Bioinformatics is branch of data science that merges biology, computer science and statistics to solve biological problems. It involves taking biological data, such as sequence data or metabolomics, and using an informatics approach. For this week’s column, I interviewed Kelsey Florek, a senior genomics and data scientist at the Wisconsin State Laboratory of Hygiene, to learn about her career journey.
“One of the things I love is one day I could be focused on coronavirus and trying to develop new visualizations or new models … and then the next day I could be talking with our IT groups or cloud support to try to figure out how we can get salmonella genomes analyzed faster using cloud technologies.” — Kelsey Florek, Wisconsin State Laboratory of Hygiene
Florek started her undergraduate studies with the intention of becoming a computer scientist but then decided to join the U.S. Navy as nuclear machinist mate. After four years in the service, she went back to Grand Valley State University in Allendale, Michigan. For two years, she worked in a lab focused on solving the structure of the Acinetobacter baumannii β-lactamase ADC-7. She said the work made her realize that she wanted to go to graduate school.
“I didn’t want to practice medicine. I didn’t want to see patients. But I really enjoyed learning more about viruses,” she said.
Designing her own degree
While interviewing with graduate programs, Florek met a student who was in an MPH/Ph.D. program, something she did not know was an option. When she started her Ph.D. at the University of Wisconsin-Madison in 2013, she did some research to see how she could get a dual degree.
“There were definitely a lot of barriers. There is a lot of work to just even get some sort of curriculum approved,” she said.
After meeting with officials at both programs, reviewing policies and coming up with a feasible plan, she was approved for a dual degree. It was an intense four years, she said, but she made it through. Florek earned her master’s in public health in 2016, and her Ph.D. in microbiology and immunology in 2017.
She then began a fellowship at the Wisconsin State Laboratory of Hygiene on campus. The fellowship is administered by the Association of Public Health Laboratories and the Centers for Disease Control and Prevention. (Learn more about APHL–CDC fellowships.)
This particular fellowship focused on antimicrobial resistance. Florek’s research focused on developing new sequence-based and molecular techniques for surveillance of antimicrobial resistance in the Midwest. She was a fellow for almost two years before being hired for the role she has now.
Life as a bioinformatician
Florek has been in her current position for almost three years, and she said each day is different. She builds workflows and pipelines or works with specific data.
“My primary role is to utilize genomics and sequencing technology and merge that with new computational technology to better understand diseases in the state of Wisconsin,” she said.
One of her first big projects involved collaborating with a team of bioinformaticians to create a repository that has everything bioinformaticians need in one place.
Since the WSLH is a state laboratory on the Madison campus, Florek can easily meet with academic researchers and has access to the university’s Center for High Throughput Computing, Amazon Cloud and Google Cloud. In addition, she uses various technologies such as like Nextflow, Python, R, Bash, Nodejs, genomics and machine learning. She also uses Docker, which allows her to containerize applications, so everything is available when she needs to run programs or applications.
I asked Florek about the steps someone in her position takes when tackling a biological problem or question. She told me:
- Select the tool, application or statistical software you need to use.
- Do testing and benchmarking to see what gives you the optimal setup.
- Construct your workflow, which is a selection of bioinformatic tools that will help you get an answer from your raw data.
- Begin the actual implementation, which is determining how you can use the information you found to provide the answers you want.
Advice for scientists who are interested in bioinformatics careers
If you are considering a bioinformatics career, now is the time, Florek said. There are many laboratories hiring, but there are not many applicants. Here are Florek’s tips:
Join a laboratory: Florek’s top recommendations is joining a laboratory to gain experience in public health or bioinformatics. She said her fellowhip helped her develop her skills, network and collaborate with other public health researchers. The fellowship she did is open to people at all education levels and lasts one to two years. Another fellowship to consider is the Epidemiologic Intelligence Service one at the CDC. It is a competitive two-year post-graduate fellowship (for those with Ph.D.s and M.D.s) in applied epidemiology that gives fellows on-the-job training. Fellows work in public health departments, at federal agencies and sometimes on temporary assignments in areas outside of the U.S.
Have a solid foundation in biology: Since bioinformatics is about solving biological problems, having a strong foundation in biology is key. Whether you are analyzing bioinformatics data to track influenza, find what variant of COVID-19 is circulating, or following a pathogen outbreak, you need to understand what is happening at the disease level.
Build your computer science skills and statistical understanding: Florek encourages scientists to learn coding, programming, R and scripting. She said even the skills she learned in her college computer science courses still help her today. “I think it’s getting harder and harder to do biology without having some sort of experience with R or a little bit of programming,” she said.
Consider additional education or certifications: If you are applying to graduate schools, consider doing a dual degree like Florek.
The future is in bioinformatics. Whether it is sequencing, genomics or machine learning, bioinformatics is becoming a major aspect of biologists’ work. This means that we need more bioinformaticians. If you want to learn more about Florek’s work, check out her website.