Vavouri’s lab, Institut Josep Carreras
August 2021 - Present
Bioinformatician & master's thesis student
Under the supervision of Dr. Tanya Vavouri, I am studying the PIWI-interacting RNAs (piRNAs), and the evolution and conservation of piRNA-producing loci. During this time, I have completed a Master’s thesis in which I studied the piRNA variation across closely related mouse species. Currently, I am finishing a PhD thesis involving the study of piRNA cluster expression, evolution and conservation across mouse strains and species.
Comparing the transcriptome and small RNA transcriptome across several inbred and outbred mouse strains we found that most piRNA variation is due to the genotype. Furthermore, polymorphisms in endogenous retrovirsues (ERVs), particularly intracisternal A particles (IAP), are responsible for the variation and emergence of piRNA production in a locus-specific manner, likely through defects in the RNA processing of the piRNA precursor transcripts.
In addition to the bulk sequencing, we decided to perform spatial transcriptomics with 10x Xenium in situ expression data, although I didn’t use this data in the thesis or related publications. For this purpose, we designed a 10x Xenium custom panel to detect several piRNA precurosr transcripts, as well as marker genes for spermatogenesis cell types. This involved the analysis of single-cell RNA-seq data as a reference, as well as the design of the probes for the piRNA precursor transcripts. The analysis of this data, although not published, involved the clustering and cell type annotation, a descriptive dissection of the data at pseudobulk, cellular and subcellular levels, and deeper experiments for subcellular transcript localization with tools such as bento, ELLA, InSTAnT and CellSP.
Tasks:
- Analyse and integrate distinct types of omics data, including bulk sequencing and 10x Xenium spatial transcriptomics.
- Development of a small RNA-seq pipeline to analyse piRNA production in several species.
- 10x Xenium spatial transcriptomics: design of probes for custom panel, analysis of single-cell RNA-seq data as reference, cellular and subcellular analysis of 10x Xenium data.
- Retrieve and analyze multiple-sequence alignments using ENSEMBL Compara Perl API to obtain orthologous regions between mouse strains and species and get the blocks without gaps in the multiple-sequence alignment.
- Mentoring of bachelor’s and master’s thesis students.
- Developing outreach activities addressed to high-school and undergraduate students.
- Scientific writting
Related works
Research papers:
- Casas, Mitjavila-Ventura, Sierra et al (2025). Genetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse. EMBO Journal. DOI: 10.1038/s44318-025-00475-4
Reviews:
- Mitjavila-Ventura and Vavouri (2026). Mechanisms seeding the emergence of new piRNAs. Trends in Genetics. DOI: 10.1016/j.tig.2026.04.004
Master’s thesis:
- Mitjavila-Ventura (2022). Analysis of the variation in piRNA expression across three Mus species. Universitat Oberta de Catalunya (UOC).