101 questions with a bioinformatician #3: Deanna Church

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

After 15 years working at the NCBI as a staff scientist, Deanna Church packed her bags and headed over to the West Coast (which some of us think of as the best coast) to join Personalis, a company that is 'pioneering genome guided medicine'. In her new role as Senior Director of Genomics and Content, Deanna is helping to improve their bioinformatics pipelines which will help lead to improved analysis of human genome data. This work will also involve supporting the move to GRCh38

If you don't know what GRCh38 is, then you've either been living under a rock or you probably have never worked with vertebrate genomes. The 'GRC' part of GRCh38 refers to the Genome Reference Consortium, an organization that Deanna was heavily involved with during her time at the NCBI. The GRC are the official 'gatekeepers of genomic light and truth' (a title which I may or may not have just invented)...the key point is that they ensure that the 'reference sequence' for the genomes of human and other species remains a trusted reference. They coordinate the incorporation of changes to the reference sequence, changes that need to be made based on the latest sequencing and genome variation data.

I think that Deanna's work in genomics can best be summarized using her very own words taken from her About.me page:

Deanna Church: making the genome a friendlier place

To find out more about Deanna, follow her on twitter (@DeannaChurch). And now, on to the 101 questions...



001. What's something that you enjoy about current bioinformatics research?

In general, I really enjoy bioinformatics for the problem solving aspects. Most of the time, even the (seemingly) smallest problem will throw you unanticipated challenges. The thing I like most about the work I’m currently doing is that I feel like I’m part of a team that is really working on processes that will have a direct impact on people’s medical care. 


010. What's something that you *don't* enjoy about current  bioinformatics research?

This could change on a day to day basis, but my current woe is managing sequence identifiers.  This is a serious problem — while I understand the convenience of reporting results as either ‘chr1’ or ‘1’ these are not robust sequence identifiers. We should be managing and exchanging data using a more robust nomenclature (e.g. by using things like accession.version) as these provide a robust and traceable history of a sequence. The current standards make it too difficult to make simple mistakes — I fear we may see a lot of this as folks transition from GRCh37 to GRCh38.


011. If you could go back in time and visit yourself as an 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

Can I give two? Keep taking the liberal arts classes as an undergrad, but work more computer programming and math into your schedule!


100. What's your all-time favorite piece of bioinformatics software, and why?

This is a little self-serving, but I really like the the GeT-RM browser. I managed the development of this tool while I was at NCBI. It is not my favorite necessarily because of the usage or impact this has had in the community, but rather for what I learned while we were doing this project. I learned a huge amount about gathering user requirements, writing specifications, agile development and testing. Plus, we’ve gotten good feedback from users so that is always a plus.  


101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality?

I think I might have to say ‘.’ for a couple of reasons. First, I’ve spent a huge amount of my career trying to fill the actual gaps in assemblies — especially the human and mouse assemblies. Second, on many of my projects I’ve been a metaphorical gap filler: project manager in some cases, backend developer in others, and even a couple of turns at web UI development. I’m not quite comfortable calling myself a jack of all trades, but I try not to be too afraid of taking on new roles. It is good to continually test yourself...and to fail every now and again.