Together with Jocelyne Demengeot, our neighbour at the Instituto Gulbenkian de Ciência, we have been studying the immunobiology of regulatory Foxp3+ T cells, as well as the molecular regulation of the efficiency of V(D)J recombination.

Together with Alberto Darszon's lab, at the Institute for Biotechnology of the UNAM in Cuernavaca (Mexico), we seek to understand how sea urchin spermatozoa find their conspecific eggs during broadcast spawning events. This involves modelling the sensorimotor system of the sperm cell as well as quantitative imaging of spermatozoa swimming in the confined to the plane or freely in three dimensions.

Together with Pedro Lima and Anders Lynn Christensen we have been trying to develop new strategies to control distributed robotic systems inspired by our models of biological systems.
This collaboration started many years ago, when Pedro and Jorge Carneiro cosupervised a student together with Michael Athans. Dejan Milutinovic modelled how the distribution of T cell receptors changed in time as a function of the ligands presented by antigen presenting cells. He develop a hybrid automata approach which he later redeployed for the control of large populations of robots. Dejan's thesis was awarded a prize by EURON which resulted in its publication as the book "On cells and robots".
More recently, together with Ander Lynn Christensen we studying the possibility of endowing collective robotic systems with distributed immune systems capable of detecting and dealing with unpredicted faults and abnormalities. This is part of the project BioInstBots, coordinated by Pedro, aiming to create a theory of collective robotic systems inspired both in biology and institutional economics.

Together with Claudine Chaouiya, at the Instituto Gulbenkian de Ciência, we are developing new formal tools to deal with the challenges that multicellular systems pose to gene regulatory network theory.
Our collaboration goes back to the work we have done together with Aurelien Naldi and Denis Thieffry on the logical modelling of the gene regulatory networks that control the differentiation of CD4+ T cells.

Adriano Henriques' research is centred on spore development in B. subtilis. This is a fascinating ancient biological process with overtones of cell differentiation, precursor maintenance, fate decision, and cell morphogenesis. Our collaboration was born from the analysis and interpretation of data on the regulation of sigma factors. During this work we discovered that we had a lot to learn with each other.

Michal Or-Guil is a physicist by training who moved into quantitative immunology to to tackle one of its most fundamental challenges: the structure and dynamics of antibody repertoires. We collaborate informally ever since. Recently, Michal and Jorge are co-supervising the doctoral research project of Tom Weber, who investigates the dynamics of germinal center reaction and the variability in cell cycle progression which plays a key role in this dynamics.

Together with Vasco Barreto, our colleague at the Instituto Gulbenkian de Ciência, we study several forms of somatic variation including V(D)J recombination, monoallelic expression of autosomal genes, and variability of specific gene products in cells populations that are otherwise homogeneous.