DNAnexus Snapshot: Five Minutes with Vince Ramey

vince rameyIn this series of Snapshot blog posts, we profile some of our fascinating team members to give you a better sense of who we are.

This week we’re talking to Vince Ramey, a scientist who joined DNAnexus in April 2012 and has been providing some biology context for the programming team working on the new DNAnexus platform.

Q: What do you do at DNAnexus?

A: The role has changed as the development stage of the new platform has changed. When we were in the R&D stage I was programming full time. Since the beta launch, now we’re engaging with some key people and I’m doing a lot more to help support some of these partnerships. I go out and meet with people and help them put their tools in the system; show them how it can change the way they do business. Part of my job is to get in the head of potential users — biologists or clinicians, say — and figure out what they need for data analysis. The scientist’s role includes things like: what kind of content do we need in terms of public data sets, how is someone going to use this tool, how do you display a variant?

 

Q: Where were you before?

A: I was doing a PhD in a biophysics program at the University of California, Berkeley. I was a genetics major in undergrad and took a detour from genomics and genetics in grad school. I joined the biophysics program because that’s where bioinformatics was housed. But my academic life took a turn when I got there and I was an electron microscopist for six years. I looked at the shapes of single proteins and tried to figure out how they work.

 

Q: What attracted you to DNAnexus?

A: DNAnexus was exactly what I was looking for: this small shop that was aiming really big; that was making something that was a general solution to a fundamental problem. It allowed me to do code and be technical but also to talk to people and engage on a lot of levels.

 

Q: What is something you’ve learned since joining that has surprised you?

A: My experience of programming was all in the academic setting; I taught myself a lot, and sometimes programmed with one or two other people. I went from that very basic understanding of what it meant to do a programming project to this shop in the heart of Silicon Valley, where there’s a cutting-edge understanding of what it takes to make something like this. I realized my conception of what it was to work on a software project was pretty rudimentary compared to the state of the art. There are so many moving parts, it’s amazing.

 

Q: If you could have any person’s genome sequenced, whose would it be?

A: Genghis Khan comes to mind. You could add a lot of factual information for today’s population in retrospect for a person like that — though I don’t think there’s a gene for pillaging so you probably wouldn’t find that.

 

Q: If you weren’t a scientist at DNAnexus, where would you be?

A: I’d pretty seriously consider building an off-the-grid house in the middle of nowhere. It’s an interesting problem, because you have to think about a lot of physical design to really pull it off — like how to catch water to meet your needs. The idea of doing something with recyclable components is appealing.

 

Q: Fill in the blank: There’s probably a genetic link to _________.

A: Thinking everything has a genetic link! This question, and the slippery slope it opens up, is frightening in a lot of ways. There’s a common perception that genetics has a huge influence on who you are, and it’s true for some specific things, but we’re much more complicated than that. The wise answer always seems to be, “everything has lots of causes.”

 

Q: Tell us one thing about yourself that nobody at DNAnexus knows.

A: When I’m in the zone I listen to the same couple of songs over and over. I’ll sit in the office and do that. When you find your groove, you gotta stick with it, you know?

Snapshot: Five Minutes with Mike Lin

Mike Lin DNAnexusIn a series of Snapshot blog posts, we are spotlighting some of our fascinating team members to give you a better sense of who we are.

Today we’re sitting down with Mike Lin, a senior software engineer who joined DNAnexus in February 2012. Mike was previously at MIT and the Broad Institute, where he worked in Manolis Kellis’s lab on comparative genomics of protein-coding genes. He comes from a computing background, but started taking biology-related course work as an undergraduate student when he realized that bioinformatics looked like an exciting and growing field.

Q: What do you do at DNAnexus?

A: I’m a software engineer, working to build our new collaborative platform for analyzing DNA data in the cloud. Right now I’m particularly focused on scaling the back-end architecture to enable it to process thousands of human genomes per month.

 

Q: Where did you work before?

A: I recently finished my PhD at MIT and the Broad Institute, where I worked on machine learning techniques to study the evolution and function of protein-coding genes in the human and fruit-fly genomes.

 

Q: What was it about DNAnexus that attracted you to the company?

A: I believe the cloud platform we’re building at DNAnexus will accelerate scientific collaboration in genomics, and thus help fulfill its potential for human health and medicine.

Genomics is a highly interdisciplinary and collaborative field, but the “big data” it produces makes collaboration really difficult at times. For example, when I was involved in research at MIT, we had access to some amazing compute facilities there. But our collaborators at other institutions used their own compute clusters (and weren’t allowed on ours anyway), so we’d have to send massive files around by e-mail or FTP. Sharing analysis software was even worse, as getting someone else’s code to compile and run often led to hair-pulling frustration. These are big problems that impede progress of the entire science.

