• A
  • A
  • A
  • ABC
  • ABC
  • ABC
  • А
  • А
  • А
  • А
  • А
Regular version of the site

International Laboratory of Bioinformatics Opens at the Faculty of Computer Science

International Laboratory of Bioinformatics Opens at the Faculty of Computer Science

© iStock

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.

Maria Poptsova
© HSE University

International Collaboration

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.

Invited Researchers

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.

Future Plans

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.

 

See also:

Scholars from Moscow and Vladivostok Join Efforts to Study Institutes and Preferences in Economic Behaviour

Applications from HSE departments for the ‘Mirror Laboratories’ open project competition are open until May 20. One of the ‘mirror laboratories’ successfully operating today was created as a result of a similar competition in 2020 by economists from HSE University and Far Eastern Federal University (FEFU) to study institutes and preferences in economic behaviour. Alexis Belianin, Head of the HSE International Laboratory for Experimental and Behavioural Economics, talked about how peers from Moscow and Vladivostok collaborate.

Stress Disorders More Prevalent among Doctors due to the Pandemic

Psychologists from HSE University have joined their peers from Ekaterinburg to look into the impact of the pandemic on the mental health of Russian doctors. They found that medical staff are suffering from stress, anxiety, and depression more often than before. The results of the study were published in International Journal of Environmental Research and Public Health.

International Laboratory of Landscape Ecology Opens at HSE University

The laboratory will be led by Robert Sandlersky, a specialist in energy and mass transfer and the study of other properties of landscapes via satellite imagery and Senior Research Fellow at the Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences. The HSE News Service spoke to Robert about the laboratory’s future activities.

New International Laboratory to Study Lighting Flashes and Volcanic Lightning

HSE University has launched a new International Laboratory for the Study and Assessment of Dangerous Geophysical Phenomena. Alexander Kostinskiy, Head of the Laboratory and Deputy Director of HSE MIEM, explains the laboratory’s future work, its important research and practical applications, and the role of international cooperation in the new laboratory.

Alexei Vagov: ‘Metamaterials Should Serve People'

The Centre for Quantum Metamaterials is one of the new international laboratories that will be launched at MIEM, HSE University, in 2022.  Alexei Vagov, Head of the Centre, speaks about the main areas of the Centre’s research, its team, and future research cooperation.

HSE University in Nizhny Novgorod to Continue Its Research into Dynamical Systems

The mega-grant awarded by the Russian government to the International Laboratory of Dynamical Systems and Applications at HSE University’s Nizhny Novgorod campus has been extended to 2022–2023. The Academic Supervisor of the laboratory is Dmitry Turaev, a leading specialist in the field of dynamical systems and Professor at Imperial College London. Professor Turaev spoke to the HSE News Service about the results achieved by the laboratory so far and its plans for the next two years.

International Laboratory of Social Neurobiology to Look at How Fake News Affects Human Behaviour

The mega-grant allocated by the Russian government to the International Laboratory of Social Neurobiology, has been extended for 2022-23. The laboratory was founded two years ago and is headed by Iiro Jaaskelainen, a leading neurobiologist from Finland. Laboratory Head Vasily Klucharev spoke to the HSE News Service about the results the lab has already achieved and the prospects for the next two years.

HSE University to Establish Four New International Labs

Two international laboratories will be created at the HSE University Institute of Electronics and Mathematics, one at the Faculty of Geography and Geoinformation Technology, and one at the Faculty of Biology and Biotechnology. The four projects were selected from a total of 17 applications.

Scholars Look at Publication Activity in Post-Soviet Countries

75% of papers published in post-Soviet countries are by Russian researchers. In total, about 3% of all papers published globally are from post-Soviet countries. The role of universities has grown over the last 30 years, with over half of all recent academic papers being made with the participation of university researchers. These are the conclusions made in a study of publication activity by scholars in post-Soviet countries.

Researchers Propose Carbon Debt System to Combat Global Warming

An international team of researchers, including Artem Baklanov, Research Fellow of the International Laboratory of Game Theory and Decision Making, HSE University, has proposed treating greenhouse gas emissions as financial debt in a new research article published in Nature. This approach could provide immediate economic incentives for enterprises to begin mitigating the harmful effects of their business activities.