Getting to know us: Jon from HAVANA

This month we are meeting Jonathan Mudge who is the Annotation Project Leader in the HAVANA group.


What is your job in Ensembl?

I’m a Team Leader in the HAVANA group. We focus on manual gene annotation of the human and mouse genomes, which forms the core of the genesets produced for these species as part of the GENCODE / Ensembl projects.


What do you enjoy about your job?

We’re pushing forward the frontiers of our field – routinely finding stuff that no-one has seen before, developing new analytical methods etc – and yet at the same time our resources remain central to pretty much all fields of genome science across the world. What we do is important.


What are you currently working on?

My own particular interests are in understanding the complexity of the human transcriptome, including alternative splicing, and gene regulation events. Right now we’re working on methods to better identify the portion of the transcriptome that encodes for protein (which seems to be less than you might think). I’m also starting to think a lot more about the intersection of our gene models with disease-associated variation datasets.


What is your typical day?

I’ll usually be found in the HAVANA office, doing whatever needs to be done. In truth, interesting science usually seems to take preference over more bureaucratic duties, though I’m working on that…


How did you end up here?

I grew up in Glasgow, then went to Edinburgh to do a degree in Genetics. Immediately after that I did a PhD on primate chromosome evolution at the Life Centre at Newcastle University, before serving a dozen or so years at the Wellcome Sanger Institute (as it is now called) as part of the HAVANA team. We moved to EMBL-EBI in 2017.


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

I knew a lot about the genebuilding efforts due to our collaborative work while at the Wellcome Sanger Institute. Nonetheless, I’d still underestimated the breadth of stuff that Ensembl actually does.


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

Did you know all our manual annotations become available to external users after 24 hours? We have a track hub for this. It means you don’t have to wait for the next release!

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