Third-generation ingle-molecule long-reads technologies (Nanopore and Pacbio) can sequence full-length transcripts, creating exciting new opportunities for genome annotation and the study of alternative transcript variants. However, the new data is not exempt of biases and novel methodologies for preprocessing, curation and statistical analysis need to be developed. My lab has been pioneering in the development of such tools. I will give an overview of the current limitations, solutions, and opportunities for long read RNA-seq highlighting the new biology revealed by these data. I will present the LRGASP project, a community-wide challenge to evaluate the potential of lrRNA-seq for transcript identification and quantification.
Institute for Integrative Systems Biology, Spanish National Research Council
Pre-eminence Professor, University of Florida
Dr. Conesa is PhD in Molecular Microbiology from the University of Leiden in the Netherlands. After a short appointment as bioinformatics project leader at TNO Quality of Life (The Netherlands), she obtained a Ramon y Cajal award to join the Valencia Agricultural Research Institute in 2003 in Spain. She moved to Prince Felipe Research Center in 2007 and became Senior Group Leader in 2010. In 2014 she was recruited as pre-eminence Professor at the University of Florida. In 2021 was obtained a Research Professor position at the Spanish National Research Council.
Dr. Conesa´s lab is interested in understanding functional aspects of gene expression at the genome-wide level and across different organisms. Her group has developed statistical methods and software tools that analyze the dynamics aspects transcriptomes, integrate these with other types of molecular data and annotate them functionally. Some of our popular software tools are Blast2GO, Paintomics, maSigPro, NOISeq, Qualimap, SQANTI, etc. She has 140 research papers that have received over 27000 citations. She is co-founder of Biobam, a bioinformatics company that commercializes user-friendly software for biologists. In her most current research, they develop statistical methods for multiomics data integration and tools for the analysis of third-generation long-reads sequencing data.