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 has announced the winners of the Project Competition in Basic Science Research for Intercampus Departments. The competition, which the university is organising for the first time, will provide funding to 10 research teams working on five topics. Four of the winning projects will be implemented by new research departments formed as a result of the competition.
An international group of scientists and medical specialists, including HSE researchers, examined the role played by microRNA (miRNA) and long non-coding RNAs on the progression of ovarian cancer. Having analysed more than a hundred tumour samples, they found that miRNA can prevent cell mutation while long non-coding RNAs have the opposite effect of enabling such mutations. These findings can help design new drugs which act by regulating miRNA concentrations. The study was published in the International Journal of Molecular Sciences.
In early September, the HSE University Faculty of Computer Science hosted the international conference Computer Methods of Cognitome Analysis. The event was organised by the International Laboratory of Algebraic Topology and Its Applications at the faculty.
Researchers of the HSE University and the Southern Federal University (SFedU) have tested a new method for studying the perception of facial emotional expressions. They suggest that asking subjects to recognise emotional expressions from dynamic video clips rather than static photographs can improve the accuracy of findings, eg in psychiatric and neurological studies. The paper is published in Applied Sciences.
Academics’ work week became even longer during the pandemic. This is true of researchers from different countries, independently of their gender and specialisation, an international research team with HSE University participation found. Their working time during the pandemic was 51 hours compared to the usual 40. The increased number of working hours per week seems to have become part of the new academic norm. The results of the study were published in the Plos One journal.
Researchers of the HSE International Laboratory of Statistical and Computational Genomics together with their international colleagues have proposed a new statistical method for analysing population admixture that makes it possible to determine the time and number of migration waves more accurately. The history of Colombians and Mexicans (descendants of Native Americans, Spaniards and Africans) features two episodes of admixture that occurred about 350 and 200 years ago for Mexicans and 400 and 100 years ago for Colombians. The results were published in the Plos Genetics journal.
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.
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.
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.
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.