We are interested in the molecular mechanisms that regulate cell fate. To study such mechanisms, we employ the laws of physics and the rules of evolution to develop and apply experimental/computational methods for determining the 3D structures of biological systems. Our current lines of research are:

Structure determination of tissues. More recently, we have started exporting our methods to study how tissues organize in space. To do so, we take as input single-cell omics datasets and used them to re-construct tissues. This line of research has been funded so far by "La Caixa" Foundation and the H2020 of the European Commision.
Structure determination of genomes. Since 2007, we have engaged collaboration with experimentalists to study the 3D organization of the chromatin. Such work is resulting in the first ever structures of genomic domains and entire genomes. This work has been funded by a HFSP Research Grant, the European Research Council, the NIH, and the Spanish Science Ministerios.
Comparative RNA structure prediction (closed in 2016). The recent interest in RNA, specially non-coding RNA molecules, has prompted us to develop a series of tools for the alignment of RNA structures and the prediction of their functions. This work was funded by a Marie Curie action, a Generalitat Valenciana research grant and the Spanish Ministerio de Ciencia e Innovación.
Protein-Ligand interactions (closed in 2012). We develop methods for comparative docking of small chemical compounds and their target proteins. Such methods have already been applied to identify drug targets in ten genomes that cause tropical diseases. This work was part of the Tropical Disease Initiative and was funded by the Spanish Ministerio de Ciencia e Innovación.