Harvard Catalyst Profiles

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Jeremy H. Gunawardena, Ph.D.

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Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
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  1. R01GM122928 (DEPACE, ANGELA H) Apr 10, 2017 - Jun 30, 2025
    NIH
    Information Integration and Energy Expenditure in Eukaryotic Gene Regulation
    Role: Co-Principal Investigator
  2. R01GM105375 (GUNAWARDENA, JEREMY) Dec 15, 2014 - Jun 30, 2023
    NIH
    Information Processing by Post-translational Modification
    Role: Principal Investigator
  3. R01GM081578 (GUNAWARDENA, JEREMY) Apr 15, 2008 - Mar 31, 2013
    NIH
    Complex Dynamics in Multisite Phosphorylation
    Role: Principal Investigator
  4. P50GM068762 (SORGER, PETER KARL) Sep 1, 2003 - Aug 31, 2014
    NIH
    Systems Biology of cell Decision Processes
    Role: Co-Principal Investigator

Bibliographic
selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Çetiner U, Gunawardena J. Reformulating nonequilibrium steady states and generalized Hopfield discrimination. Phys Rev E. 2022 Dec; 106(6-1):064128. PMID: 36671125.
    Citations:    Fields:    
  2. Nam KM, Martinez-Corral R, Gunawardena J. The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems. Interface Focus. 2022 Aug 06; 12(4):20220013. PMID: 35860006; PMCID: PMC9184966.
    Citations:    
  3. Biddle JW, Martinez-Corral R, Wong F, Gunawardena J. Allosteric conformational ensembles have unlimited capacity for integrating information. Elife. 2021 06 09; 10. PMID: 34106049.
    Citations: 10     Fields:    Translation:AnimalsCells
  4. Gershman SJ, Balbi PE, Gallistel CR, Gunawardena J. Reconsidering the evidence for learning in single cells. Elife. 2021 01 04; 10. PMID: 33395388; PMCID: PMC7781593.
    Citations: 11     Fields:    
  5. Biddle JW, Gunawardena J. Reversal symmetries for cyclic paths away from thermodynamic equilibrium. Phys Rev E. 2020 Jun; 101(6-1):062125. PMID: 32688527.
    Citations: 2     Fields:    
  6. Nam KM, Gyori BM, Amethyst SV, Bates DJ, Gunawardena J. Robustness and parameter geography in post-translational modification systems. PLoS Comput Biol. 2020 05; 16(5):e1007573. PMID: 32365103; PMCID: PMC7224580.
    Citations: 5     Fields:    Translation:Cells
  7. Dexter JP, Prabakaran S, Gunawardena J. A Complex Hierarchy of Avoidance Behaviors in a Single-Cell Eukaryote. Curr Biol. 2019 12 16; 29(24):4323-4329.e2. PMID: 31813604.
    Citations: 23     Fields:    Translation:AnimalsCells
  8. Park J, Estrada J, Johnson G, Vincent BJ, Ricci-Tam C, Bragdon MD, Shulgina Y, Cha A, Wunderlich Z, Gunawardena J, DePace AH. Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity. Elife. 2019 06 21; 8. PMID: 31223115; PMCID: PMC6588347.
    Citations: 20     Fields:    Translation:AnimalsCells
  9. Biddle JW, Nguyen M, Gunawardena J. Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA. Elife. 2019 02 14; 8. PMID: 30762521; PMCID: PMC6375704.
    Citations: 13     Fields:    Translation:AnimalsCells
  10. Dexter JP, Ward PS, Dasgupta T, Hosios AM, Gunawardena J, Vander Heiden MG. Lack of evidence for substrate channeling or flux between wildtype and mutant isocitrate dehydrogenase to produce the oncometabolite 2-hydroxyglutarate. J Biol Chem. 2018 12 28; 293(52):20051-20061. PMID: 30381394.
    Citations: 10     Fields:    Translation:HumansCells
  11. Wong F, Dutta A, Chowdhury D, Gunawardena J. Structural conditions on complex networks for the Michaelis-Menten input-output response. Proc Natl Acad Sci U S A. 2018 09 25; 115(39):9738-9743. PMID: 30194237; PMCID: PMC6166846.
    Citations: 6     Fields:    
  12. Dexter JP, Biddle JW, Gunawardena J. Model discrimination for Ca2+ -dependent regulation of myosin light chain kinase in smooth muscle contraction. FEBS Lett. 2018 08; 592(16):2811-2821. PMID: 30066333.
