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She believes the future of medicine lies in fully understanding human DNA. As a new Assistant Professor at Faculty of Informatics MU, she is working to connect biology with modern computational methods and expand collaboration between scientists. In addition to research, she is promoting a new degree program in Bioinformatics. She is also a laureate of this year's Czexpats in Science Award, which aims to support and publicly recognise the work and achievements of Czech scientists abroad. Mgr. Monika Čechová, Ph.D., shares her experiences from international research, what awaits future students of bioinformatics and how artificial intelligence is transforming DNA analysis.

On your website you mention: "I am interested in the most complex parts of the human genome. I believe complete Telomere-To-Telomere assemblies are the future of genomics that is happening now." What exactly do you mean by that?

Until recently, we did not have the technology or the algorithms to read complete human DNA. For example, we are interested in regions such as centromeres, which are important for cell division, or telomeres, which protect the ends of chromosomes and limit how many times a cell can divide. Today, the situation is different. Each of us may have our entire genome, the DNA from all 46 chromosomes, but this is in the proof of concept stage. I would like to see us move from testing for genetic predispositions to individual diseases to simply having our genome as part of our medical records. Which is the future, but a future that is certainly possible. The future of genomics, which is happening on the scientific scene right now.

You have been involved in the decoding of the Y chromosome within the Telomere-to-Telomere Consortium. Please tell us more about this consortium and your role in this research.

The Telomere-To-Telomere Consortium read the first complete human genome (called CHM13), almost exactly three years ago. It was a group of scientists from around the world with a common vision - to read and describe the last remaining 8% of human DNA. The founders of the consortium are Karen Miga and Adam Phillippy; fittingly, their main interests are repetitive DNA (i.e. DNA containing repetitive sequences - author's note) and new algorithms for genomics. But the Y chromosome was still missing, the repetitive half, which is like putting together a blue-sky puzzle. I enthusiastically joined the project - I was particularly interested in the structure of palindromes, large repetitive pieces of DNA that contain genes whose deletion can potentially result in infertility. 

In 2020, you were interviewed for the FI Alumni Gallery, in which we discussed your academic beginnings and your work at Pennsylvania State University. Where have you moved in your career since then, and what have these experiences brought you?

The most significant experience for me was another extended stay overseas, this time in California. I worked as a postdoc in the lab of Associate Professor Karen Miga, founder of the aforementioned Telomere-To-Telomere consortium. As a supervisor, she was incredibly inspiring, always thinking not about what science can do today, but what it can do tomorrow, a year from now, a decade from now, and how to scale projects for use in practice. In her lab, I had access to the latest technologies, sometimes before they were even brought to market. I often felt like I was living in a sci-fi version of the future. It made me realize how I wanted to guide my own students and what kind of research I wanted to do. After returning to the Czech Republic, I joined the Faculty of Informatics here as an Assistant Professor. I am working to ensure that bioinformatics research continues to expand, is open to collaborations between scientists and towards the public, and that we can solve interesting biological problems using informatics - for which we have great support here. 

In 2020, you also published an article "Ten simple rules for biologists initiating a collaboration with computer scientists" in the journal PLOS Computational Biology, in which you formulate ten rules for successful collaboration between biologists and computer scientists?Are you succeeding in fulfilling these rules? Would you make any additions today, additional rules?

I would say that the article is still relevant and probably will be for a long time. Although I have to say that ChatGPT and similar models, as well as modern data libraries, have now greatly simplified the checking, cleaning and formatting of data, as well as the technical part of the analysis, which can be largely automated. The human factor is now even more critical - for a computer scientist, this might be a detailed conversation with someone who has collected the data being analysed. I'm convinced that in the future the boundaries of disciplines will become even more blurred, and all research will be interdisciplinary.  

As part of your studies at FI, you literally designed your own studies in bioinformatics when it was not yet common in undergraduate studies. How do you perceive the creation of a new study programme in Bioinformatics, which FI is launching from the next academic year in cooperation with the Faculty of Science MU?

I think it's great, especially for community building. The courses cover about 60% informatics subjects, and 40% biology, across the faculties. It will also mean more lectures for our students, more invited guests, workshops, leisure activities, maybe eventually even a summer school. I believe this will enhance the attractiveness of the field and the satisfaction and employability of our graduates.  

What can students look forward to in the new programme?  

