/about

curriculum.md

gabrielvpina@me.log:~$ cat curriculum.md

Whoami

Bioinformatician working where virology meets genomics. PhD student in Genetics and Molecular Biology at the Universidade Estadual de Santa Cruz (UESC), in Ilhéus, Bahia — the same program where I finished my master’s.

Most of my work comes down to one idea: the viruses are already in the data, and somebody has to go look. I build the tools that make that search routine.

Research

Viral discovery and surveillance from public data. Mining RNA-Seq libraries deposited for entirely different purposes, and recovering the viral sequences hiding in them.

Metagenomics and metatranscriptomics. Characterizing viral diversity across hosts — plants, arthropods and fermentation-associated microbial communities.

Endogenous viral elements and small RNAs. Tracing ancient viral integrations in bee genomes, and the small RNA pathways that respond to infection.

Plant immunity. Identification of resistance genes in Theobroma cacao, and the study of their expression under various conditions.

Education

PhD in Genetics and Molecular Biology

Universidade Estadual de Santa Cruz · Ilhéus, BA · 2025 — present

Building the next generation of ViralQuest, and extending viral discovery to new hosts and datasets.

MSc in Genetics and Molecular Biology

Universidade Estadual de Santa Cruz · Ilhéus, BA · 2023 — 2025

Emphasis on bioinformatics. Viral genomic surveillance of Theobroma cacao using public data, screening putative novel viral sequences across RNA-Seq libraries.

BSc in Interdisciplinary Sciences

Universidade Federal do Sul da Bahia · Itabuna, BA · 2018 — 2022

Skills

Sequencing data — NGS analysis; genome and transcriptome assembly and curation; differential expression; gene set enrichment (GSEA); small RNA analysis.

Engineering — bioinformatics pipeline development; reproducible environments with Docker and pixi; data mining from public sequence repositories; Linux server administration for research.

Languages — R, Python and Bash, with Git and GitHub for everything.

Software

viralquest

An interactive, accessible pipeline for viral sequence analysis and curation. Designed so that finding viruses in a contig set does not require being a bioinformatician first. Published in BMC Bioinformatics.

viralfetch

Query and download viral taxonomy, metadata and sequences — the tedious part of every virome project, automated.

slin

A terminal interface for the SLURM workload manager, for people who live on a cluster.

dataViz

Figures and visualizations from published papers, kept in the open so the plots are reproducible.

Publications

Work on cocoa viromes, bee endogenous viral elements, stingless bee miRNAs and the ViralQuest pipeline itself — the full list lives on the publications page.

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