    Citations: 1     Fields:    Translation:HumansAnimals
  13. Wong F, Amir A, Gunawardena J. Energy-speed-accuracy relation in complex networks for biological discrimination. Phys Rev E. 2018 Jul; 98(1-1):012420. PMID: 30110782.
    Citations: 9     Fields:    Translation:Cells
  14. Estrada J, Wong F, DePace A, Gunawardena J. Information Integration and Energy Expenditure in Gene Regulation. Cell. 2016 Jun 30; 166(1):234-44. PMID: 27368104; PMCID: PMC4930556.
    Citations: 51     Fields:    
  15. Malleshaiah M, Padi M, Rué P, Quackenbush J, Martinez-Arias A, Gunawardena J. Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation. Cell Rep. 2016 Feb 09; 14(5):1181-1194. PMID: 26832399.
    Citations: 11     Fields:    Translation:AnimalsCells
  16. Malleshaiah M, Gunawardena J. Cybernetics, Redux: An Outside-In Strategy for Unraveling Cellular Function. Dev Cell. 2016 Jan 11; 36(1):2-4. PMID: 26766437.
    Citations: 3     Fields:    Translation:Animals
  17. Dexter JP, Dasgupta T, Gunawardena J. Invariants reveal multiple forms of robustness in bifunctional enzyme systems. Integr Biol (Camb). 2015 Aug; 7(8):883-94. PMID: 26021467.
    Citations: 5     Fields:    Translation:Cells
  18. Dexter JP, Xu P, Gunawardena J, McClean MN. 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. 2015 Mar 25; 9:17. PMID: 25888817.
    Citations: 6     Fields:    Translation:AnimalsCells
  19. Ahsendorf T, Wong F, Eils R, Gunawardena J. A framework for modelling gene regulation which accommodates non-equilibrium mechanisms. BMC Biol. 2014 Dec 05; 12:102. PMID: 25475875; PMCID: PMC4288563.
    Citations: 24     Fields:    Translation:AnimalsCells
  20. Prabakaran S, Hemberg M, Chauhan R, Winter D, Tweedie-Cullen RY, Dittrich C, Hong E, Gunawardena J, Steen H, Kreiman G, Steen JA. Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun. 2014 Nov 18; 5:5429. PMID: 25403355.
    Citations: 25     Fields:    Translation:AnimalsCells
  21. Gunawardena J. Beware the tail that wags the dog: informal and formal models in biology. Mol Biol Cell. 2014 Nov 05; 25(22):3441-4. PMID: 25368417; PMCID: PMC4230599.
    Citations: 3     Fields:    Translation:Humans
  22. Prabakaran S, Gunawardena J, Sontag E. Paradoxical results in perturbation-based signaling network reconstruction. Biophys J. 2014 Jun 17; 106(12):2720-8. PMID: 24940789.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  23. Gunawardena J. Models in biology: 'accurate descriptions of our pathetic thinking'. BMC Biol. 2014 Apr 30; 12:29. PMID: 24886484.
    Citations: 90     Fields:    Translation:HumansAnimals
  24. Dasgupta T, Croll DH, Owen JA, Vander Heiden MG, Locasale JW, Alon U, Cantley LC, Gunawardena J. A fundamental trade-off in covalent switching and its circumvention by enzyme bifunctionality in glucose homeostasis. J Biol Chem. 2014 May 09; 289(19):13010-25. PMID: 24634222.
    Citations: 12     Fields:    Translation:HumansAnimals
  25. Gunawardena J. Time-scale separation--Michaelis and Menten's old idea, still bearing fruit. FEBS J. 2014 Jan; 281(2):473-88. PMID: 24103070.
    Citations: 29     Fields:    Translation:HumansAnimalsCells
  26. Mirzaev I, Gunawardena J. Laplacian dynamics on general graphs. Bull Math Biol. 2013 Nov; 75(11):2118-49. PMID: 24018536.
    Citations: 22     Fields:    
  27. Gunawardena J. Biology is more theoretical than physics. Mol Biol Cell. 2013 Jun; 24(12):1827-9. PMID: 23765269.
    Citations: 9     Fields:    
  28. Hao N, Budnik BA, Gunawardena J, O'Shea EK. Tunable signal processing through modular control of transcription factor translocation. Science. 2013 Jan 25; 339(6118):460-4. PMID: 23349292.
    Citations: 75     Fields:    Translation:AnimalsCells
  29. Dexter JP, Gunawardena J. Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli. J Biol Chem. 2013 Feb 22; 288(8):5770-8. PMID: 23192354.