A secure cloud platform on which you can instantly share data and analysis software, and run analyses at scale without huge upfront investments in hardware and pipeline engineering, will really make a difference — and that’s what we’re building. Of course, there are also amazing commercial opportunities when you think about millions of people having their genomes sequenced in this decade.

 

Q: What have you learned since joining the company?

A: I’m continuing to learn a ton about working on a team of professional software engineers, which I didn’t have much experience with in the past. “Agile” sprint planning, continuous integration testing, distributed source control, and the human elements of keeping everyone focused and coordinated — all examples of important professional practices that are quite hard to get right, and weren’t really on the radar in academia.

 

Q: What would you do if you weren’t a software engineer?

A: If I hadn’t come to DNAnexus, I probably would have stayed in academia for postdoctoral research. Failing that, let me say airline pilot!

 

Q: What person had the greatest influence on where you are today?

A: I owe a great deal to my PhD advisor Manolis Kellis, who taught me not only everything about genomics, but also about the importance of taking risks and staying positive.

 

Q: Fill in the blank; there is probably a genetic link to _____

A: Circadian rhythms; I think there really are “morning people” and “night people.” I’m the latter.

 

Q: If you could have anyone in history’s genome sequenced, whose would it be? Why?

A: It’s hypothesized that there were actually a “Y-chromosomal Adam” and an “X-chromosomal Eve.” Genetic models of human populations would probably be quite a bit more precise if we could get our hands on those. And there’s the not-unrelated “Genghis Khan Effect.”

 

Q: If you had your genome sequenced, what would you hope to find (or not find)?

A: Like a substantial fraction of people of East Asian descent, I seem to have a lousy ALDH2 gene that severely curtails my participation in certain common social activities. In fact, I suspect I have not one but two bum alleles. I’d like to know for sure!

 

Q: Tell us one thing about yourself that nobody at DNAnexus knows.

A: I used to drive a purple car. It was a Volkswagen with a pearl-coat paint that on a cloudy day looked blue, but in the sunlight showed unmistakable purple streaks. Of course, I bought it on a cloudy day.

Snapshot: Five Minutes with Lee Bendekgey

In a series of Snapshot blog posts, we are spotlighting some of our fascinating team members to give you a better sense of who we are.

DNAnexus Lee BendekgeyThis month we sat down with Lee Bendekgey, Vice President of Business Operations here at DNAnexus. Lee joined the company in June 2011, coming from Nuvelo, a publicly traded biopharmaceutical company where he served as Chief Financial Officer and General Counsel. Lee earned his BA from Kalamazoo College and his JD from Stanford Law School.

 

Q: What do you do at DNAnexus?

A: I manage the company’s financial and legal functions.

 

Q: Where did you work before?

A: I’ve worked at lots of places. Probably most relevant to DNAnexus are the six years I spent at Incyte, which was one of the first-generation genomics companies. The thing that’s exciting right now is that we’re seeing the results of work that was started in the mid ’90s. Everyone expected that when the genome was sequenced, there would be all of these immediate changes to how illness was treated — and when that didn’t happen a lot of people dismissed it as hype. It’s happening and we’re seeing it now.

 

Q: What was it about DNAnexus that attracted you to the company?

A: I have always worked at companies whose goal was to create a new product category that addresses an unmet need.

 

Q: What have you learned since joining the company?

A: When I joined DNAnexus about 18 months ago, it was an earlier-stage company than any of the others for whom I’ve worked. As a result, I’ve learned how rewarding it is to make an impact on a company that is on such a steep growth trajectory.

 

Q: What would you do if you weren’t VP of business operations?

A: If I could do anything or be anyone, I would be Bruce Springsteen.

 

Q: What person had the greatest influence on where you are today?

A: My wife. I’ve had a pretty adventurous career in Silicon Valley, where there’s a lot of change and risk. It’s much easier to take career risks when you are able to go home to a person who makes you feel secure.

 

Q: Fill in the blank; there is probably a genetic link to _____

A: Creativity.

 

Q: If you could have anyone in history’s genome sequenced, whose would it be?  Why?

A: Leonardo da Vinci.  See previous answer.

 

Q: If you had your genome sequenced, what would you hope to find (or not find)?

A: I would want to find out about any health care risks that I can do something to mitigate.

 

Q: Tell us one thing about yourself that nobody at DNAnexus knows.

A: When I was in high school I was interested in music and theater, like those kids on Glee.