Jeremy Gunawardena

Jeremy Gunawardena is a mathematician and systems biologist^[2] who is Associate Professor in the Department of Systems Biology at Harvard Medical School.^[3] His lab focuses on cellular information processing.^[4]

Jeremy Gunawardena
Alma mater	University of Cambridge (Ph.D.)
Known for	Little b linear framework[1]
Scientific career
Fields	Systems biology, Mathematical biology, Algebraic topology
Institutions	Harvard

Education

He received a BSc degree in mathematics from Imperial College, London, where he was awarded the Sir John Lubbock Memorial Prize for the highest-ranked first class degree in the University of London.^[5] He did Part III of the Mathematical Tripos at Trinity College, Cambridge, for which he was awarded a J T Knight Prize in Class 1, and went on to do his PhD in algebraic topology with Frank Adams at Cambridge.^[6]

Career

He was elected to a research fellowship in Pure Mathematics at Trinity College.^[7][8] Before taking up his Fellowship, he spent two years as L.E. Dickson Instructor in the Department of Mathematics at the University of Chicago.^[9] He subsequently spent several years in industrial research at HP Labs in Bristol, UK.^[10][11] He also served as a Member of Council of the UK's Engineering and Physical Sciences Research Council (EPSRC).^[12] In 2002, Gunawardena become a Visiting Scientist at the Bauer Center for Genomics Research at Harvard.^[13] In 2003, he joined the newly formed Department of Systems Biology at Harvard Medical School.^[14]

Work

Gunawardena's PhD thesis led to the solution, with Frank Adams and Haynes Miller, of the Segal conjecture for elementary abelian groups,^[15] which provided the algebraic starting point for Gunnar Carlsson's solution of the full conjecture.^[16] At the University of Chicago, he helped to set up the first computer science courses at the University.^[17] At HP Labs, Gunawardena created the Basic Research Institute in the Mathematical Sciences (BRIMS), a pioneering academic-industrial partnership with the University of Bristol and the Isaac Newton Institute for Mathematical Sciences in Cambridge.^[18][19]

One of his most cited papers, "Multisite protein phosphorylation makes a good threshold but can be a poor switch" in Proceedings of the National Academy of Sciences, ^[20] has received 280 citations according to Google Scholar.^[21]

Gunawardena introduced, with Aneil Mallavarapu, the programming-with-models approach to virtual cells, which led to the programming language little b.^[22]Together with Marc Kirschner, Lew Cantley, Walter Fontana and Johan Paulsson, he helped set up and co-taught Systems Biology 200, one of the first courses to discuss the core mathematical ideas needed in systems biology.^[23] He also founded the weekly series of Theory Lunch chalk talks, which has been running since 2003 and has brought some of the culture of the mathematical sciences into systems biology.^[24]

At Harvard Medical School, Gunawardena's lab studies information processing in eukaryotic cells, with a focus on mechanisms like post-translational modification, gene regulation and allostery.^[25] Gunawardena has had a long-standing interest in the interface between mathematics and biology, on which he has written several perspectives.^[26] Gunawardena's essay, “Models in biology: ‘accurate descriptions of our pathetic thinking’,” published in BMC Biology, critiques the limitations of mathematical models in biological research.^[27] He argues that many models fail to accurately represent nature and emphasizes the importance of verifiability and falsifiability in their components and conclusions.^[28]

Gunawardena's lab has developed over several years a mathematical approach for analyzing biomolecular systems called the 'linear framework in which theorems can be proved about biological processes.^[29]

Gunawardena has been exploring the concept of cellular learning, bringing ideas from cognitive science and psychology to bear on the behavior of individual cells.^[30] He was awarded a European Research Council synergy grant to study this, 'CeLEARN: learning in single cells through dynamical internal representations', together with Aneta Koseska, Dietmar Schmucker and Jordi Garcia-Ojalvo.^[31]

Selected publications

• Gunawardena, Jeremy (2014-04-30). "Models in biology: 'accurate descriptions of our pathetic thinking'". BMC Biology. 12 (1): 29. doi:10.1186/1741-7007-12-29. ISSN 1741-7007. PMC 4005397. PMID 24886484.
• Gunawardena, Jeremy (2013). "Biology is more theoretical than physics". Molecular Biology of the Cell. 24 (12): 1827–1829. doi:10.1091/mbc.E12-03-0227. ISSN 1939-4586. PMC 3681688. PMID 23765269.
• Gunawardena, Jeremy (2012-02-15). "Some lessons about models from Michaelis and Menten". Molecular Biology of the Cell. 23 (4): 517–519. doi:10.1091/mbc.e11-07-0643. ISSN 1059-1524. PMC 3279381. PMID 22337858.
• Nam, Kee-Myoung; Gunawardena, Jeremy (2023-11-03). "The linear framework II: using graph theory to analyse the transient regime of Markov processes". Frontiers in Cell and Developmental Biology. 11. doi:10.3389/fcell.2023.1233808. ISSN 2296-634X. PMC 10656611. PMID 38020901.
• Nam, Kee-Myoung; Martinez-Corral, Rosa; Gunawardena, Jeremy (2022-08-06). "The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems". Interface Focus. 12 (4). doi:10.1098/rsfs.2022.0013. ISSN 2042-8901. PMC 9184966. PMID 35860006.
• Gunawardena, Jeremy (2012-05-14). "A Linear Framework for Time-Scale Separation in Nonlinear Biochemical Systems". PLOS ONE. 7 (5): e36321. doi:10.1371/journal.pone.0036321. ISSN 1932-6203. PMC 3351455. PMID 22606254.
• Gershman, Samuel J; Balbi, Petra EM; Gallistel, C Randy; Gunawardena, Jeremy (2021-01-04). "Reconsidering the evidence for learning in single cells". eLife. 10: e61907. doi:10.7554/eLife.61907. ISSN 2050-084X. PMC 7781593. PMID 33395388.
• Gunawardena, Jeremy (2022). "Learning Outside the Brain: Integrating Cognitive Science and Systems Biology". Proceedings of the IEEE. 110 (5): 590–612. doi:10.1109/JPROC.2022.3162791.
• Estrada, Javier; Wong, Felix; DePace, Angela; Gunawardena, Jeremy (2016). "Information Integration and Energy Expenditure in Gene Regulation". Cell. 166 (1): 234–244. doi:10.1016/j.cell.2016.06.012. PMC 4930556. PMID 27368104.