Helena Klein

Helena Klein

Helena Klein

Track: Bioinformatics
Undergrad: University of Oregon, Eugene, OR - Biology
Internship: Phylagen
Current Job Title: Software Developer at Phylagen

How did you find yourself at Oregon? What about the program attracted you?
I’ve always loved biology, and before coming to the program I tried out researching a diverse set of focus areas including plant conservation, host-bacterial interactions, and even some clinical research. I thought that perhaps I would like to be a medical doctor (yes I took the MCAT). I had heard about the program from a professor earlier in undergrad, but it wasn’t until my final year when working on my honors thesis that I realized all of the questions I most wanted to answer required more computational skills. My project involved sequencing bacterial genomes to look for newly evolved mutations, which in practice meant that I had millions of short reads that I needed to filter and compare to the reference to begin to make any sense of the data, in short, I needed bioinformatics skills. To help with this, I took a class in Python for biologists and I was hooked. Turns out coding is fun when you have an interesting, biological problem you want to solve and it’s actually not very difficult compared to benchwork. Plus you can wear sandals.

What was the intensive summer like for you?
The summer intensive was fun. I like a good challenge, and collaborating with a like-minded cohort to tackle the exercises from the instructors was fantastic. It set us up for success both with our projects in the fall as well as our future internships. I also ended up with some great friendships since we spent so many hours together working on coursework and playing games in our free time.

Where was your internship?
Phylagen, a ~20 person start-up in San Francisco.

What was your internship like? What are you responsible for? What is a typical day like?
My internship was exciting. When working at such a small company every member of the team has the opportunity to make a big impact- including the intern. My first project was performing analysis on microbial data for a report that went directly to a customer. From there, I had the opportunity to build automation tools for our lab, help brainstorm new directions for our product, build databases, and design APIs. By the end of my internship, I was also supervising the next set of data science interns and running our production bioinformatics pipeline.

Do you feel the program prepared you for the internship? In what ways?
This program gave me the tools I needed to find the answers I wanted, both in bioinformatics and software development as a whole. In our projects, we were given a task and had a lot of freedom to pick out the best tools and use them to solve a problem. This required reading a ton of documentation, both well written and not as much, from a variety of sources which helped me immensely in my internship. Many of my tasks involved solving problems that not only had I not encountered before, but were new for the whole company. Having experience with finding and using new tools was invaluable.

How did your internship prepare you for your current position/career path?
Because there was so much that needed to be done at the company, and not enough hands to do it, I had a lot of freedom to pick what to tackle next. Over time, I realized that I was drawn more to the information management and access portion of work since I was spending so much time wrangling the data to produce a single plot. I wanted to optimize that process, which is why I’ve transitioned to biology-adjacent software development. I still use bioinformatics every day, especially when helping design sequencing quality control viewers and everything associated with them, this is just a variation on that path.

Do you have any advice for prospective students?
Apply! And once you’re in, I would recommend focusing as much time and energy as you can on your projects and your fellow students during the first 9 months of classes. It’s a unique space to collaborate, discuss ideas, and focus on learning.