This week we’re talking to Andrew Carroll, a scientist who has been with DNAnexus for the past two years. Andrew has instrumental roles in collaborating with our academic customers as well as building the tool portfolio for the platform.
Q: What do you do at DNAnexus?
A: My title is scientist. On a day-to-day basis, that involves working with our partners: understanding what they want to do scientifically, and helping them put that into DNAnexus and run it. For example, I work with Baylor College of Medicine on one set of projects relating to Mendelian diseases. I helped them take the pipeline for that analysis and get it up and running within DNAnexus. At the end they get a set of genetic variants in their cohort, and their scientists evaluate those to see which might be causative. My other main responsibility is to find open-source academic tools and port them to DNAnexus so that anybody will be able to run them. I find these by interacting with the community — talking to people we work with, reading the literature, attending conferences. Then I assess the tools myself to see which generate good, robust results.
Q: Where were you before?
A: I completed a postdoc at Lawrence Berkeley National Laboratory. Before that I was getting my PhD in molecular biology at Stanford. I was in Chris Somerville’s lab doing research relating to bioenergy and plant biology.
Q: What attracted you to DNAnexus?
A: I really enjoy tricky computational work and computational challenges. I like working on any hard problem relating to information. Through Stanford I knew one of the DNAnexus founders, Arend Sidow, and realized that this company offered an opportunity where I could come in and have a lot of freedom to work on hard problems and have the solutions be applied in real research. Being here has exceeded my expectations. These partnerships have been incredibly rewarding and include work I might not have gotten to do anywhere else, such as run 3 million CPU hours for a project. That’s pretty remarkable.
Q: What have you learned since joining the company?
A: Since I come from a plant background, I’ve learned an immense amount about operating in the human health world. Things that people care about in these cohort studies, such as keeping data private, were just never a concern in plant biology. Also, I feel that we have some of the best engineers in the world on the team and getting to interact with them on a daily basis has greatly improved my computational ability.
Q: If you weren’t a scientist at DNAnexus, where would you be?
A: I would be a scientist somewhere; it’s way too in my blood to ask scientific questions. If I couldn’t be in biology, I’d be involved in the field of large-scale machine learning and neural networks. I’m fascinated by the way brains process information.
Q: Fill in the blank: There is probably a genetic link to ______.
A: Personality. I find it quite interesting that in the evolution of humans there must have been strong pressure on maintaining certain personalities. There were much smaller networks of people early on, so there would have been pressure to maintain compatible groups of personalities and diversity of skills and strengths.
Q: If you could have any person’s genome sequenced, whose would it be?
A: I wouldn’t choose a person, because the things that make a single person really special and unique and notable aren’t in our genes. I’d go for something novel, perhaps something in the tree of life that’s underrepresented. I don’t think we have a fern genome yet, so it would be good to fill that gap.
Q: Tell us one thing about yourself that nobody at DNAnexus knows.
A: I’m actually scared of heights, but I try not to let that change anything I do. When I hiked Half Dome in Yosemite National Park, the first time I looked at the cables I thought, there is no chance I’m doing that. But the second time I went I made it to the top, and it was terrifying but not nearly as bad as I thought it was going to be. It gave me an extreme sense of accomplishment.