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. Banerjee et al. 2023. Rethinking tipping points in spatial ecosystems. arXiv preprint.
    2. CHOSEN by Jilles Verwoerd.
  2. Brun et al. 2001. Practical identifiability analysis of large environmental simulation models. Water Res. Research.
    3. CHOSEN by Giovanni Ghisalberti.
  3. Castro & de Boer. Testing structural identifiability by a simple scaling method. PLos Comp. Biol.
  4. Siteur et al. 2016. Ecosystems off track: rate-induced critical transitions in ecological models. Oikos.
    5. CHOSEN by Barber Vos.
  5. Bastiaansen et al. 2018. Multistability of model and real dryland ecosystems through spatial self-organization. PNAS.
    6. CHOSEN by Raul Alvarez Candas.
  6. Staver & Levin. 2012. Integrating Theoretical Climate and Fire Effects on Savanna and Forest Systems. American Naturalist.
    7. CHOSEN by Emma Erkocevic.
  7. Sherratt. Pattern solutions of the Klausmeier Model for banded vegetation in semi-arid environments I. Nonlinearity. 2010 CHOSEN by Xizhi Tian. .
  8. Armstrong et al. A continuum approach to modelling cell-cell adhesion. J. Theor. Biol. 2006. CHOSEN by Arjen Schipper.
  9. Potts and Lewis. Spatial Memory and Taxis-Driven Pattern Formation in Model Ecosystems. Bull. Math. Biol. 2019.. CHOSEN by Tara Perovic.
  10. Xue and Othmer. Multiscale models of taxis-driven patterning in bacterial chemotaxis. SIAM J Appl Math. 2007
  11. Shinar and Feinberg. Structural sources of robustness in biochemical reaction networks. Science 2010. + Supplement + additional (more readable) background into the theory Gunawardena, 2003.
  12. Hofer et al. Resolving the chemotactic wave paradox: a mathematical model for chemotaxis of Dictyostelium amoebae. J. Biol. Systems. 1995. CHOSEN by Vincent Kuhlmann.
  13. 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 Xiaojen Chen.
  14. Grünbaum. Advection-diffusion equations for internal state-mediated random walks. SIAM J. Appl. Math. 2000..
  15. Boldin and Diekmann. Superinfections can induce evolutionarily stable coexistence of pathogens. J. Math. Biol. 2008. CHOSEN by Laura Haverkorn..
  16. 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.. CHOSEN by Jochem van Dam.
  17. Umulis et al. Robustness of Embryonic Spatial Patterning in Drosophila melanogaster. Book chapter (long!).
  18. Boettiger et al. The neural origins of shell structure and pattern in aquatic mollusks. PNAS. 2009 and the mathematical appendix. CHOSEN by David Bakker.
  19. Berestycki et al. Can a species keep pace with climate change? Bull. Math. Biol. 2009. CHOSEN by Rita Mak.
  20. Pachepsky et al. Persistence, spread and the drift paradox. Theor. Pop. Biol. 2005. . CHOSEN by Willem Kalkman.
  21. Enciso and Sontag. On the stability of a model of testosterone dynamics. J. Math. Biol. 2004..
  22. 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 Kejun Xiao.
  23. Popatov and Lewis. Climate and competition: the effect of moving range boundaries on habitat invasibility. Bull. Math. Biol. 2003..
  24. Liu et al. Phase separation explains a new class of selforganized spatial patterns in ecological systems. PNAS 2013. + SI. CHOSEN by Leander Post. .
  25. Shahrezaei and Swain. Analytical distributions for stochastic gene expression. PNAS. 2008. CHOSEN by Destin Nobach. .
  26. Sherratt and Lord. Nonlinear dynamics and pattern bifurcations in a model for vegetation stripes in semi-arid environments. Theor. Pop. Biol. 2007.
  27. Oke, Matadi and Xulu. Optimal Control Analysis of a Mathematical Model for Breast Cancer. Math. Comp. Appl. 2018. CHOSEN by Bidayatul Masulah. .
  28. F. Knauer, Th. Stiehl & A. Marciniak-Czochra (2019) Oscillations in a white blood cell population with multiple differentiation stages, J. Math. Biology. CHOSEN by Myrthe van Leeuwen.
  29. W. Jaeger, S. Kroemker & B. Tang (1994) Quiescence and transient growth dynamics in chemostat models, Math. Biosci. 119, pp.225-239. .
  30. Steidinger & Peay. Optimal Allocation Ratios: A Square Root Relationship between the Ratios of Symbiotic Costs and Benefits. CHOSEN by Laura van Schijndel.
  31. K. Painter. 2009. Continuous Models for Cell Migration in Tissues and Applications to Cell Sorting via Differential Chemotaxis. Bull. Math. Biol. CHOSEN by Andrew Moyer.