Getting to know us: Irina from Variation

Today we are meeting Irina, who joined the Variation team earlier this year. She talks about how she came to Ensembl, her interests, experience so far and more.

What is your job in Ensembl?

I am a Bioinformatician in the Ensembl Variation team and I work on the annotation and interpretation of DNA variants in the context of existing phenotypes. Our team handles the production and maintenance of the Ensembl Variation databases covering a variety of species, as well as the development of tools related to variation data like the Variant Effect Predictor (VEP), Haplosaurus, LD Calculator and others. My personal interest lies in the interpretation of human DNA variants for clinical diagnosis and direct impact to human health.

What do you enjoy about your job?

I really enjoy the team and work culture in Ensembl. Everyone is very knowledgeable and open to share their insight with you. I enjoy working on variation data and the mix between our individual and common responsibilities. At the individual level each of us has an area of work where we spend most of the time and become experts; and at the same time we are jointly responsible for the periodical Ensembl Variation database releases and for supporting the people using our resources. Each of us takes turn in coordinating the release and helpdesk.

What are you currently working on?

I work on improving the phenotype data linked to genes and specific variants. This work involves a constant cycle of revisiting what resources are available, what data can be extracted and how best to represent and make it available through the web interface or programmatic REST access. My latest work implied an expanded and improved data import from ClinVar, a variation resource containing links between human variation and observed health status. I also developed and expanded the phenotype and population REST API endpoints for easier data retrieval.

What is your typical day?

A typical day for me starts with a quick recap of the previous day, what was done / what needs to be done next and a brief catch-up meeting with the other Variation team members, which makes me aware of what everyone else is working on, or the status of the next Ensembl release. Then I’m free to organise my rest of the day as long as things are done in time. Depending on the day, we might have Ensembl or Variation team meetings, or I might be interested in attending one of the many high-quality scientific talks on the campus, or one of the STEM Ambassadors training sessions, a scheme I recently joined.

How did you end up here?

After studying Computer Science in high school in Targu Mures, Romania, I knew I wanted to continue in a related field. Whilst researching for university degree courses a Bioinformatics course in Hagenberg, Austria, caught my eye. Biology so far had presented itself to me as a universe of unknown rules and principles, and Bioinformatics had the promise of breaking down biological questions into parts and structuring biological knowledge into clear rules and principles. As part of the four-year undergraduate degree I did an internship at EMBL-EBI working as part of IntAct on protein interactions; this was my first introduction to EMBL-EBI and research in Cambridge.

After a PhD in Proteomics and Bioinformatics in Cambridge, I felt the desire to explore other areas of Bioinformatics, and worked on de-novo assembly and gene set definition as part of Ensembl Metazoa. This period overlapped the time when the phase 3 of the 1000 Genomes Project was reaching its final analysis stages, highlighting the implications of large DNA variation sets.

An exciting post-doctoral opportunity to work in Boston on the evaluation of human protein truncating variants in the team that created gnomAD, one of the free resources of genomic variation data with high impact on clinical diagnosis, led me away from EMBL-EBI. I returned earlier this year in the Ensembl Variation team where I continue to work on improved interpretation of variation in the context of existing data, this time looking at all variation classes and their phenotypic impact.

What surprised you most about Ensembl when you started working here?

The main aim of the Ensembl team is the release of the Ensembl databases and support of the associated tools, however there are a lot of smaller projects going on in parallel. This diversity leads to a variety of skill sets represented in the team. It appears to me that everyone has a unique combination of experiences and skills that they are willing to share and contribute to the success of Ensembl.

What is the coolest tool or data type in Ensembl that you think everybody should know about?

The Variant Effect Predictor (VEP) is one of the coolest tools and, in combination with the Haplosaurus tool that uses genotype data, has great power for correctly predicting the effect of variation. I think some of the most exciting work is happening on the phenotype front. The G2P plugin is a great example of this; it uses variant allelic level requirements to predict the variant’s impact on genes and their disease phenotypes. I think there are great opportunities ahead to assess and improve the evaluation of specific variation effect on the human disease phenotype, so stay tuned for future work!

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