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281 results on '"Szekely, Tamas"'

17. Conserved transcriptomic profiles underpin monogamy across vertebrates

Author

Young, Rebecca L., Ferkin, Michael H., Ockendon-Powell, Nina F., Orr, Veronica N., Phelps, Steven M., Pogány, Ákos, Richards-Zawacki, Corinne L., Summers, Kyle, Székely, Tamás, Trainor, Brian C., Urrutia, Araxi O., Zachar, Gergely, O’Connell, Lauren A., and Hofmann, Hans A.

Published
2019

19. Stochastic modelling and simulation in cell biology

Author

Szekely, Tamas, Burrage, Kevin, and Erban, Radek

Subjects
571.6, Biology, Computational biochemistry, Cell Biology (see also Plant sciences), Biology and other natural sciences (mathematics), Computer science (mathematics), Mathematical biology, Probability theory and stochastic processes, Stem cells (clinical sciences), Biology (medical sciences), Chemical kinetics, Stochastic simulation, tau-leap, higher-order stochastic methods, stem cells, population dynamics
Abstract

Modelling and simulation are essential to modern research in cell biology. This thesis follows a journey starting from the construction of new stochastic methods for discrete biochemical systems to using them to simulate a population of interacting haematopoietic stem cell lineages. The first part of this thesis is on discrete stochastic methods. We develop two new methods, the stochastic extrapolation framework and the Stochastic Bulirsch-Stoer methods. These are based on the Richardson extrapolation technique, which is widely used in ordinary differential equation solvers. We believed that it would also be useful in the stochastic regime, and this turned out to be true. The stochastic extrapolation framework is a scheme that admits any stochastic method with a fixed stepsize and known global error expansion. It can improve the weak order of the moments of these methods by cancelling the leading terms in the global error. Using numerical simulations, we demonstrate that this is the case up to second order, and postulate that this also follows for higher order. Our simulations show that extrapolation can greatly improve the accuracy of a numerical method. The Stochastic Bulirsch-Stoer method is another highly accurate stochastic solver. Furthermore, using numerical simulations we find that it is able to better retain its high accuracy for larger timesteps than competing methods, meaning it remains accurate even when simulation time is speeded up. This is a useful property for simulating the complex systems that researchers are often interested in today. The second part of the thesis is concerned with modelling a haematopoietic stem cell system, which consists of many interacting niche lineages. We use a vectorised tau-leap method to examine the differences between a deterministic and a stochastic model of the system, and investigate how coupling niche lineages affects the dynamics of the system at the homeostatic state as well as after a perturbation. We find that larger coupling allows the system to find the optimal steady state blood cell levels. In addition, when the perturbation is applied randomly to the entire system, larger coupling also results in smaller post-perturbation cell fluctuations compared to non-coupled cells. In brief, this thesis contains four main sets of contributions: two new high-accuracy discrete stochastic methods that have been numerically tested, an improvement that can be used with any leaping method that introduces vectorisation as well as how to use a common stepsize adapting scheme, and an investigation of the effects of coupling lineages in a heterogeneous population of haematopoietic stem cell niche lineages.

Published
2014

37. Polygamy slows down population divergence in shorebirds

Author

Jackson, Josephine D’Urban, dos Remedios, Natalie, Maher, Kathryn H., Zefania, Sama, Haig, Susan, Oyler-McCance, Sara, Blomqvist, Donald, Burke, Terry, Bruford, Michael W., Székely, Tamás, and Küpper, Clemens

Published
2017

41. Sex ratios

Author

Jennions, Michael, Székely, Tamás, Beissinger, Steven R., and Kappeler, Peter M.

Published
2017
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47. Introduction

Author

Balshine, Sigal, Kempenaers, Bart, and Székely, Tamás

Published
2002

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