My research focuses in the computational analysis of eukaryotic genome sequences: development of genome and transcriptome assembly protocols, modeling signal delimiting functional regions (splice-sites, regulatory regions, and so on…); finding and annotating gene exonic structures and their splicing isoforms; modeling protein-protein interaction and genetic regulatory networks; as well as integrating and developing software tools for the visualization and data integration from those analyses.
|WoS Researcher ID||B-3877-2014|
|SCOPUS Author ID||7004394733|
|Open Researcher & Contributor ID (ORCID)||0000-0001-7793-589X|
I’ve got my MSc in Biology in 1998 (UB) and started my research career in Dr R. Guigó’s lab (IMIM/UPF). My PhD thesis, defended in May, 2005 (UPF), encompassed three key aspects of Genomics: the visualization of gene and genome annotations, the study of splicing signals, and the assessment of the eukaryotic computational gene-finding tools. Among visualization tools it is worth to mention gff2ps that opened us the doors to collaborations with genome annotation consortiums. I was also involved in three of the big four community assessment experiments of gene-finding software: GASP, for the 2,4Mbp region of Adh gene in Drosophila melanogaster; EGASP, the extension of the previous experiment over 1% of the human genome within the ENCODE project; and RGASP, for the evaluation of gene-finding tools able to manage RNA-seq evidences.
Being awarded with a “Juan de la Cierva” post-doctoral fellowship, I moved into Dr E. Saló’s lab (UB) in January 2006. There I began Bioinformatic analyses on Schmidtea mediterranea; proteomics datasets from mass-spectrometry experiments were processed to chase candidate genes specific of neoblasts. We assembled and annotated one of the first published transcriptomes for this species, based on 454 sequencing technology. That sequence catalog was useful later on, serving as transcript reference set for subsequent projects, like the differential expression analysis in three neoblasts populations by means of DGE-tags. With the experience acquired, we were able to integrate distinct transcriptomes already available for this species into an interologs network (PlanNET), projected from the human interactome. Such tool has become useful to navigate through the planarian molecular pathways and to connect sequences from different transcriptome experiments retrieved from the planarian community. We have recently extended to cope with complex RNA-seq data sets such those produced from Single-Cell transcriptomics (PlanExp).
For the period 2010-12 I was awarded with a research project grant as starting group, and, in June 2009, we engaged into the Bioinformatics Unit of the Instituto de Biomedicina of Barcelona University (IBUB). Same year the Computational Genomics Lab web site was started, with the aim of serving our analysis tools and datasets to the public domain. Since its origin, we have been actively collaborating with different groups from the former Genetics department (now one of the sections of the Genetics, Microbiology & Statistics dept.), as we were able to apply tools and protocols, initially developed for genomic research on planarian, to other biological problems. It is worth to mention works on Drosophila genes, on human disease driver genes networks (RPGeNet), on integration of variation and promoter profiling (SiNoPsis), on basal metazoan genome annotation, on novel species characterization from viral whole-genome shotgun metagenomics, and so on.