International Laboratory of Bioinformatics

The laboratory was established in 2018 to develop the field of bioinformatics at the faculty of computer science. The international laboratory of bioinformatics is actively engaged in the development and application of the most advanced methods of machine learning and artificial intelligence for the analysis of omics data in molecular biology.

Main directions of the laboratory's scientific activity

1. Fundamental research into the role of secondary DNA structures and their interrelationship with the epigenetic code. Practical application of the research is directed towards the development of drugs that regulate the function of flipons - secondary DNA structures that control the operation of the genome. In particular, a potential cancer drug has been proposed that regulates the function of the genome through the activation of one of the flipons - Z-DNA.

2. Development of a pipeline for analyzing genomic data from sequencing, genetic panels. Comprehensive analysis from variant to phenotype. Since 2019, the laboratory has been collaborating with medical institutions and pharmaceutical companies in this area of activity.

3. Machine learning in bioinformatics. Work in this area has been underway since 2018. The International Laboratory of Bioinformatics collaborates with major industrial partners.

4. Genetic research in the field of cardiogenetics, focused on creating a catalog of mutations in patients with cardiovascular diseases. In 2020, the "Cardiovascular Disease Genetics" Consortium was established.

5. Creation of AI systems in bioinformatics. Development of AI systems for predicting diagnosis and disease progression based on patients' clinical data. Since 2020, as part of this line of activity, the laboratory has developed the first systems for predicting side effects of anticoagulants, antidepressants, and antipsychotics. This direction is finding application in pharmaceutical companies.

The results of the laboratory's research work are published in Russian and international journals. Various scientific and educational events on the subject of research are regularly held, such as scientific seminars on machine learning methods in bioinformatics, summer and winter schools on bioinformatics, round tables, conferences, and the annual interdisciplinary forum of the "Cardiovascular Disease Genetics" Consortium. The International Laboratory of Bioinformatics actively collaborates with leading laboratories worldwide.

Analysis of genetic information can help prevent complications after a heart attack

Two HSE University projects received financial support for commercialization development

The interdisciplinary forum "Cardiogenetics and Bioinformatics: The Realities of 2024" took place

Latest Publications

Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping

Alternative DNA conformation formed by sequences called flipons potentially alter the readout of genetic information by directing the shape-specific assembly of complexes on DNA The biological roles of G-quadruplexes formed by motifs rich in guanosine repeats have been investigated experimentally using many different methodologies including G4-seq, G4 ChIP-seq, permanganate nuclease footprinting (KEx), KAS-seq, CUT&Tag with varying degrees of overlap between the results. Here we trained large language model DNABERT on existing data generated by KEx, a rapid chemical footprinting technique performed on live, intact cells using potassium permanganate. The snapshot of flipon state when combined with results from other in vitro methods that are performed on permeabilized cells, allows a high confidence mapping of G-flipons to proximal enhancer and promoter sequences. Using G4-DNABERT predictions,with data from ENdb, Zoonomia cCREs and single сell G4 CUT&Tag experiments, we found support for a model where G4-quadruplexes regulate gene expression through chromatin loop formation.

Authors: Maria Poptsova, Alan Herbert, Dmitry Konovalov, Dmitry Umerenkov