Meet data scientist Kelsey Florek

Bioinformatics is a branch of data science that merges biology, computer science, and statistics to solve biological problems. This involves taking biological data, such as sequence or metabolomics data, and using a computational 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 more about her professional background.

“One of the things that I love is that one day I could focus on the coronavirus and try to develop new visualizations or new models… and then the next day I could talk with our IT groups or our cloud support to try to understand how we can get salmonella genomes analyzed faster using cloud technologies. – Kelsey Florek, Wisconsin State Hygiene Laboratory

Florek began her undergraduate studies with the intention of becoming a computer scientist, but then decided to join the US Navy as a second 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 resolving the structure of the β-lactamase ADC-7 of Acinetobacter baumannii. She said the job made her realize that she wanted to go to college.

“I didn’t want to practice medicine. I didn’t want to see any patients. But I really liked knowing more about viruses, ”she said.

Design your own diploma

During an interview 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 doctorate. at the University of Wisconsin-Madison in 2013, she researched how she might get a double degree.

“There were definitely a lot of obstacles. It takes a lot of work to even get some sort of program approved, ”she said.

After meeting with those responsible for both programs, reviewing policies, and developing a workable plan, she was approved for a double degree. It’s been four intense years, she said, but she’s managed to pull through. 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 scholarship is administered by the Association of Public Health Laboratories and the Centers for Disease Control and Prevention. (Learn more about APHL-CDC scholarships.)

This particular scholarship focused on antimicrobial resistance. Florek’s research has focused on the development of novel molecular and sequence-based techniques for antimicrobial resistance surveillance in the Midwest. She was a scholarship holder for almost two years before being hired for the role she now occupies.

The life of a bioinformatician

Florek has been in her current role for almost three years and she says every day is different. It creates workflows and pipelines or works with specific data.

“My primary role is to use genomics and sequencing technology and merge them with new computer technology to better understand diseases in the state of Wisconsin,” she said.

One of his first big projects involved working with a team of bioinformaticians to create a repository that brings together everything bioinformaticians need in one place.

With the WSLH being a state lab on the Madison campus, Florek can easily meet university researchers and has access to the university’s Center for High Throughput Computing, Amazon Cloud, and Google Cloud. In addition, 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 actions a person takes in their position when they tackle a biological problem or issue. She said:

  1. Select the tool, application, or statistical software you want to use.
  2. Do some benchmarking and testing to see what gives you the optimal setup.
  3. Build your workflow, which is a selection of bioinformatics tools that will help you get an answer from your raw data.
  4. Begin the actual implementation, which determines how you can use the information you find to provide the answers you want.

Advice to scientists interested in careers in bioinformatics

If you are considering a career in bioinformatics, now is the time, said Florek. There are a lot of labs that are hiring, but there aren’t a lot of applicants. Here are tips from Florek:

Join a laboratory: Florek’s main recommendation is to join a laboratory to gain experience in public health or bioinformatics. She said her fellowship had helped her develop her skills, network and collaborate with other public health researchers. The scholarship she performed is open to people of all levels of education and lasts one to two years. Another scholarship to consider is that of the CDC’s Epidemiological Intelligence Service. This is a competitive two-year graduate scholarship (for doctoral and doctoral 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 regions outside of the United States

Have a solid foundation in biology: Since bioinformatics is all about solving biological problems, having a solid foundation in biology is essential. Whether you are analyzing bioinformatics data to track the flu, find which variant of COVID-19 is circulating, or track a pathogen outbreak, you need to understand what’s going on 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 learned in college computer science classes 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 training or certifications: If you are applying 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 that we need more bioinformaticians. If you want to learn more about Florek’s work, check out his website.

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