Research Experience

At IGTP I worked on the analysis of DNA methylation arrays for colorectal cancer and expression arrays for lung cancer data. I mainly used R on my analysis, including the Keras library which serves as an interface to TensorFlow.

My research project at the IRB tried to find the correct protein modelling/molecular dynamics protocol to predict the resistance towards different drugs of the HIV-1 protease.

At the CRG, I worked on the study of protein-DNA complexes, basically using FoldX to predict the binding affinity of mutants. I was involved in several European projects like Megatools, ZNIP and EMERGENCE. Below, an example of the analysis of the effect of mutations on the stability of Pax6. Mutations to Pax6 are linked to several eye diseases.

Below, the I-CreI scaffold, example of a meganuclease we used to design mutants with new DNA-binding capabilities.

During my stage at the CNIO, I worked mainly on developing web applications. We developed a pair of apps that convert gene, clone or protein IDs into other IDs. This can be done with IDconverter, an application that was initially developed by Patricio Yankilevich. We managed to speed up this application by pre-generating the tables thanks to a Python script I wrote. IDClight is an application with the same purpose, but it can be easily linked from other applications as the IDs are passed with the URL. Try it and tell me what you think about it.

Also we developed PaLS (Pathway and Literature Strainer). PaLS is a tool that filters, from a list or a set of lists of gene/clone/protein identifiers, those that meet certain criteria related to their references to articles in PubMed, Gene Ontology terms and KEGG and Reactome pathways.

Previously, while I was at The Burnham Institute, in the nicest place you can find (La Jolla, USA), I collaborated with Marc Robinson-Rechavi (now at the University of Lausanne). The output was an article in Journal of Molecular Biology. My contribution to the paper was an analysis of 3D protein structures of a thermophilic bacteria (Thermotoga maritima) and compare them with those of homologous proteins from mesophilic bacteria. I used networks (graphs) to characterize these structures and arrived to the conclusion that the thermostability of proteins is nicely linked to their compactness (measured by the connectivity of the networks). I still have some plans to explore this field when I have time...

Before that, a couple of experiences in companies and my PhD. The title: Chemical Evolution of the Galaxy and the Problem of Light Elements. If interested, pass by and I'll explain it to you.