Simone Rubinacci

DPhil Candidate in Systems Biology

Short Bio

Currently I am a Phd student (Systems Biology DTC) at the University of Oxford, St Catherine’s College. My DPhil is supervised by Prof. Jonathan Marchini. My research is focused on speeding up Bayesian inference methods in statistical genetics area using GPU computing.


I was a Chaste developer during my master. Here you can find a paper as a result of my time spent in the Computational Biology Group.

Bimib group

I was part of the BIMIB group, until October 2016. We are still working together on a spatio-temporal logic project. Details will be available soon!

Imputation and phasing using PBWT and GPU computing

Imputation and phasing are two key problems in the statistical genomics area. We aim to speed-up the current methods using succint data structures (Positional Burrows Wheeler Transform) and GPU computing.

View Project*

*can still be a private repository, in case just wait for any news.


A Chaste plugin for the multiscale simulation of Gene Regulatory Networks driving the spatial dynamics of tissues and cancer.

View Project

Education and previous experiences

Junior research fellow

Università degli studi di Milano Bicocca, March 2015 - October 2015

  • Position funded by the scholarship "Analysis off-lattice and in-lattice simulation traces using spatio-temporal logics", under the supervision of Prof. Marco Antoniotti.

Master of Science

Università degli studi di Milano Bicocca, March 2015

  • Thesis title:Noisy Random Boolean Networks dynamics for cellular differentiation using the Chaste modelling environment.
  • Supervisors:Prof. Marco Antoniotti (Università degli studi di Milano Bicocca) and Dr Joe Pitt-Francis (University of Oxford)
  • The Master's thesis was in co-tutorship between Università degli studi di Milano Bicocca and the University of Oxford

Teaching assistant

Università degli studi di Milano Bicocca, October 2012 - September 2013

  • Teaching assistant for the course “Foundation of Informatics” (“Fondamenti dell’informatica”) for the Bachelor’s degree in Computer Science, first year. The course was held by Professor Ugo Moscato.
  • Main tasks: assistance during the lessons, preparation of the learning materials and assistance during the exams.


EXTRA scholarship

  • EXTRA Project was born in 2007 and provides grants to young talents for preparation of Master's theses in co-tutorship outside of Italy.
  • In my case, it was aimed to finance my Master's thesis project at the University of Oxford.


Peer-reviewed Journal articles