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Research Articles

2014

J P Dexter, P Xu, J Gunawardena, M N McClean, "Robust network structure of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae", submitted, 2014.

J P Dexter*, T Dasgupta*, J Gunawardena, "Invariants reveal multiple forms of robustness in bifunctional enzyme systems", submitted, 2014.

T Ahsendorf, F Wong, R Eils, J Gunawardena, "A framework for modelling gene regulation which accommodates non-equilibrium mechanisms", BMC Biol, 12:102 2014. Provisional online version

S Prabakaran*, M Hemberg*, R Chauhan*, D Winter, R Tweedie-Cullen, C Dittrich, E Hong, J Gunawardena, H Steen, G Kreiman, J A Steen, "Quantitative profiling of peptides from RNAs classified as non-coding", Nat Commun doi:10.1038/ncomms6429 2014. Preview   Paper  Supplementary Information

S Prabakaran, J Gunawardena, E Sontag, "Paradoxical results in perturbation-based biological network reconstruction", Biophys J 106:2720-8 2014. Paper   Supplementary Information

J Gunawardena, "Models in biology: 'accurate descriptions of our pathetic thinking'", BMC Biol 12:29 2014. Invited review. Full text   Paper   Blog     F1000   Nature

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 by enzyme bifunctionality in glucose homeostasis", J Biol Chem, 289:13010-25 2014. Paper

J Gunawardena, "Time-scale separation: Michaelis and Menten's old idea, still bearing fruit", FEBS J, 281:473-88 2014. Invited review. Paper

2013

S L Field, T Dasgupta, H Bulsara, R S Savage, J Adebayo, M Cummings, J Gunawardena, N M Orsi, "Bayesian modelling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine inflammatory networks in vivo", submitted, 2013.

J Estrada*, N Andrew*, D Gibson, F Chang, F Gnad, J Gunawardena, "Cellular interrogation: multiple questions discriminate molecular mechanisms in mammalian cells", submitted, 2013.

I Mirzaev, J Gunawardena, "Laplacian dynamics on general graphs", Bull Math Biol, 75:2118-49 2013. Paper

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.   Paper   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. Paper, supplementary Mathematica notebook and accompanying Mathematica package.

2012

Y Xu, J Gunawardena, "Heterogeneity, bimodality and the dose-time trade off in EGF signalling", submitted, 2012.

Y Xu, J Gunawardena, "Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited", J Theor Biol, 311:139-52 2012. Paper.

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. Paper   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. Paper.

J Gunawardena, "A linear framework for time-scale separation in nonlinear biochemical systems", PLoS ONE, 7:e36321 2012.
The published version of this paper on the PLoS ONE site had typesetting and figure reference errors that were introduced by PLoS ONE during publication. These errors have finally been corrected in the online version and in the Paper.   Supplementary information.

F Gnad, J. Estrada, J Gunawardena, "Proteus: a web-based, context-specific modelling tool", Bioinformatics, 28:1284-6 2012. Full text   Paper.

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   Paper.

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   Paper. This was a featured paper in Molecular Systems Biology.

2010

F Gnad, J Gunawardena, M Mann, "PHOSIDA 2011: the posttranslational modification database", Nucleic Acids Res, 39:253-60 2010. Paper. 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. Paper

2009

M. Thomson, J Gunawardena, "The rational parameterisation theorem for multisite post-translational modification systems", J Theor Biol, 261:626-36 2009. Paper

M Thomson, J Gunawardena, "Unlimited multistability in multisite phosphorylation systems", Nature, 460:274-7 2009. doi:10.1038/nature08102. Paper   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. Paper

2008 and earlier

A Manrai, J Gunawardena, "The geometry of multisite phosphorylation", Biophys J, 95:5533-43 2008. Paper 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. Paper

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. Paper

J Gunawardena, "Distributivity and processivity in multisite phosphorylation can be distinguished through steady-state invariants", Biophys J, 93:3828-34 2007. Paper

J Gunawardena, "Multisite protein phosphorylation makes a good threshold but can be a poor switch", PNAS 102:14617-22 2005. Paper

Essays

J Gunawardena, "Beware the tail that wags the dog: informal and formal models in biology", Mol Biol Cell, 25:3441-4 2014. Invited perspective. Paper

J Gunawardena, "Biology is more theoretical than physics", Mol Biol Cell, 24:1827-9 2013. Invited perspective. Paper

J Gunawardena, "Silicon dreams of cells into symbols", Nat Biotech 30:838-40 2012. Paper. 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. Paper

J Gunawardena, "Biological systems theory", Science 328:581-2 2010. Paper. News & Views on G Shinar, M Feinberg, "Structural sources of robustness in biochemical reaction networks", Science 327:1389-91 2010.

Book chapters

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, pages 243-67. Volume 9 of E Egelman (editor), Comprehensive Biophysics, Academic Press, Oxford. 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. Paper

Preprints & technical reports

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. Paper

J Gunawardena, "Notes on Metabolic Control Analysis", 2002. Paper

 

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