, 2009.
M Thomson, J Gunawardena, "Unlimited multistability in multisite phosphorylation systems", Nature, doi:10.1038/nature08102, 2009. PDF
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
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. doi:10.1098/rsif.2008.0205, 2008. PDF PubMed
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, "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
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
A Mallavarapu, "Caring about sharing: little b, a language for building modular models", Alife Boston, 2005. PPT
J Gunawardena, "In-silico biology: from virtual genomes to virtual cells", BioIT World 2005. PDF
J Gunawardena, "Fluorescence correlation spectroscopy in single mammalian cells", Systems Biology Department Retreat 2005. PDF
J Gunawardena, "The low road to systems biology", Whitehead Institute BioFrontiers 2004. PDF
A Mallavarapu & J Gunawardena, "little b - a language for modular, shareable models of biological systems", Systems Biology Department Retreat 2004. PDF