Within the Bachelor's degree, we offer a specialization in Applied Bioinformatics and Bioinformatics Software Development. Master's students can look forward to three majors. Sequential Bioinformatics (represented at FI by myself and Assoc. Prof. Matej Lexa), Computational Systems Biology (Assoc. Prof. David Šafránek) and Structural Bioinformatics and Drug Design. Each of these directions is represented by a different group of scientists from several institutions, including the Central European Institute of Technology (CEITEC) and the National Center for Biomolecular Research (NCBR). So it will be really diverse. I am particularly fascinated by DNA and especially the complex, repetitive regions of DNA and the accurate reading of complete chromosomes, especially human.

Recently, the media reported on the emergence of Evo 2, a new AI model focused on biology. How do you see this progress? Will you use this tool in your teaching or your research? 

I'm definitely intrigued, but I haven't had the opportunity to try out the tool yet. However, I do use ChatGPT in my teaching and research. When used properly, it increases productivity. If someone is skeptical of similar models, then I presume their experience is either old or they haven't spent enough time getting familiar with the model. Part of sequence bioinformatics involves processing and converting data that previously required writing code. This can now be generated automatically by the right prompt and then only minimally modified. This takes us from hours to minutes for some tasks. 

Since February this year, you have been an Assistant Professor at the Department of Machine Learning and Data Processing at FI MU. What are your main tasks?

Tasks are classically divided into research, teaching and supervising students. I am also working on establishing new collaborations in Brno, greater networking within the Brno bioinformatics community, and international projects - especially those I started at American universities, i.e. Penn State and University of California, Santa Cruz (UCSC). I also want to get more involved in public outreach and give talks at events such as Masaryk University's TEDx or the University of the Third Age. I want to see the answer to a question "What can we learn from our DNA?" eventually become part of general knowledge, similar to what the field of bioinformatics is for.  

What research are you involved in at FI?

I have been at FI for a short time so far, so I expect to get involved in more activities gradually. However, I have collaborated with Associate Professor Lexa in the past and we have a recent joint paper on repetitions in DNA and their arrangement in the 3D space of the cell. Associate Professor Šafránek is the guarantor of the Bioinformatics undergraduate program here at FI that I am helping to promote. And the collaboration with our Office for External Relations is also great.  

In the broader "bio" category, there is a small group of us who meet for lunch together, organized by my colleague Sam Pastva. So I think we will see more joint projects and grants in the future. I'm also still working on several projects with American colleagues, particularly a project looking at the intergenerational inheritance of centromeres, telomeres and other regions of DNA that are accessible to us today because of technological advances, as well as advances in DNA processing algorithms. 

Thanks to your successful work abroad, you are the winner of this year's Czexpats in Science Award, which will be presented on 16 April 2025 at Masaryk University in Brno. What can we look forward to in your lecture on that occasion and how do you perceive this award? 

I'm thrilled about the award. The Czexpats community is really great, it brings together scientists with international experience. I look forward to their Christmas conference: Konerence pod stromeček every year - sometimes it's lonely overseas. Czexpats also helps with the integration of scientists after they return from abroad, which has its own pitfalls too, so sharing experiences is invaluable. But first and foremost, it is a community that provides a huge amount of enthusiasm, inspiration and drive to advance Czech science. 

In my talk I will discuss complete human genomes and the inheritance of repetitive DNA across generations. 

Are you going to invite any interesting guests from the field to the informatics colloquia that FI regularly organizes? Possibly who?

I would love to invite my mentors from UCSC: Karen Mig and Benedict Paten. Benedict develops algorithms and tools for bioinformatics. He is a big fan of Adam Ondra, so a visit to Brno is not unrealistic. 

That's good to know, we will be happy to help you organize such a meeting. Is there anything left that you would like to share?  

I would like to assure FI students that there is no need to be afraid of the prefix bio. If someone is intrigued by bioinformatics, they can enroll in one of the intro courses, no matter what field they are studying. It is also possible to do a bioinformatics undergraduate thesis or dissertation and join the Systems Biology Lab (Sybila), which also studies bioinformatics. For example, you can create a software tool that solves a specific problem in modern biology through DNA analysis. 

Ultimately, DNA is a text file like any other - specifically about 6 GB of data with the ability to affect our lives.  

Thank you for the interview and I wish you success in your future work.

Author: Marta Vrlová, Office for External Relations and Partnerships at FI MU