Mathematical Biology papers

The final project consists of choosing a paper, writing an essay about it and giving a presentation to us all on it. Below you find a list of possible choices. You are free to choose a paper or topic yourself. If you have something specific in mind, or would like us to look for a paper on a subject you are particularly interested in, let us know and we will try to find a paper for you.

Papers to choose from for your final project

  1. D. F. Anderson et al. Stochastic analysis of biochemical reaction networks with absolute concentration robustness. Royal Soc. Interface. 2015. CHOSEN by Finn van Vlaardingen.
  2. Bastiaansen et al. 2018. Multistability of model and real dryland ecosystems through spatial self-organization. PNAS. CHOSEN by Marta Amaro Catalayud.
  3. Staver & Levin. 2012. Integrating Theoretical Climate and Fire Effects on Savanna and Forest Systems. American Naturalist. CHOSEN by Samuel Heras de Paz.
  4. Sherratt. Pattern solutions of the Klausmeier Model for banded vegetation in semi-arid environments I. Nonlinearity. 2010. .
  5. Armstrong et al. A continuum approach to modelling cell-cell adhesion. J. Theor. Biol. 2006. CHOSEN by Simone Denti.
  6. Potts and Lewis. Spatial Memory and Taxis-Driven Pattern Formation in Model Ecosystems. Bull. Math. Biol. 2019..
  7. Xue and Othmer. Multiscale models of taxis-driven patterning in bacterial chemotaxis. SIAM J Appl Math. 2007
  8. Shinar and Feinberg. Structural sources of robustness in biochemical reaction networks. Science 2010. + Supplement + additional (more readable) background into the theory Gunawardena, 2003.
  9. Hofer et al. Resolving the chemotactic wave paradox: a mathematical model for chemotaxis of Dictyostelium amoebae. J. Biol. Systems. 1995. CHOSEN by Arnoud Melse.
  10. Culshaw et al. A mathematical model of cell-to-cell spread of HIV-1 that includes a time delay. J. Math. Biol. 2003.. CHOSEN by Zoé Dekker.
  11. Grünbaum. Advection-diffusion equations for internal state-mediated random walks. SIAM J. Appl. Math. 2000.. CHOSEN by Anne-Wil van den Heuvel.
  12. Boldin and Diekmann. Superinfections can induce evolutionarily stable coexistence of pathogens. J. Math. Biol. 2008.. CHOSEN by Hengyi Li.
  13. Wortel et al. Metabolic states with maximal specific rate carry flux through an elementary flux mode. FEBS Journal. 2014. together with Planqué et al. Maintaining maximal metabolic flux by gene expression control. PLoS Comp Biol. 2018..
  14. Umulis et al. Robustness of Embryonic Spatial Patterning in Drosophila melanogaster. Book chapter (long!). CHOSEN by Alessandro Acquarone.
  15. Boettiger et al. The neural origins of shell structure and pattern in aquatic mollusks. PNAS. 2009 and the mathematical appendix. CHOSEN by Ans Huizing.
  16. Berestycki et al. Can a species keep pace with climate change? Bull. Math. Biol. 2009.. CHOSEN by Beatrice Zovico.
  17. Pachepsky et al. Persistence, spread and the drift paradox. Theor. Pop. Biol. 2005. . CHOSEN by Max Bertman.
  18. Enciso and Sontag. On the stability of a model of testosterone dynamics. J. Math. Biol. 2004.. CHOSEN by Melvin van Beuzekom.
  19. Trapman and Bootsma. A useful relationship between epidemiology and queueing theory: The distribution of the number of infectives at the moment of the first detection. Math. Biosciences 2009.. CHOSEN by Emily Teng.
  20. Popatov and Lewis. Climate and competition: the effect of moving range boundaries on habitat invasibility. Bull. Math. Biol. 2003. CHOSEN by Niels van Dijk.
  21. Liu et al. Phase separation explains a new class of selforganized spatial patterns in ecological systems. PNAS 2013. + SI. CHOSEN by Aron Folkersma.
  22. Shahrezaei and Swain. Analytical distributions for stochastic gene expression. PNAS. 2008. CHOSEN by Wijnand van Essen.
  23. Sherratt and Lord. Nonlinear dynamics and pattern bifurcations in a model for vegetation stripes in semi-arid environments. Theor. Pop. Biol. 2007.
  24. Oke, Matadi and Xulu. Optimal Control Analysis of a Mathematical Model for Breast Cancer. Math. Comp. Appl. 2018. CHOSEN by Merel Wilms Floet. .
  25. F. Knauer, Th. Stiehl & A. Marciniak-Czochra (2019) Oscillations in a white blood cell population with multiple differentiation stages, J. Math. Biology. CHOSEN by Zias Kool.
  26. W. Jaeger, S. Kroemker & B. Tang (1994) Quiescence and transient growth dynamics in chemostat models. CHOSEN by Lorenzo Bonetti.
  27. K. Painter. 2009. Continuous Models for Cell Migration in Tissues and Applications to Cell Sorting via Differential Chemotaxis. Bull. Math. Biol. CHOSEN by Ottavia Comacchio.
  28. D. Angeli et al. 2007. A Petri net approach to the study of persistence in chemical reaction networks. Math. Biosciences 210. CHOSEN by Nancy Ntawumenyumunsi.
  29. G. B. Ermentrout and J. D. Cowan. 1979. Mathematical Theory of Visual Hallucination Patterns. Biol. Cybernetics. CHOSEN by Sarah Betto.