Jeremy Gunawardena

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Beware the tail that wags the dog: informal and formal models in biology
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115
    Mol Biol Cell 25:3441-4. 2014
  2. pmc Models in biology: 'accurate descriptions of our pathetic thinking'
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, USA
    BMC Biol 12:29. 2014
  3. pmc Biology is more theoretical than physics
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Biol Cell 24:1827-9. 2013
  4. pmc A linear framework for time-scale separation in nonlinear biochemical systems
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e36321. 2012
  5. pmc Some lessons about models from Michaelis and Menten
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Biol Cell 23:517-9. 2012
  6. pmc Multisite protein phosphorylation makes a good threshold but can be a poor switch
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 102:14617-22. 2005
  7. pmc Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding
    Sudhakaran Prabakaran
    Department of Systems Biology, Harvard Medical School, Boston, MA, USA
    Wiley Interdiscip Rev Syst Biol Med 4:565-83. 2012
  8. pmc The geometry of multisite phosphorylation
    Arjun Kumar Manrai
    Department of Physics, Harvard University, Cambridge, Massachusetts, USA
    Biophys J 95:5533-43. 2008
  9. pmc Time-scale separation--Michaelis and Menten's old idea, still bearing fruit
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA, USA
    FEBS J 281:473-88. 2014
  10. pmc Proteus: a web-based, context-specific modelling tool for molecular networks
    Florian Gnad
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 28:1284-6. 2012

Collaborators

Detail Information

Publications20

  1. pmc Beware the tail that wags the dog: informal and formal models in biology
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115
    Mol Biol Cell 25:3441-4. 2014
    ..Here I suggest to the contrary that progress in biology requires a better integration of the formal with the informal. ..
  2. pmc Models in biology: 'accurate descriptions of our pathetic thinking'
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, USA
    BMC Biol 12:29. 2014
    ..I will discuss three models from this perspective, each of which yields biological insights, and this will lead to some guidelines for prospective model builders...
  3. pmc Biology is more theoretical than physics
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Biol Cell 24:1827-9. 2013
    ..Here, ideas from a previous essay are expanded upon to suggest, to the contrary, that the second kind of theory has always played a critical role and that biology, therefore, is a good deal more theoretical than physics...
  4. pmc A linear framework for time-scale separation in nonlinear biochemical systems
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e36321. 2012
    ..We show that elimination of internal complexity is feasible when the relevant graph is strongly connected. The framework provides a new methodology with the potential to subdue combinatorial explosion at the molecular level...
  5. pmc Some lessons about models from Michaelis and Menten
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Biol Cell 23:517-9. 2012
    ..Michaelis and Menten's classic 1913 paper on enzyme kinetics is used to draw some lessons about the relationship between mathematical models and biological reality...
  6. pmc Multisite protein phosphorylation makes a good threshold but can be a poor switch
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 102:14617-22. 2005
    ....
  7. pmc Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding
    Sudhakaran Prabakaran
    Department of Systems Biology, Harvard Medical School, Boston, MA, USA
    Wiley Interdiscip Rev Syst Biol Med 4:565-83. 2012
    ..We focus particularly on examples other than the well-known 'histone code', to emphasize the pervasive use of information encoding in molecular biology. Finally, we touch briefly on new methods for measuring mod-form distributions...
  8. pmc The geometry of multisite phosphorylation
    Arjun Kumar Manrai
    Department of Physics, Harvard University, Cambridge, Massachusetts, USA
    Biophys J 95:5533-43. 2008
    ..We anticipate that this approach will have much wider applications in biological modeling...
  9. pmc Time-scale separation--Michaelis and Menten's old idea, still bearing fruit
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, MA, USA
    FEBS J 281:473-88. 2014
    ..The framework offers new capabilities for mathematical analysis and helps to do justice to Michaelis and Menten's insights about individual enzymes in the context of multi-enzyme biological systems. ..
  10. pmc Proteus: a web-based, context-specific modelling tool for molecular networks
    Florian Gnad
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 28:1284-6. 2012
    ..A wide variety of context-specific models may thereby be rapidly built, modified and explored...
  11. pmc Quantitative profiling of peptides from RNAs classified as noncoding
    Sudhakaran Prabakaran
    1 Proteomics Center, Boston Children s Hospital, Boston, Massachusetts 02115, USA 2 Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Commun 5:5429. 2014
    ..These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential...
  12. pmc Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria
    Florian Gnad
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell Proteomics 9:2642-53. 2010
    ..Thus, the phosphoproteome reflects major events in the evolution of life...
  13. pmc Programming with models: modularity and abstraction provide powerful capabilities for systems biology
    Aneil Mallavarapu
    Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Cambridge, MA 02115, USA
    J R Soc Interface 6:257-70. 2009
    ..We have developed a computational infrastructure that accomplishes this. We show here why such capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously...
  14. pmc Information Integration and Energy Expenditure in Gene Regulation
    Javier Estrada
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Cell 166:234-44. 2016
    ..Our approach is grounded in fundamental physics, leads to testable experimental predictions, and suggests how a quantitative paradigm for eukaryotic gene regulation can be formulated. ..
  15. pmc Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions
    Sudhakaran Prabakaran
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 7:482. 2011
    ..This combined MS strategy provides an optimal mixture of accuracy and coverage for quantifying distributions, but positional isomers remain a challenging problem...
  16. pmc Paradoxical results in perturbation-based signaling network reconstruction
    Sudhakaran Prabakaran
    Department of Systems Biology, Harvard Medical School, Boston Massachusetts
    Biophys J 106:2720-8. 2014
    ....
  17. pmc A fundamental trade-off in covalent switching and its circumvention by enzyme bifunctionality in glucose homeostasis
    Tathagata Dasgupta
    From the Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
    J Biol Chem 289:13010-25. 2014
    ..We suggest that bifunctionality of PFK-2/FBPase-2 complements the metabolic zonation of the liver by ensuring coherent switching in response to insulin and glucagon. ..
  18. doi request reprint Complex-linear invariants of biochemical networks
    Robert L Karp
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    J Theor Biol 311:130-8. 2012
    ..Finally, we outline a systematic procedure for using complex-linear invariants to analyse molecular networks of any deficiency...
  19. pmc Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited
    Yangqing Xu
    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
    J Theor Biol 311:139-52. 2012
    ..The methods introduced here are widely applicable to other reversible modification systems...
  20. pmc Distributivity and processivity in multisite phosphorylation can be distinguished through steady-state invariants
    Jeremy Gunawardena
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
    Biophys J 93:3828-34. 2007
    ..We discuss the experimental and theoretical challenges in extending these results...