Jeremy Gunawardena

Last updated
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

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]

Contents

Education

He received a BSc 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]

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. [20] Gunawardena has had a long-standing interest in the interface between mathematics and biology, on which he has written several perspectives. [21] 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. [22] He argues that many models fail to accurately represent nature and emphasizes the importance of verifiability and falsifiability in their components and conclusions. [23]

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. [24]

Gunawardena has been exploring the concept of cellular learning, bringing ideas from cognitive science and psychology to bear on the behavior of individual cells. [25] 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. [26]

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, [27] has received 280 citations according to Google Scholar. [28]

Gunawardena introduced, with Aneil Mallavarapu, the programming-with-models approach to virtual cells, which led to the programming language little b. [29]

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. [30] 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. [31]

Selected publications

Related Research Articles

<span class="mw-page-title-main">Computational biology</span> Branch of biology

Computational biology refers to the use of techniques in computer science, data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and data science, the field also has foundations in applied mathematics, molecular biology, cell biology, chemistry, and genetics.

<span class="mw-page-title-main">Systems biology</span> Computational and mathematical modeling of complex biological systems

Systems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach to biological research.

<span class="mw-page-title-main">Mathematical and theoretical biology</span> Branch of biology

Mathematical and theoretical biology, or biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of living organisms to investigate the principles that govern the structure, development and behavior of the systems, as opposed to experimental biology which deals with the conduction of experiments to test scientific theories. The field is sometimes called mathematical biology or biomathematics to stress the mathematical side, or theoretical biology to stress the biological side. Theoretical biology focuses more on the development of theoretical principles for biology while mathematical biology focuses on the use of mathematical tools to study biological systems, even though the two terms are sometimes interchanged.

<span class="mw-page-title-main">Marc Kirschner</span> American biologist (born 1945)

Marc Wallace Kirschner is an American cell biologist and biochemist and the founding chair of the Department of Systems Biology at Harvard Medical School. He is known for major discoveries in cell and developmental biology related to the dynamics and function of the cytoskeleton, the regulation of the cell cycle, and the process of signaling in embryos, as well as the evolution of the vertebrate body plan. He is a leader in applying mathematical approaches to biology. He is the John Franklin Enders University Professor at Harvard University. In 1989 he was elected to the National Academy of Sciences. In 2021 he was elected to the American Philosophical Society.

<span class="mw-page-title-main">Walter M. Elsasser</span> German-American physicist

Walter Maurice Elsasser was a German-born American physicist, a developer of the presently accepted dynamo theory as an explanation of the Earth's magnetism. He proposed that this magnetic field resulted from electric currents induced in the fluid outer core of the Earth. He revealed the history of the Earth's magnetic field by the study of the magnetic orientation of minerals in rocks. He is also noted for his unpublished proposal of the wave-like diffraction of electron particles by a crystal. The subsequent Davisson–Germer experiment showing this effect led to a Nobel Prize in Physics.

<span class="mw-page-title-main">Pattern formation</span> Study of how patterns form by self-organization in nature

The science of pattern formation deals with the visible, (statistically) orderly outcomes of self-organization and the common principles behind similar patterns in nature.

<span class="mw-page-title-main">Tom Rapoport</span> German-American cell biologist (born 1947)

Tom Abraham Rapoport is a German-American cell biologist who studies protein transport in cells. Currently, he is a professor at Harvard Medical School and a Howard Hughes Medical Institute investigator. Born in Cincinnati, Ohio, he grew up in East Germany. In 1995 he accepted an offer to become a professor at Harvard Medical School. In 1997 he became an investigator of the Howard Hughes Medical Institute. He is a member of the American and German National Academies of Science.

<span class="mw-page-title-main">Aviv Regev</span> Bioinformatician

Aviv Regev is a computational biologist and systems biologist and Executive Vice President and Head of Genentech Research and Early Development in Genentech/Roche. She is a core member at the Broad Institute of MIT and Harvard and professor at the Department of Biology of the Massachusetts Institute of Technology. Regev is a pioneer of single cell genomics and of computational and systems biology of gene regulatory circuits. She founded and leads the Human Cell Atlas project, together with Sarah Teichmann.

Johan Paulsson is a Swedish mathematician and systems biologist at Harvard Medical School. He is a researcher in systems biology and stochastic processes, specializing in stochasticity in gene networks and plasmid reproduction.

<span class="mw-page-title-main">Turing pattern</span> Concept from evolutionary biology

The Turing pattern is a concept introduced by English mathematician Alan Turing in a 1952 paper titled "The Chemical Basis of Morphogenesis" which describes how patterns in nature, such as stripes and spots, can arise naturally and autonomously from a homogeneous, uniform state. The pattern arises due to Turing instability which in turn arises due to the interplay between differential diffusion of chemical species and chemical reaction. The instability mechanism is unforeseen because a pure diffusion process would be anticipated to have a stabilizing influence on the system.

