Tina Toni

Contact Details

I have moved to Department for Biological Engineering, Massachusetts Institute of Technology. My new email address is ttoni@mit.edu.

I obtained my undergraduate degree in Mathematics at the University of Ljubljana, Slovenia and a Masters degree in Interdisciplinary Mathematics at the University of Warwick, UK. My masters thesis examined probabilistic models of gene regulatory networks, focusing particularly on Bayesian networks.

For my PhD I worked on the systems biology of cellular signaling processes. My main focus was on the development of statistical and computational tools that allow us to learn the structure and parameters of signaling networks from biological time-course data. In particular, I have been working with Approximate Bayesian Computation algorithms based on Sequential Monte Carlo (ABC SMC), which I applied to dynamical systems.

I applied these parameter estimation and model selection techniques to prokaryotic and eukaryotic signal transduction and stress response pathways, in particular JAK-STAT signaling, the dynamics of MAPK and Erk/Mek signaling, and the Phage Shock Protein stress response in Escherichia coli.

I defended my PhD thesis in March 2010, and from July 2010 I am working as a Wellcome Trust-MIT Postdoctoral Fellow at the Department of Biological Engineering at Massachusetts Institute of Technology with Professor Bruce Tidor and Professor Ron Weiss.

Publications:

M. Huvet, T. Toni, X. Sheng, T. Thorne, G. Jovanovic, C. Engl, M. Buck, J.W. Pinney, M.P.H. Stumpf. Mapping the evolution of the Phage shock protein (Psp) response system: interplay between protein function, genomic organization and system function, Molecular Biology Evolution (In Press)

N. Joly, C. Engl, G. Jovanovic, M. Huvet, T. Toni, X. Sheng, M. P. H. Stumpf, M. Buck. Managing membrane stress: the Phage shock protein (Psp) response, from molecular mechanisms to physiology, FEMS Microbiology Reviews, 34 (5), 797-827, 2010. PDF file

J. Liepe, C. Barnes, E. Cule, K. Erguler, P. Kirk, T. Toni§, M. P. H. Stumpf§. ABC- SysBio - approximate Bayesian computation in Python with GPU support, Bioinformatics, 26(14), 1797-1799, 2010. PDF file

T. Toni. The beauty of biology at single molecule resolution; book review, Human Genomics, 5(5)2010 .

T. Toni, M. P. H. Stumpf. Simulation-based model selection for  dynamical systems in systems and population biology, Bioinformatics,  26 (1), 104-110, 2010. PDF file

M. Secrier*, T. Toni*, M. P. H. Stumpf. The ABC of reverse engineering biological signalling systems, Molecular BioSystems, 5, 1925-1935, 2009. PDF file

M. Huvet*, T. Toni*, H. Tan, G. Jovanovic, C. Engl, M. Buck, M. P. H. Stumpf. Model-based evolutionary analysis: The natural history of phage shock stress response, Biochemical Society Transactions, 37,
762-767, 2009. PDF file

T. Toni, M. P. H. Stumpf. Parameter inference and model selection in signal transduction models.
Book chapter for Topics in Computational Biology Methods in Molecular Biology Series, Humana Press, 2009 (accepted). PDF file

T. Toni, D. Welch, N. Strelkowa, A. Ipsen and M. P. H. Stumpf. Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society Interface, 6, 187-202, 2009. PDF file  (or PDF file in arXiv)

 P. Kirk, T. Toni, M. P. H. Stumpf. Parameter inference for biochemical systems that undergo a Hopf bifurcation. Biophysical Journal, 95, 540-549, 2008. PDF file

* joint first author
§ joint corresponding author