Amina Echchiki

Research interests

PhD student in Evolutionary Bioinformatics (UNIL/SIB), bioinformatics trainer (Elixir/SIB) and teaching assistant at (UNIL/SIB). I actively promote networking and exchange of knowledge among fellow researchers, by contributing as trainer and/or organizer for classes, workshops, scientific events and mentoring activities within my area of expertise. I am also active in academic life as PhD students representative (CUSO/UNIL) and as manager of departmental sharing-based platforms for scientific visibility, monitoring the usage of internal computing servers, and introducing these platforms to newcomers.

Since my very first encounter with bioinformatics, I have been fascinated by the diversity of topics at the interface of computer technology and biological sciences. I try to keep myself updated - especially on the technical side - through literature, and active in Q&A forums and social media.

You can find me on:

Twitter: https://twitter.com/aechchiki
LinkedIn: https://www.linkedin.com/in/amina-echchiki-9b829912a/

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.