Dr Saeed Farjami
About
Biography
I completed my bachelor's (2010) and master's (2012) degrees at Isfahan University of Technology. In 2017, I graduated from the University of Auckland, New Zealand, with a PhD in mathematics under supervision of Prof. Hinke M. Osinga and A/Prof. Vivien Kirk. The main focus of my research was on investigating underlying mechanisms of transient responses of slow-fast systems to brief perturbations. In particular, I developed an algorithm for computing the stable manifold of a saddle slow manifold (transient stable manifold) to prove its key role in determining the number of oscillations in such responses. In March 2018, I moved to McGill University, Canada, where I held a Post Doctoral Research Fellow position in the lab of A/Prof. Anmar Khadra. My main research was focused on exploiting ordinary differential equations (ODEs) in particular geometric singular perturbation theory (GSPT), to explain and predict some of the peculiar behaviours in cerebellar stellate cells. In December 2019, I joined the research group of Dr. Andrea Rocco at University of Surrey as a Research Associate to design and develop mathematical models of gene expression of stem cells during development.
Publications
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence suggest alternatives to the standard framework based on Waddington's epigenetic landscape. The models allow us to suggest two generic dynamical scenarios that describe the differentiation process. In the first scenario gradual variation of a single control parameter is responsible for both entering and exiting the oscillatory regime. In the second scenario two control parameters vary: one responsible for entering, and the other for exiting the oscillatory regime. We analyse the standard repressilator and four variants of it and show the dynamical behaviours associated with each scenario. We present a thorough analysis of the associated bifurcations and argue that gene regulatory networks with these repressilator-like characteristics are promising candidates to describe cell fate selection through an oscillatory process.
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically motivated mathematical models for cell differentiation that generically generate oscillations and hence suggest alternatives to the standard framework based on Waddington's epigenetic landscape. The models allow us to suggest two generic dynamical scenarios that describe the differentiation process. In the first scenario, gradual variation of a single control parameter is responsible for both entering and exiting the oscillatory regime. In the second scenario, two control parameters vary: one responsible for entering, and the other for exiting the oscillatory regime. We analyse the standard repressilator and four variants of it and show the dynamical behaviours associated with each scenario. We present a thorough analysis of the associated bifurcations and argue that gene regulatory networks with these repressilator-like characteristics are promising candidates to describe cell fate selection through an oscillatory process.
Neural crest cells are crucial in development, not least because of their remarkable multipotency. Early findings stimulated two hypotheses for how fate specification and commitment from fully multipotent neural crest cells might occur, progressive fate restriction (PFR) and direct fate restriction, differing in whether partially restricted intermediates were involved. Initially hotly debated, they remain unreconciled, although PFR has become favoured. However, testing of a PFR hypothesis of zebrafish pigment cell development refutes this view. We propose a novel ‘cyclical fate restriction’ hypothesis, based upon a more dynamic view of transcriptional states, reconciling the experimental evidence underpinning the traditional hypotheses.
Additional publications
Saeed Farjami, Ryan Alexander, Derek Bowie, Anmar Khadra, Bursting in cerebellar stellate cells induced by pharmacological agents: Non-sequential spike adding, PLoS Computational Biology, 16 (2020), e1008463, https://doi.org/10.1371/journal.pcbi.1008463
Saeed Farjami, Ryan Alexander, Derek Bowie, Anmar Khadra, Switching in Cerebellar Stellate Cell Excitability in Response to a Pair of Inhibitory/Excitatory Pre-synaptic Inputs: A dynamical systems perspective, Neural Computation, 32 (2020), 626-658, 10.1162/neco_a_01261
John Mitry, Ryan Alexander, Saeed Farjami, Derek Bowie, Anmar Khadra, Modeling Excitability in Cerebellar Stellate Cells: Temporal Changes in Threshold, Latency and Frequency of Firing, Communications in Nonlinear Science and Numerical Simulation, 82 (2020), 105014, 10.1016/j.cnsns.2019.105014
Saeed Farjami, Vivien Kirk, Hinke M. Osinga, Interactions between a locally separating stable manifold and a bursting periodic orbit, The European Physical Journal Special Topics 227 (2018), 603-614, 10.1140/epjst/e2018-00138-1
Saeed Farjami, Vivien Kirk, Hinke M. Osinga, Computing the Stable Manifold of a Saddle Slow Manifold, SIAM Journal of Applied Dynamical Systems, 17 (2018), 350-379, 10.1137/17M1132458
Saeed Farjami, Vivien Kirk, Hinke M. Osinga, Transient Spike Adding in the Presence of Equilibria, The European Physical Journal Special Topics 225 (2016), 2601-2612, 10.1140/epjst/e2015-50332-9