Wendell Lim is an American biochemist who is the Byer's Distinguished Professor of Cellular and Molecular Pharmacology at the University of California, San Francisco. He is the director of the UCSF Cell Design Institute. He earned his A.B. in chemistry from Harvard University working with Jeremy Knowles on enzyme evolutionary optimization. He obtained his Ph.D. in biochemistry and biophysics from Massachusetts Institute of Technology under the guidance of Bob Sauer using genetic and biophysical approaches to understand the role of hydrophobic core interactions in protein folding. He then did his postdoctoral work with Frederic Richards at Yale University on the structure of protein interaction domains. Lim's work has focused on cell signaling, synthetic biology, and cell engineering, particularly in immune cells.

<span class="mw-page-title-main">Dana Pe'er</span> Bioinformatician

Dana Pe'er, Chair and Professor in Computational and Systems Biology Program at Sloan Kettering Institute is a researcher in computational systems biology. A Howard Hughes Medical Institute (HHMI) Investigator since 2021, she was previously a professor at Columbia Department of Biological Sciences. Pe'er's research focuses on understanding the organization, function and evolution of molecular networks, particularly how genetic variations alter the regulatory network and how these genetic variations can cause cancer.

<span class="mw-page-title-main">James Ferrell (biologist)</span> American biologist (born 1955)

James Ellsworth Ferrell is an American systems biologist. He is a Professor of Chemical and Systems Biology and Biochemistry at Stanford University School of Medicine. He was Chair of the Dept. of Chemical and Systems Biology from its inception in 2006 until 2011.

<span class="mw-page-title-main">John J. Tyson</span> American mathematical biologist

John J. Tyson is an American systems biologist and mathematical biologist who serves as university distinguished professor of biology at Virginia Tech, and is the former president of the Society for Mathematical Biology. He is known for his research on biochemical switches in the cell cycle, dynamics of biological networks and on excitable media.

Cell-based models are mathematical models that represent biological cells as discrete entities. Within the field of computational biology they are often simply called agent-based models of which they are a specific application and they are used for simulating the biomechanics of multicellular structures such as tissues. to study the influence of these behaviors on how tissues are organised in time and space. Their main advantage is the easy integration of cell level processes such as cell division, intracellular processes and single-cell variability within a cell population.

The Novak–Tyson Model is a non-linear dynamics framework developed in the context of cell-cycle control by Bela Novak and John J. Tyson. It is a prevalent theoretical model that describes a hysteretic, bistable bifurcation of which many biological systems have been shown to express.

Li Zhang is a biologist currently working at University of Texas at Dallas. She is a professor of Biological Sciences and the Cecil H. and Ida Green Distinguished Chair in Systems Biology Science at the University of Texas at Dallas. During her 20+ years of independent research, Li Zhang has made major contributions to the understanding of Heme signaling and function in gene regulation, neuronal differentiation and survival, and lung cancer bioenergetics.

Trisha Nell Davis is an American biochemist and the former Earl Davie/ZymoGenetics Chair of the department of biochemistry at the University of Washington. Her early research focused on Calmodulin, though the primary focus of her lab has since shifted to the molecular machinery of cell division in budding yeast, especially the microtubule organizing centers and the kinetochores. She retired in 2024 after 11 years serving as the Chair.

<span class="mw-page-title-main">Stacey Finley</span> American biologist and geneticist

Stacey Finley is the Nichole A. and Thuan Q. Pham Professor and associate professor of chemical engineering and materials science, and quantitative and computational biology at the University of Southern California. Finley has a joint appointment in the department of chemical engineering and materials science, and she is a member of the USC Norris Comprehensive Cancer Center. Finley is also a standing member of the MABS Study Section at NIH. Her research has been supported by grants from the NSF, NIH, and American Cancer Society.

Matt Thomson is an American computational biologist, academic, and entrepreneur. He works in the fields of computational biology, biophysics, and machine learning.

