Quick Q&A with NCBI’s Evolutionary Genomics Research Group

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Quick Q&A with Igor B. Rogozin and Sanjarbek Hudaiberdiev
Question Igor B. Rogozin, PhD Sanjarbek Hudaiberdiev, PhD
headshot of Igor Rogozin casual headshot of Sanjarbek Hudaiberdiev
In lay terms, what is the focus of your NLM research? My goal is to use pro- and eukaryotic genomes to track changes in genetic sequences in different species. This approach is called comparative genomics. I study comparative genomics at different timescales: from population genomics to comparison of different forms of life. In general, we study the evolutionary roots of microbial genetic selfish elements and defense systems. This allows us to understand the intricate relationships between the so-called “mobile genetic elements,” as well as the evolutionary arms race between the hosts and parasites (e.g., bacteria and viruses).

We are capable of extracting the biological rules behind the immense amount of data we are being poured, by combining the computational resources of NCBI and modern computational methods of data mining. As such, one of my projects involves analyzing the conserved neighborhoods in prokaryotic genomes. The idea behind this is that it can be observed that oftentimes the genes which encode functionally coupled units tend to be located close to each other on the genomes of their host organisms.

Why is your research significant, in your opinion? Located at the intersection of several sciences, comparative genomics provides an integrative, multidisciplinary shortcut to help us better understand the relationship between DNA structure, protein functions (including functional innovations), and phenotypes, including cases of complex human conditions. Analyzing the evolutionary roots and relationships between the microbial genomes and their parasites, together with defense systems, enables us to build comprehensive censuses.

These censuses help us better understand the biological processes, as well as generate ideas to be tested later in the wet labs. In addition, it allows us to ask if there are more systems like that out in the vast ocean of life, and if so, how can we search for them.

As an example, we recently made a study, where we analyzed a particular protein called Cas4, which is one of the building blocks of the CRISPR-Cas defense systems. The thing which makes this protein interesting is that it is present not in all of the hitherto discovered CRISPR-Cas system types and is observed in different genomic contexts with varying predicted functions. As a result of the study, we came to the conclusion that Cas4 proteins, in addition, take part in a wide range of systems, such as adaptive immunity, Restriction-Modification systems, and DNA damage-repair systems in microbes as well as in bacteriophages.

What or who inspired you to pursue your career? Mathematical sophistication was a family value. My father, the co-author of the Kolmogorov-Rogozin inequality, took my education seriously and had hopes (I guess) that I would follow his footsteps. However, I undertook the study of biology instead. Ultimately, my research rests on both disciplines equally. I’ve been keen on science since high school. Being on the school’s team for participating in a nationwide Olympics in physics allowed me to study physics and math more than the average student in my school. This granted me access to “specialized cabinets,” where we had primitive computers, through which I got to like programming. But the computers were always magic to me. I found it fascinating that, by using the electric circuits, you could build a machine to which you could give written instructions and make it do different tasks. So I decided to study computer engineering and was lucky to get a scholarship.

But throughout my undergraduate studies, I kept reading texts on general physics, and I would sneak into classes from the physics department.

So, there was not one single thing that inspired me to pursue my career, but rather a natural flow of my life—just the way I grew up.

How did you get started in your career? I studied bumblebee populations under the supervision of the zoologist Dr. Valentine Zaika during my first year at Novosibirsk University. I noticed a reduced variability of bumble bees. It was already known that in bumble bee species sex is determined by haplodiploidy (the vast majority of males are haploid). Together with my classmate, Andrey Karpenko, we designed simulation and analytical models that may explain the observed reduced variability by haplodiploidy. After graduating from the university, I took graduate classes at Istanbul Technical University to study machine learning, a field which was just gaining popularity. There I learned about bioinformatics as an application field of machine learning techniques.

But then I went back home to work as a software developer in Bishkek, Kyrgyzstan. During my four years or so of software developer experience, I concluded that I wanted to pursue a career in science and not in a “pure programming” environment. Around that time, I got an invitation to do a PhD in Italy, under the supervision of Prof. Sandor Pongor at ICGEB, Trieste. That’s how my scientific career started.

What really gets you jazzed about science and research? Obtained results frequently prove opposite to your expectations. At NLM/NCBI, I find it joyful to work among so many bright and talented people. I realized that it’s like a person trying to master chess. It helps if the majority of people in the room are much better than you in chess. It gives you the necessary stimulus and means to improve. So, my main focus here is to capitalize on that, and learn as much as possible.
If you weren’t doing what you’re doing now, what else might you be doing? Soccer is one of my favorite sports. An idea to play professionally and eventually coach sometimes crossed my mind when I was a child. I probably would go on being a software developer. Although I sometimes catch myself thinking that I could be a historian.
Tell us something surprising about yourself. I am Erdös2. Erdös numbers have been a part of the folklore of mathematicians throughout the world for a long time. I feel good about being Erdös2. (Although some mathematicians think that biologists should be excluded from the Erdös collaborative network, this reflects problems with network analyses.) I got this “rank” because of the following paper:

Rogozin I.B., Makarova K.S., Murvai J., Czabarka E., Wolf Y.I., Tatusov R.L., Szekely L.A., Koonin E.V. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res., 2002, V.30, N 10, 2212-2223

Dr. Laszlo Szekely is Erdös1.

I’m native to three cuisines and speak five languages.

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More Information About NCBI’s Evolutionary Genomics Research Group

Focus on NLM Scientists: Dr. Kira Makarova Makes Her Mark, NLM in Focus (Jan 8, 2018)
Lofty Goal, Amazing Discoveries: NCBI’s Work with CRISPR-Cas, NLM in Focus (Aug 7, 2017)
Adventures of a Computational Biologist in the Genome Space, NLM Musings from the Mezzanine (Jan 2, 2018)
Exploring the Brave New World of Metagenomics, NLM Musings from the Mezzanine (Jan 9, 2018)
Eugene Koonin’s Continued Role in CRISPR, by Way of Yogurt, The NIH Catalyst (Jan-Feb 2016)

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