articles | essays | chapters | preprints | posters
M M Slabodnick, J G Ruby, S B Reiff, E C Swart, S Gosai, S Prabakaran, E Witkowska, G E Larue, S Fisher, R M Freeman Jr, J Gunawardena, W Chu, N A Stover, B D Gregory, M Nowacki, J Derisi, S W Roy, W F Marshall, P Sood, "The macronuclear genome of Stentor coeruleus reveals tiny introns in a giant cell", Curr Biol27:569-75 2017. PDF.
H Qi, C Despres, S Prabakaran, F X Cantrelle, B Chambraud, J Gunawardena, G Lippens, C Smet-Nocca, I Landrieu, "The study of posttranslational modifications of Tau protein by nuclear magnetic resonance spectroscopy: phosphorylation of Tau protein by ERK2 recombinant kinase and rat brain extract, and acetylation by recombinant CREB-binding protein", Methods Mol Biol1253:179-213 2017. PDF.
J Estrada, F Wong, A DePace, J Gunawardena, "Information integration and energy expenditure in gene regulation", Cell 166:234-44 2016. Full text (valid until 19 August 2016; there are MathML errors in the online version when it is viewed in some browsers; the pdf version is free of those errors) PDF Supplemental Information. For his contribution to this paper, Javier Estrada was awarded the Young Investigator Award at ICSB 2016.
J Estrada*, N Andrew*, D Gibson, F Chang, F Gnad, J Gunawardena, "Cellular interrogation: exploiting cell-to-cell variability to discriminate regulatory mechanisms in oscillatory signalling", PLoS Comput Biol 12:e1004995 2016. Full text PDF.
H Qi, S Prabakaran, F-C Cantrelle, B Chambraud, J Gunawardena, G Lippens, I Landrieu, "Characterization of neuronal tau protein as a target of extracellular-signal-regulated kinase", J Biol Chem 291:7742-53 2016. PDF.
M Malleshaiah, M Padi, P Rué, J Quackenbush, A Martinez-Arias, J Gunawardena, "Nac1 coordinates a sub-network of pluripotency factors to regulate embryonic stem cell differentiation", Cell Reports 14:1181-94 2016. Full text PDF.
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", BMC Syst Biol 9:76 2015. Full text PDF Amalgamated Additional Files.
J P Dexter*, T Dasgupta*, J Gunawardena, "Invariants reveal multiple forms of robustness in bifunctional enzyme systems", Integr Biol 7:883-94 2015. PDF Cover Supplementary Mathematica notebook.
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", BMC Syst Biol 9:17 2015. Full text PDF Supplementary Information.
T Ahsendorf*, F Wong*, R Eils, J Gunawardena, "A framework for modelling gene regulation which accommodates non-equilibrium mechanisms", BMC Biol, 12:102 2014. Full text PDF Additional File BMC Biology commentary.
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 PDF Supplementary Information.
S Prabakaran, J Gunawardena, E Sontag, "Paradoxical results in perturbation-based biological network reconstruction", Biophys J 106:2720-8 2014. PDF Supplementary Information.
J Gunawardena, "Models in biology: 'accurate descriptions of our pathetic thinking'", BMC Biol 12:29 2014. Invited review. Full text PDF 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. PDF.
J Gunawardena, "Time-scale separation: Michaelis and Menten's old idea, still bearing fruit", FEBS J, 281:473-88 2014. Invited review. PDF.
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. Editor's choice in Sci Signal and research highlight in Nat Rev Genet.
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.
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.
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 Supplementary Information. 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.
M. Malleshaiah J Gunawardena, "Cybernetics redux: an outside-in strategy for unraveling cellular function", Dev Cell 36:2-4 2016. PDF. Preview of Mitchell, Wei & Lim, "Oscillatory stress stimulation uncovers Achilles' heel of the yeast MAPK signaling network", Science 350:1379-83 2015.
J Gunawardena, "Beware the tail that wags the dog: informal and formal models in biology", Mol Biol Cell, 25:3441-4 2014. Invited perspective. PDF.
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.
G Lippens, J Gunawardena, I Landrieu, C Smet-Nocca, S Prabakaran, B Parent, A Leroy, I Huvent, "Post-translational modifications of the proteome: the example of tau in the neuron and the brain". In J Loscalzo, A-L Barabási, E K Silverman (editors), Network Medicine. Complex Systems in Human Disease and Therapeutics, Harvard University Press, Cambridge MA USA, 2017. HUP.
J Gunawardena, "Models in systems biology: minimalist versus exhaustive strategies". In B Engquist (editor), Encyclopedia of Applied and Computational Methods, Springer-Verlag, Berlin, Germany, 2015. Springer.
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.
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.
C J DeHart, L Fornelli, O S Skinner, L C Anderson, P D Compton, C L Hendrickson, P M Thomas, G Lahav, J Gunawardena, N L Kelleher, "Mapping p53 proteoforms by native and denaturing top-down mass spectrometry", American Society for Mass Spectrometry Annual Conference, San Antonio, Texas, June 2016. Poster.
M Malleshaiah, M Padi, P Rue, J Quackenbush, A Martinez-Arias, J Gunawardena, "Nac1 coordinates a sub-network of pluripotency factors to regulate embryonic stem cell differentiation", International Society for Stem Cell Research Conference, San Francisco, June 2016. Poster.
Gunawardena Lab, "Cellular information processing", Harvard Undergraduate Life Sciences Research Fair, 2016. Poster.
M Cummings, T Dasgupta, J Adebayo, G Mappa, R Hutson, N Wilkinson, J Gunawardena, N M Orsi, "Cytokine networks in endometrial carcinogenesis", UK Pathological Society, Dublin, Ireland, June 2015. Poster. Awarded 2nd prize by the UK Pathological Society.