Statistical and Computational Genomics Projects at HSE University

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Vladimir Shchur, Head and a Senior Research Fellow at the International Laboratory of Statistical and Computational Genomics, talks about the lab, its research projects and their practical applications.

Vladimir Shchur

Genomics is one of the most promising types of contemporary interdisciplinary science. We are interested in a variety  of problems related to the study of genomes, primarily the development of new mathematical models and methods for genomics data analysis (at present, we rely on probability theory, statistics, machine learning and numerical methods).

We are interested in the history of population development and interaction: traces of genetic bottleneck (events when there was a significant decrease in population size e.g., when a small group of our ancestors left Africa, and their descendants settled throughout the rest of the globe) and traces of ancient introgression (the mixing of populations e.g., inbreeding of Neanderthals and Denisovans).

For example, we started a joint project with our Chilean colleagues on traces of natural selection in their genes

A lot of research is being done on the coronavirus, and this concerns how virus populations develop within human populations. As we have a large array of data, we work on methods to predict potential variances of concern with respect to viral spread rates at the DNA level. We develop large genealogies of the virus and then look at its different evolutionary properties. Since this research involves working with data, certain projects deal with data processing. The sequencing technologies are imperfect. With this in mind, it is necessary to come up with preprocessing and analysis methods for data after it has been sequenced.

Practical Applications and Possible Future Projects

In the case of coronavirus, we are learning how to detect new variants as early as possible. For example, the earlier we can detect that a certain variant has an increased rate of infection, the earlier we can recommend paying special attention to it.

We also analyze the effectiveness of restrictive measures (e.g., the closing of borders), which, in turn, can be used to reduce negative economic effects. Such studies require new methods. We recently developed a viral genealogy simulator, which operates as a tool for method validation.

Our simulator is flexible enough to take into account many important complexities for modelling the spread of COVID-19: population structure, interacting genetic variants and cross-immunity

As for the study of human populations, we all wonder who our ancestors were. It is a basic human curiosity. We want to build the most complete and accurate picture of the world so that we can analyze the processes of adaptation and consider what mechanisms of natural selection were involved throughout history.

When there is an understanding of these mechanisms, we can better understand what is important in our genome and what is not. One gene can affect several traits—neutral or those under natural selection—and they can be complexly connected. If we figure out how to untangle this, our understanding of genetic disease and other phenotypes will largely improve.

I personally would like to work with oncology. Tumors are also a population (of cells) that develops, and the process of chemotherapy acts similar to a natural selection

I am also interested in how to personalize the use of drugs and treatment tactics based on evolutionary studies of genetic tumor genetic variation. Maybe someday we could get further engaged in such research with the Faculty of Biology and Biotechnology.

Achievements and Collaboration Plans

I am proud of our research team, which is currently being formed. If the first year of work was under a super manual mode, now I can say ‘guys, please calculate this’. We have around 20 students working with us who say they did not initially think that scientific work was so interesting but now want to continue to do science.

There is a stereotype that it is impossible to earn enough money in science, but when our students start creating something, they understand that everything is possible. Outstanding students get to work as research assistants—some get involved through project work, and others through thesis papers

For the upcoming year, we are planning several research projects (possible intersections of interests) with the Faculty of Biology and Biotechnology, but I am not ready to talk about the details yet. I hope that something will come about soon. My other personal goal is to educate specialists for the laboratory, since this field of science is quite new. Right now, we mainly work with mathematicians.