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I enjoy understanding and benchmarking methods for genomic/transcriptomic data analysis, learning new approaches and implementing solutions for biological questions.
My main research topic at the moment focuses on the Analysis of the Mediterranean amphioxus genome and transcriptome. We are using Amphioxus (Branchiostoma lanceolatum) as a model to study the evolution of function in the chordate-vertebrate transition. We are closely collaborating with the Amphiencode team to (1) build a chromosome-level resolution reference genome with annotation, (2) get a more realistic estimate of protein-coding genes in this organism, using orthology-based and expression-based validations. Ultimately, we aim to deliver (1) a full synteny map with vertebrate lineages, and (2) an in-depth survey of in-paralog genes in the amphioxus branch. We also hope to get more insight, in general, on The relation between expression patterns and function in animals, to understand which aspects of gene expression are most informative about the function of both genes and the anatomical structures where they are expressed in.
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