My scientific work concentrates in the fields of bioinformatics and computational biology, with a special emphasis on the structural and mechanistic aspects of complex systems. Over the last fifteen years, two main pillars have emerged: (a) development of novel methods, tools and databases to study proteins at different levels (sequence, structure, folding, function, interactions) and (b) application of the methods to solve biologically relevant questions in different contexts. These aspects reinforce one another, as the development of novel methods is guided by specific biological questions which in turn benefit from methodological advances. In all instances, the structural aspects of proteins are leveraged to propose novel biological mechanisms. Recently, a focus is emerging on understanding the fundamental principles underlying complex systems, such as signaling in neurons or cancer development, as a deterministic (and predictable) process based on emerging properties. The vision for my future research is to try to uncover the evolutionary “logic gates” used in protein interactions to perform cellular functions of bewildering complexity.