Virtual Cell Program

Home / Papers

articles | essays | chapters | preprints

Research Articles

2014

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", J Biol Chem, doi:10.1074/jbc.M113.546515 2014. Paper

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

2013

J P Dexter, P Xu, J Gunawardena, M N McClean, "Robust architecture of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae", submitted, 2013.

S Prabakaran, M Hemberg, R Chauhan, D Winter, R Tweedie-Cullen, C Dittrich, E Hong, J Gunawardena, H Steen, G Kreiman, J A Steen, "Peptides from RNAs classified as non-coding", submitted, 2013.

S Prabakaran, J Gunawardena, E Sontag, "Paradoxical results in perturbation-based biological network reconstruction", submitted, 2013.

T Ahsendorf, F Wong, R Eils, J Gunawardena, "A framework for modelling gene regulation that accommodates non-equilibrium mechanisms", 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. PDF

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, supplementary Mathematica notebook and accompanying Mathematica package.

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.
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 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.

2011

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.

2010

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

2009

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

Essays

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

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.

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. PDF

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. PDF

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

 

Home | Research | Systems Timeline | Teaching
Papers | People | Positions
Events | Theory Lunch | Contact