Meet Data Scientist Kelsey Florek
Bioinformatics is a branch of data science that merges biology, computer science, and statistics to solve biological problems. It involves taking biological data, such as sequence or metabolomics data, and using a computational approach. For this week’s column, I interviewed Kelsey Florek, senior genomics and data scientist at the Wisconsin State Laboratory of Hygiene, to learn more about her professional journey.
“One of the things that I like is that one day I could focus on the coronavirus and try to develop new visualizations or new models… then the next day I could talk with our IT groups or our cloud support to try to understand how we can analyze Salmonella genomes faster using cloud technologies. — Kelsey Florek, Wisconsin State Hygiene Laboratory
Florek began her undergraduate studies with the intention of becoming a computer scientist, but later decided to join the United States Navy as a nuclear machinist. After four years of service, she returned to Grand Valley State University in Allendale, Michigan. For two years, she worked in a laboratory focused on solving the structure of the ADC-7 β-lactamase from Acinetobacter baumannii. She said the job made her realize she wanted to go to graduate school.
“I didn’t want to practice medicine. I didn’t want to see any patients. But I really enjoyed learning about viruses,” she said.
Design your own diploma
During interviews with graduate programs, Florek met a student who was in an MPH/Ph.D. program, something she didn’t 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 certainly a lot of obstacles. There is a lot of work to get some sort of program approved,” she said.
After meeting with both programs, reviewing policies, and developing a workable plan, she was approved for a dual degree. It was four intense years, she says, but she got through it. Florek obtained his master’s degree in public health in 2016 and his doctorate. 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 the APHL-CDC scholarships.)
This particular fellowship focused on antimicrobial resistance. Florek’s research has focused on developing new molecular and sequence-based techniques for monitoring antimicrobial resistance in the Midwest. She was a fellow for nearly two years before being hired for the position she now holds.
The life of a bioinformatician
Florek has been in her current role for nearly three years and she said every day is different. She builds workflows and pipelines or works with specific data.
“My primary role is to take genomics and sequencing technology and merge it with new computer technology to better understand diseases in the state of Wisconsin,” she said.
One of his first big projects was to collaborate with a team of bioinformaticians to create a repository with everything bioinformaticians need in one place.
Because WSLH is a state lab 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. Moreover, it uses various technologies such as Nextflow, Python, R, Bash, Nodejs, genomics and machine learning. She also uses Docker, which allows her to containerize apps, so everything is available when she needs to run programs or apps.
Basics of bioinformatics
I asked Florek about the steps a person in their position takes when tackling a biological problem or question. She said:
- Select the tool, app or statistical software you need to use.
- Perform tests and benchmarking to see what gives you the optimal configuration.
- Build your workflow, which is a selection of bioinformatics tools that will help you get an answer from your raw data.
- Begin the actual implementation, which involves figuring out how you can use the information you’ve found to provide the answers you want.
Advice for scientists interested in careers in bioinformatics
If you’re considering a career in bioinformatics, now is the time, Florek said. There are lots of labs hiring, but there aren’t many applicants. Here are Florek’s tips:
Join a lab: Florek’s main recommendation is to join a lab to gain experience in public health or bioinformatics. She said her fellowship helped her develop her skills, network and collaborate with other public health researchers. The scholarship she made is open to people of all levels of education and lasts for one to two years. Another scholarship to consider is that of the CDC Epidemiological Intelligence Service. This is a competitive two-year postdoctoral fellowship (for PhD and MD graduates) in applied epidemiology that provides fellows with on-the-job training. Fellows work in public health departments, federal agencies, and sometimes on temporary assignments in areas outside the United States
Have a solid foundation in biology: Since bioinformatics is about solving biological problems, it is essential to have a solid foundation in biology. Whether you’re analyzing bioinformatics data to track the flu, find out which variant of COVID-19 is circulating, or track a pathogen outbreak, you need to understand what’s happening at the disease level.
Develop your computer skills and statistical understanding: Florek encourages scientists to learn coding, programming, R and scripting. She said even the skills she picked up in her college computer classes still help her today. “I think it’s getting harder and harder to do biology without having some kind of experience with R or a bit of programming,” she said.
Consider additional training or certifications: If you apply to graduate schools, consider doing a double degree like Florek.
The future is in bioinformatics. Whether it is sequencing, genomics or machine learning, bioinformatics is becoming a major aspect of the work of biologists. This means we need more bioinformaticians. If you want to know more about Florek’s work, check out his website.