    Citations: 11     Fields:    Translation:Cells
  30. Gunawardena J. Silicon dreams of cells into symbols. Nat Biotechnol. 2012 Sep; 30(9):838-40. PMID: 22965055.
    Citations: 5     Fields:    Translation:Cells
  31. Prabakaran S, Lippens G, Steen H, Gunawardena J. Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. Wiley Interdiscip Rev Syst Biol Med. 2012 Nov-Dec; 4(6):565-83. PMID: 22899623.
    Citations: 132     Fields:    Translation:HumansAnimalsCells
  32. Xu Y, Gunawardena J. Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited. J Theor Biol. 2012 Oct 21; 311:139-52. PMID: 22828569.
    Citations: 14     Fields:    Translation:Cells
  33. Karp RL, Pérez Millán M, Dasgupta T, Dickenstein A, Gunawardena J. Complex-linear invariants of biochemical networks. J Theor Biol. 2012 Oct 21; 311:130-8. PMID: 22814477.
    Citations: 12     Fields:    Translation:Cells
  34. Gunawardena J. A linear framework for time-scale separation in nonlinear biochemical systems. PLoS One. 2012; 7(5):e36321. PMID: 22606254.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  35. Gnad F, Estrada J, Gunawardena J. Proteus: a web-based, context-specific modelling tool for molecular networks. Bioinformatics. 2012 May 01; 28(9):1284-6. PMID: 22426344.
    Citations: 3     Fields:    Translation:AnimalsCells
  36. Gunawardena J. Some lessons about models from Michaelis and Menten. Mol Biol Cell. 2012 Feb; 23(4):517-9. PMID: 22337858.
    Citations: 20     Fields:    
  37. Harvey SL, Enciso G, Dephoure N, Gygi SP, Gunawardena J, Kellogg DR. A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast. Mol Biol Cell. 2011 Oct; 22(19):3595-608. PMID: 21849476.
    Citations: 42     Fields:    Translation:AnimalsCells
  38. Prabakaran S, Everley RA, Landrieu I, Wieruszeski JM, Lippens G, Steen H, Gunawardena J. Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions. Mol Syst Biol. 2011 Apr 12; 7:482. PMID: 21487401.
    Citations: 24     Fields:    Translation:AnimalsCells
  39. Gnad F, Gunawardena J, Mann M. PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res. 2011 Jan; 39(Database issue):D253-60. PMID: 21081558.
    Citations: 208     Fields:    Translation:HumansCells
  40. Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria. Mol Cell Proteomics. 2010 Dec; 9(12):2642-53. PMID: 20688971.
    Citations: 41     Fields:    Translation:HumansAnimalsCells
  41. Gunawardena J. Systems biology. Biological systems theory. Science. 2010 Apr 30; 328(5978):581-2. PMID: 20431005.
    Citations: 6     Fields:    Translation:Cells
  42. Thomson M, Gunawardena J. The rational parameterization theorem for multisite post-translational modification systems. J Theor Biol. 2009 Dec 21; 261(4):626-36. PMID: 19765594.
    Citations: 28     Fields:    Translation:HumansAnimalsCells
  43. Thomson M, Gunawardena J. Unlimited multistability in multisite phosphorylation systems. Nature. 2009 Jul 09; 460(7252):274-7. PMID: 19536158.
    Citations: 108     Fields:    Translation:Cells
  44. Mallavarapu A, Thomson M, Ullian B, Gunawardena J. Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface. 2009 Mar 06; 6(32):257-70. PMID: 18647734.
    Citations: 33     Fields:    Translation:AnimalsCells
  45. Manrai AK, Gunawardena J. The geometry of multisite phosphorylation. Biophys J. 2008 Dec 15; 95(12):5533-43. PMID: 18849417; PMCID: PMC2599844.
    Citations: 24     Fields:    Translation:Cells
  46. Gunawardena J. Distributivity and processivity in multisite phosphorylation can be distinguished through steady-state invariants. Biophys J. 2007 Dec 01; 93(11):3828-34. PMID: 17704153; PMCID: PMC2084251.
    Citations: 16     Fields:    Translation:Cells
  47. Gunawardena J. Multisite protein phosphorylation makes a good threshold but can be a poor switch. Proc Natl Acad Sci U S A. 2005 Oct 11; 102(41):14617-22. PMID: 16195377; PMCID: PMC1253599.
    Citations: 117     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.