Ángel Goñi

I studied Computer Engineering (sort of computer science mixed with electrical engineering) at the Polytechnic University of Madrid, before gaining my Ph.D in Computational Biology from the same institution (did a Master in Artificial Intelligence along the way). In 2010 I moved to Manchester Metropolitan University as a postdoctoral researcher; and back to Madrid in 2013 to work at the National Centre for Biotechnology (CNB-CSIC) where I am at the moment.

My research deals with engineering devices in a cell inspired by electronic components: such as logic gates. It is required then to characterize functional genetic elements, as promoters, that will be part of the toolkit to use for that purpose. While I use my engineering background to design these genetic machines, it is computer science that allows me to perform the needed in-silico analysis before the wet-lab work begins.

The circuits can consists of intra-celullar devices where a network of genes and promoters are arraged in a predefined way (e.g. a negatively regulated promoter and a downstream reporter can form an inverter) and/or inter-cellular connectivities to engineer distributed computations in populations (e.g. two cells establish a connection so that the output of one of them becomes the input of the other). I also make use of mathematical modelling and computational simulations in order to: 1) aid the design process mentioned above; and 2) deconvolute information obtained from experiments. Both features help gaining a better understanding of the underlying dynamics of molecular processes to an extent that is not possible otherwise. I use a wide variety of mathematical procedures for those two purposes, such as differential equations, stochastic algorithms, optimisations or agent-based spatial simulations. For the wet-lab implementation of the circuits I rely on the expertise of my colleagues, as I am still a rookie regarding molecular engineering procedures (but learningn!).

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Caption: The circuit design is a logic function: AND (two gene-promoter pairs for input reading). The model for one of the parts is depicted above (promoter-regulator dynamics). Then the model is placed ‘inside’ each cell of the DiSCUS package (for population-based simulations). The circuit that belongs to one of the cells is measured over time below.