References

  1. ↑ Nam, Kee-Myoung; Gunawardena, Jeremy (3 November 2023). "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 . PMC   10656611 . PMID   38020901.
  2. ↑ "Jeremy Gunawardena – Learning and cognition in single biological cells (2 June 2022)". Trinity Japan. 24 January 2022.
  3. ↑ Leigh, Doug; Watkins, Ryan; Gunawardena, Jeremy (17 March 2020). "The Minds of Single-celled Organisms – Jeremy Gunawardena". Parsing Science. doi:10.6084/m9.figshare.12006792.
  4. ↑ "Jeremy Gunawardena gave an online talk titled "Following the energy in cellular information processing" at the IBS Biomedical Mathematics Colloquium". Biomedical Mathematics Group. 18 November 2021.
  5. ↑ Cameron, David. "Biology Enters The Matrix Through New Computer Language". Lab Manager.
  6. ↑ "Jeremy Harin Charles Gunawardena". Mathematics Genealogy Project. Retrieved January 17, 2022.
  7. ↑ "CDS Lecture Series". isr.umd.edu. Retrieved January 17, 2022.
  8. ↑ "Crick Lecture | Jeremy Gunawardena". Crick. 9 July 2024.
  9. ↑ "Jeremy Gunawardena". Biomedical Mathematics Group. Retrieved 2024-07-27.
  10. ↑ "A non-equilibrium view of cellular information processing | BioQuant". www.bioquant.uni-heidelberg.de.
  11. ↑ "Invited seminar at BRIMS, Hewlett-Packard Laboratories". University of Portsmouth.
  12. ↑ "Systems Biology Seminar". UT Southwestern Events Calendar.
  13. ↑ "Biology, Biology and Physics, Biotechnology, and Biotech Management". Nature. 414 (6866): 4. December 2001. doi:10.1038/nj6866-04a.
  14. ↑ "Biology enters 'The Matrix' through new computer language". Phys Org.
  15. ↑ https://math.mit.edu/~hrm/papers/adams-gunawardena-miller-segal-conjecture.pdf THE SEGAL CONJECTURE FOR ELEMENTARY ABELIAN p-GROUPS J. F. ADAMS, J. H. GUNAWARDENA and H. MILLER
  16. ↑ Lück, Wolfgang (2020-04-23). "The Segal conjecture for infinite discrete groups". Algebraic & Geometric Topology. 20 (2): 965–986. arXiv: 1901.09250 . doi:10.2140/agt.2020.20.965. ISSN   1472-2739.
  17. ↑ "Talk of Prof. Jeremy Gunawardena | Event | Apr 30, 2019 | Institute for Systems Theory and Automatic Control | University of Stuttgart". www.ist.uni-stuttgart.de. Retrieved 2024-11-18.
  18. ↑ "Jeremy Gunawardena – Giovanni Armenise Harvard Foundation" . Retrieved 2024-11-18.
  19. ↑ Gunawardena, J; N Hao; B A Budnik; E K O'Shea (2013). "Tunable signal processing through modular control of transcription factor translocation". Science. 339 (6118): 460–4. Bibcode:2013Sci...339..460H. doi:10.1126/science.1227299. PMC   3746486 . PMID   23349292.
  20. ↑ Tyson, John J.; Novák, Béla (2015-07-01). "Models in biology: lessons from modeling regulation of the eukaryotic cell cycle". BMC Biology. 13 (1): 46. doi: 10.1186/s12915-015-0158-9 . ISSN   1741-7007. PMC   4486427 . PMID   26129844.
  21. ↑ Gunawardena, J; Y Xu (2012). "Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited". J Theor Biol. 311: 139–152. Bibcode:2012JThBi.311..139X. doi:10.1016/j.jtbi.2012.07.012. PMC   3432734 . PMID   22828569.
  22. ↑ "Models in biology: 'accurate descr ... | Article | H1 Connect". archive.connect.h1.co. Retrieved 2025-01-23.
  23. ↑ Woolston, Chris (2014). "Maths reality check resonates online". Nature. 509 (7500): 263. doi:10.1038/509263e. ISSN   1476-4687.
  24. ↑ Martinez-Corral, Rosa; Nam, Kee-Myoung; DePace, Angela H.; Gunawardena, Jeremy (2024-05-28). "The Hill function is the universal Hopfield barrier for sharpness of input–output responses". Proceedings of the National Academy of Sciences. 121 (22): e2318329121. doi:10.1073/pnas.2318329121. PMC   11145184 . PMID   38787881.
  25. ↑ "Cells that learn: ERC Synergy Grant fuels revolutionary… - MAX PLANCK INSTITUTE FOR NEUROBIOLOGY OF BEHAVIOR — CAESAR". mpinb.mpg.de. Retrieved 2024-12-13.
  26. ↑ "Dynamical Systems Biology lab". Dynamical Systems Biology lab. Retrieved 2024-12-13.
  27. ↑ PNAS full text
  28. ↑ "Google Scholar".
  29. ↑ "Little b - Programming language". pldb.io. Retrieved 2024-11-18.
  30. ↑ "Jeremy Gunawardena | Systems, Synthetic, and Quantitative Biology". ssqbiophd.hms.harvard.edu. Retrieved 2024-11-18.
  31. ↑ "2023 Seminars | Applied Mathematics". appliedmath.brown.edu. Retrieved 2024-11-18.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.