Experience on Adrià Mitjavila Ventura

Bioinformatician & PhD student

Mon, 01 Jan 0001 00:00:00 +0000

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.

Bioinformatitian

Mon, 01 Jan 0001 00:00:00 +0000

Pasini’s lab, Istituto Europeo di Oncologia

*July 2019 - July 2021
Bioinformatician

During my stage in Dr. Diego Pasini’s lab, I investigated several molecular signaling pathways and epigenetic mechanisms underlying cellular differentiation and oncogenesis.

Tasks:

Comparison of different ATAC-seq peak callers.
Comparison of different sequencing depths in RNA-seq for differential expression analysis.
Development of a Snakemake pipepline for ATAC-seq. The code can be visualized here (unmaintained).
Development of a ShinyApp to allow wetlab members to visualize the omics produced in the lab in an easy way. The code can be visualized here (unmaintained).
Analysis of bulk RNA-seq, ChIP-seq and ATAC-seq data.

Master's thesis student

Mon, 01 Jan 0001 00:00:00 +0000

Gene expression lab, Instituto de Biomedicina de Sevilla

September 2017 - October 2018
Master's thesis student and research assistant

In the context of the master’s thesis (MSc in Molecular Genetics & Biotechnology), under the supervision of Dr. Sebastián Chávez de Diego and Dr. Gabriel Gutierrez Pozo and within Dr. Victoria Begley’s PhD project, I started studying Xrn1, a protein involved in the degradation of mRNA, and it’s role in the nucleosome localization and transcription in Saccharomyces cerevisiae. Using MNase-seq and following a DANPOS-based analysis, we found that the Xrn1 knockout mutant strains had higher nucleosome occupancy around TSS, which we related with a lower transcription initiation compared to WT strains, whereas in the gene body, the nucleosome occupancy was diminished as a consequence of RNA pol II backtracking. Results were validated using MNase-qPCR of two selected genes in Xrn1 conditional mutants.

Bachelor's thesis student

Mon, 01 Jan 0001 00:00:00 +0000

Molecular Microbiology, Microbial, S.L.

September 2016 - June 2017
Internship and Bachelor's thesis student

In the context of my bachelor’s thesis (BSc in Biotechnology) and under the supervision of Prof. Jesús García-Gil, I studied the diversity of the ileal mucosa-related microbiota of colorectal cancer patients submitted to an ileostomy and its changes after a butyrate treatment. Using DNA extracted from human biopsies of ileal mucosa, we performed qPCR and high-throughput sequencing followed by a SPSS-based statistical analysis to search for the differences between the butyrate-treated, placebo-treated and untreated groups, and we found that some healthy-related butyrate-producing bacteria increased in proportion after the butyrate-treated, but not in the other groups. At the same time, different disease-related bacteria were found to decrease in the butyrate group after the treatment compared to the other groups. Although the changes weren’t higly robust in terms of significancy, the short-period of the treatment (4 weeks) and its conditions (ileostomy allows oxigen to enter the ileum, while it is supposed to be an anoxic environment) made us think that a long-term butyrate treatment could improve microbiological conditions in the studied patients.