Aneta Žáčková: From French to bioinformatic analysis

At first, RECETOX student Aneta Žáčková wanted to study International Relations, but then she decided on Computational Biology and Biomedicine. As her studies began during the covid pandemic, she was looking for an opportunity to apply the theoretical knowledge she gained online in practice. During the second year of her Bachelor's, she was involved in a research study focusing on bioinformatics analysis of gene mutations in patients with neuromuscular disease. The codes and methods she created will be used in further research at the University Hospital Brno.

31 Mar 2022 Marie Hošťálková

Why did you decide to study Computational Biology and Biomedicine? What is your specialization?

I studied International Relations at the Matyáš Lerch Gymnasium in Brno. I always thought my strengths were in the humanities. Still, in the third year, I really enjoyed the mathematics and genetics courses, so I decided to submit applications to both the Faculty of Social Studies and RECETOX’s Computational Biology and Biomedicine program - which I found on the Masaryk University website.

The specialization was chosen before the university entrance exam. I decided on Biomedical Bioinformatics because it was closer to my heart, and I think it was a good choice.

You assisted in a research study during your undergrad. Is practical training compulsory for undergraduate students of Computational Biology and Biomedicine?

The training is not compulsory during the bachelor’s studies. Still, since the first year, I was interested in practically applying the theoretical knowledge gained in my studies. In my first year, the covid pandemic started, so everything was online. Without meeting my classmates and teachers, I was puzzled about how the study subjects would be used in actual research. So, I got in touch with a doctor working at the Cancer Outpatient Clinic at St. Anne's, FNUSA-ICRC, and asked if he knew of anyone working in bioinformatics or data analysis. A few days later, I was contacted by Dr. Réblová, a bioinformatician at the Brno University Hospital and CEITEC MUNI in the Medical Genomics group. At our first meeting, she told me about a project she had been thinking about for some time. Even though the doctor warned me that it is only an idea that may not necessarily result in anything interesting, we started working together. However, it worked out great, and currently, I am working on my bachelor’s thesis on the topic of this specific project, which Dr. Réblová also supervises. I am very grateful that she invited me to the project and that I can learn from her.

What is the project about?

We work with data from patients with various neuromuscular diseases. It is one of the largest groups of monogenic inherited diseases, i.e., diseases caused by a single mutation in a person's genetic information. The Centre for Molecular Biology and Genetics under the Faculty of Medicine Brno has provided us with sequences of patients who have symptoms of one of these diseases. Still, the possible causes have not yet been found in their genetic information. We are looking at the possibility that the disease is caused by a combination of several mutations, rather than limited to a single mutated gene.

First, it was necessary to perform bioinformatics analyses to detect the mutations in each patient. Then, we used the codes we had created in Python and Bash to produce all possible combinations of the patients' two mutations. This resulted in files with 1,250,000,000 lines, about 40 GB in size, for each patient. The codes and methods used in this work were so efficient that they will be used in other research on patients with autoimmune hemolytic anemia.

How did you manage to combine practice and school?

In the covid pandemic, I could combine both very well - I had time to do both online school and research. I mainly worked from home and had online consultations with the doctor. As a researcher, I combine the theoretical knowledge from school with a practical project. Because I enjoy it, I don't feel like I'm doing anything extra. Moreover, I am in my third year, and thanks to this project, I worked on my bachelor's thesis in my second year. During the Fall semester of the third year, when most students were just getting familiarized with their topics, I had already written more than half of my thesis.

How has the practical work affected your studies?

Thanks to the research, I can realistically imagine my future work. Also, the research motivates me to see the practical part of my studies. But I know that I was fortunate to have participated in such an exciting project. On the other hand, I had to step out of my comfort zone to ask for the opportunity to "try out" my field of study in practice. It became clear to me that even though individual courses in the first year may not make sense at first sight and students may not know why they should study them, everything is connected - each course has a purpose.

What about the future? Are you planning to study Computational biology and biomedicine in your master’s studies?

Yes, I want to continue at the master’s level in my field.

What about a Ph.D.?

I must finish my bachelor’s first. Laugh. In my first year, it seemed totally unrealistic. Now I know I want to stay in science and research, I'm not ruling out a Ph.D. But I must take it one step at a time. Laugh.

And how do you spend your spare time?

I've been doing French theatre since I was in high school. I'm a member of the alumni ensemble of the Matyáš Lerch Gymnasium. We meet once a month and rehearse all weekend. I studied French intensively in high school, and as an actress, I can stay in touch with the language. Plus, the group of people around the theatre is great, and it's always a lot of fun.

Aneta, thank you for such a pleasant interview.

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