About
About me and my career.
Whilst my formal academic training was in Biological Sciences, I have always been a computer geek and an enthusiastic GNU/Linux and open source user. Hence, Computational Biology is the perfect combination of my two main passions and professional interests.
I was awarded with an FPI fellowship to conduct my PhD in Genetics at the University of Barcelona under the supervision of Dr. Emili Saló and Dr. Josep F. Abril, and defended my thesis, entitled Characterization of the Neoblast as a Stem Cell Model, in 2016, obtaining the cum laude distinction for my work studying regeneration and stem cells through proteomics and next generation sequencing (NGS). Even though most of my work was focused on the computational analyses of the data, I also devoted part of my time to learn and apply several experimental techniques related to NGS and the validation of its results. My background in Biology together with my skills and training in Bioinformatics, provides me an integrative understanding of both fields, which allows me to link the experimental research with the computational analysis to make the most of the data.
That knowledge was the perfect and necessary combination to successfully face the challenges of the newborn single cell genomics era, making me the perfect fit to join the recently created Single Cell Genomics Team at the National Center for Genomic Analysis (CNAG) in 2014. As the first and only bioinformatician of the group, I was in charge to develop all the computational pipelines and protocols required for the data processing and analysis of the different single cell sequencing technologies performed in our lab. I was responsible for testing and implementing new pipelines in this fast evolving field, updating existing ones, and providing the rest of the members of our growing group, as well as external collaborators, with high quality data. The data processing comprised from the quality control of the raw sequencing reads to the generation of the final reports with the analyses. It required a good comprehension of the technologies and the protocols, a fluid and close communication with the members of the sequencing service and the laboratory technicians and, lastly, with the final recipient of the data, in order to deliver the expected results.
I took advantage of the JIP workflow manager (based on Python) together with my own Perl programs and Bash scripts, integrating them with the Slurm workload manager and the LIMS database of the laboratory for an automated processing of the samples. During those years, I acquired extensive experience in working with HPCs, the usage of job scheduling systems such and parallel distributed file systems like Lustre, mandatory for an efficient processing of big amounts of data.
The great potential of the single cell technologies rapidly attracted the attention of the scientific community. Together with our own research projects, we established collaborations with many other renowned research groups, most of them focused on cancer and biomedicine with clinical applications. Thus, as a postdoc, I was not only in charge of the data management. I also participated in the experimental design and analysis of many projects, from the development of new methods (Guillaumet-Adkins et al., Iacono et al., Massoni-Badosa et al.) to clinical research in cancer (Martinez-Marti et al., Barriga et al.), among others, together with international projects such as the Human Cell Atlas initiative, for the generation of a comprehensive atlas of all the human cell types, or the International Cancer Genome Consortium for the study of the Chronic Lymphocytic Leukaemia.
In 2018 I was awarded with a Juan de la Cierva Fellowship to extend my work as a postdoc two more years at the Single Cell Genomics Team and after the end of my stay as a postdoc at the CNAG, I joined the Cancer Genomics Group at the Vall d'Hebron Institute of Oncolgy (VHIO) in 2020 to apply my knowledge of the NGS technologies on translational research, with a direct impact on cancer patients.
Since December 2021, I am a member of the IrsiCaixa research group for Neoantigens and Vaccines against Cancer, where I focus my efforts on new strategies for the generation of personalized therapeutic vaccines with clinical application in patients with cancer.