International Laboratory of Bioinformatics Opens at the Faculty of Computer Science
On January 25, 2021, an International Laboratory of Bioinformatics opened at the Faculty of Computer Science. The main goal of the laboratory is to determine the role of alternative DNA structures in the genome.
Maria Poptsova, Associate Professor at the Big Data and Information Retrieval School will head the laboratory. Prof. Alan Herbert (USA), president and founder of InsideOutBio company, will be the lab’s academic supervisor. Prof. Herbert earned his PhD from the University of Auckland and has worked at MIT in the laboratory of Dr. Alexander Rich, who discovered Z-DNA, as well as at Boston University. Prof. Herbert is credited with discovering a protein that bonds with Z-DNA.
Maria Poptsova describes what the new laboratory will do.
At our Research and Study Laboratory of Bioinformatics, we were building neural network models of deep learning that detect Z-DNA on the basis of omics data. As a result of our research, we published a paper in Scientific Reports. The principal author of the paper was Nazar Beknazarov, an intern at the laboratory and second-year Master’s student at HSE University. It turned out that Alan Herbert was one of the reviewers of our paper, and he liked what we had done, so we started up a correspondence. I read his papers on flipons – secondary DNA structures, which rapidly appear, do their work, and disappear. Alan invented the term ‘flipon’ (from ‘flip on’). This concept was very close to mine: the regulatory role of secondary DNA structures is turning on and off different genomic processes: our lab was doing research specifically on the role of secondary DNA structures. I invited Alan to become an academic consultant for our laboratory, and he agreed. Our online summer school on machine learning in bioinformatics played a major role in his positive decision. Alan joined us from Boston and was impressed both by the speakers and the students.
We have already started our joint work: Alan got our laboratory involved in a research project with Fox Chase Cancer Center in Philadelphia. They had experimental data on protein bonding regions with Z-DNA in mouse genomes after the impact of certain agents, and the laboratory students are already actively working on analysing this data. They found that Z-DNA plays a huge role in regulating the internal cell immunity — a kind of immunity that works inside the cell, by detecting an alien virus DNA or RNA. This is a new and thrilling area of work for the Laboratory of Bioinformatics.
We received a grant for opening an international laboratory, which allowed us to invite international experts. Alexey Shaitan, head of the Integrative Biology Group at the MSU Faculty of Biology Bioengineering Department has joined us. Alexey used to work in the USA at the renowned National Center for Biotechnology Information NIH. Today, his group is studying nucleosomes, and particularly, performs molecular modelling of nucleosome dynamics. We are planning a joint project on the role of secondary DNA structures as nucleosome barriers. Ivan Antonov, a graduate of the Faculty of Bioengineering and Bioinformatics, who earned his PhD at Georgia Institute of Technology under the supervision of Mark Borodovsky, has also joined us. Dr. Antonov works as the director of the Centre for Bioinformatics at Georgia Tech and currently heads the Department of Bioinformatics at MIPT.
The laboratory is going to continue studying the role of secondary DNA structures. We are going to test the newest deep learning algorithms in their application to problems in genomics. Thanks to Alan, we hope to get an opportunity to analyze the latest experimental data generated at laboratories across the globe.
In addition, our laboratory participates in projects by the Consortium for Genetics of Cardiovascular Diseases. At our Research and Study Laboratory of Bioinformatics, we have begun work on projects in personalized medicine. As part of our cooperation with the RMAPO Institute of Personalized Medicine (of which the area supervisor is Rector Dmitry Sychev), we are building machine learning models to predict individual intolerance to drugs. We are also planning a project on genotyping patients with cardiovascular diseases as part of our cooperation with the Central State Medical Academy of the Department of Presidential Affairs (area supervisor Dmitry Zateishikov). The goal of all projects is to create a database of national mutations. A model for us in this endeavour is the Cardiovascular Disease Knowledge Portal created by Harvard and MIT.
HSE University researchers have identified the genes that play a crucial role in breast cancer metastasis. The results of the study were published in the journal PLOS ONE.
In celebration of Russia’s Year of Science and Technology, we continue our series about HSE University’s international laboratories, which are headed by world-class scientists and scholars. The first of these, the Laboratory of Algebraic Geometry and Its Applications, was established in October 2010. Below, Laboratory Head Dmitry Kaledin discusses the Lab’s history, research, achievements, and current activities.
In Russia, 2021 was declared the Year of Science and Technology. HSE has always paid special attention to the development of science, and more than 40 international laboratories have played an important role in the development of the university as a world research centre. One of the University’s first such laboratories was theRonald F. Inglehart Laboratory for Comparative Social Research (LCSR), named after its academic supervisor at the time, American sociologist and political scientist Ronald Inglehart. HSE News Service spoke with LCSR Laboratory Head and professor of sociology Eduard Ponarin (HSE – St. Petersburg) about the Laboratory’s work over the past decade.
During the pandemic, countries have endeavoured to protect their citizens without hurting their economies with excessive restrictions. At the seminar ‘Living with Covid-19: Optimal Lockdown Policies’, Hubert Kempf, academic supervisor of HSE University’s International Laboratory for Macroeconomic Analysis, presented a mathematical model that can be used to calculate the optimal level of restrictions.
On February 9, the HSE International Laboratory 'Russia’s Regions in Historical Perspective' hosted Janet Hartley (London School of Economics), who presented her recent monograph The Volga: A History of Russia’s Greatest River. The presentation was part of a joint lecture series between the Laboratory and The Mikhail Prokhorov Foundation. HSE news service spoke with Janet Hartley about her interest in Russia, her experience travelling and doing research in Russia, and the books she has written on Russia.
Mapping Empire and Environment in Siberia: International Laboratory ‘Russia’s Regions in Historical Perspective’ Hosts Erika Monahan
How does an American researcher become interested in the history of enterprise in Siberia? Does knowing Alaska give one a good understanding of the Siberian temperament? If there is one book that provides a good history of Russia, what is it? HSE News Service asked these and other questions to Erika Monahan, Associate Professor of History at the University of New Mexico, who recently gave a talk at the seminar of the HSE International Laboratory ‘Russia’s Regions in Historical Perspective’
This year’s HSE competition for the creation of international laboratories which considered proposals for the period of January 1, 2021 – December 21, 2023, was conducted from June 15 to December 15, 2020.
In October, Professor Holger Kusse, Leading Research Fellow of the International Laboratory for the Study of Russian and European Intellectual Dialogue lectured at the seminar ‘West and East: The Universalism of Culture’. We spoke with Holger Kusse about his work in Germany and Europe, his research, and his plans for the 2020-2021 academic year.
The number of international laboratories run in cooperation with leading international scholars is set to expand at HSE University. The competition aims to support the existing and create new research teams. Applications will be accepted from July 10 to August 31, 2020.
The first research seminar of the International Laboratory of Statistical and Computational Genomics had been postponed almost a month due to COVID-19. In April, however, the event finally took place. Laboratory Head Vladimir Shchur discusses what life is like for scientists in self-isolation during the pandemic, what genomics is, and why gesturing is important when teaching online.