Head of Genomics of Gene Expression Lab (UFL)
Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville (USA)
Currently, I lead the Genomics of Gene Expression Lab at the University of Florida (USA). I am interested in understanding the functional aspects of gene expression at the genome-wide level. For that I have developed statistical methods and software tools that analyze the (dynamics aspects of) transcriptome data, integrate these with other types of molecular data and annotate them functionally. I have applied these methods to gene expression characterization in both biomedical and model organism settings, as in non-model species -specially plants-, for which I have extensively collaborated with scientists in Europe, USA, South Africa and South America.
My current research uses NGS technologies to investigate the functional implications of gene expression and regulation. I am developer of popular software tools such as Blast2GO (functional annotation of novel sequence data), Paintomics (visualization of integrated pathway data), and Qualimap (quality control of mapped NGS data) and SQANTI (quality control of transcriptomes assembled from long sequencing reads), and have published statistical tools for gene expression analysis such as maSigPro (time series analysis), minAS (multivariate feature selection), ASCA-genes (multivariate multifactorial gene expression analysis), SEA (user-friendly software and functional analysis of time course gene expression data analysis), and NOIseq (RNA-seq differential expression analysis). At present I am leading several research projects where high-throughput sequencing is used to analyze gene expression from different points of view. Some of them are focused on the integration of multi-omic data types to better understand diseases or phenotypes, and others study the functional role of isoforms. Next to my research, I have an intensive activity in bioinformatics education and training and I have also been involved in the formation of two spin-off companies in the area of biotechnology and bioinformatics.