Seminars 2026
15.01.2026 [online] Distribution Analysis of microRNA Seed Binding Sites Across Functional Regions of the Human Genome
Zoom
Speaker: Artyom Bashkatov, Junior Research Fellow
This report presents a genome-wide analysis evaluating the localization of microRNA (miRNA) binding sites within various genomic functional and regulatory elements, with a specific focus on retrotransposons (LTR, SINE, LINE). The analysis reveals a non-uniform distribution of miRNA binding sites within retrotransposons, characterized by distinct density peaks.
21.01.2026 [online] Non-canonical DNA structures collaborate with canonical motifs for the function of HOT loci
Zoom
Speaker: Zenobio Antonio Viana de Barros, Research Fellow
We mapped and characterized non-B DNA structures (flipons)—including Z-DNA, G-quadruplexes, and triplexes—across high-occupancy target (HOT) loci, which are genomic regions bound by unusually high numbers of transcription factors. By integrating structural predictions with multi-omics data and applying rigorous statistical modeling, we found that different flipon types play distinct roles in transcriptional regulation and chromatin accessibility. Our results suggest that flipons are an integral component of the regulatory machinery within these active genomic regions, working alongside sequence motifs to influence transcription.
28.01.2026 [online] Characterization of LG4 regions
Zoom
Speaker: Dmitrii Konovalov, Junior Research Fellow
It is known that a large proportion of sequences in the human genome are represented by repeats. This report presents the results of characterization of long G-quadruplex-like regions (LG4)—regions with a high content of the GGG motif separated by long loops. Their potential role in the regulation of gene expression is investigated.
04.02.2026 [online] Colocalization Analysis of microRNA Binding Sites and G-quadruplexes in Human Gene Promoters
Zoom
Speaker: Artyom Bashkatov, Junior Research Fellow
This report investigates the colocalization patterns of conserved human microRNAs (miRNAs) and G-quadruplex structures within promoter regions. The analysis utilizes core and tissue-specific promoter tracks predicted via DeepGQ deep learning models. The results are visualized as a heatmap demonstrating the statistical significance of miRNA binding site enrichment or depletion relative to G-quadruplex motifs.
11.02.2026 [online] Flipons and the epigenetic landscape: a genome-wide analysis of DNA structure and chromatin context
Zoom
Speaker: Zenobio Antonio Viana de Barros, Research Fellow
We are applying a similar mapping framework to investigate how flipons relate to the broader epigenetic landscape. The goal is to systematically analyze the co-occurrence and potential interplay between flipons and epigenetic markers—such as histone modifications (e.g., H3K4me1, H3K27ac), chromatin accessibility states, and DNA methylation patterns. This will help clarify whether flipons act as structural scaffolds that recruit or stabilize epigenetic signals, and how these interactions might contribute to gene regulation across different genomic contexts.
25.02.2026 [online] The role of "kissing" loops of guanine quadruplexes in the regulation of gene expression
Zoom
Speaker: Dmitrii Konovalov, Junior Research Fellow
Quadruplex loop interactions can stabilize enhancer-promoter loops. In addition to stacking interactions between tetrads, quadruplex loops can interact via hybridization, similar to the interaction of "kissing" hairpin loops. This report presents the results of a study of such interactions and examines their potential role in the regulation of gene expression.
04.03.2026 [online] Microbiome combination with proteome
Zoom
Speaker: Alexandra Kozlova, Research Assistant
The presentation reviewed the combined use of metagenomic and proteomic studies. Metagenomics reveals which genes and microorganisms are present, while proteomics reveals which are truly active and functional. Together, they allow us to link community composition to its actual biological activity. This provides a more comprehensive understanding of processes in ecosystems, medicine, and biotechnology. The presentation described a workflow for primary data processing, metagenome analysis, and integrating the resulting data with proteomic sequencing. Available software for performing the corresponding analysis was also presented.
11.03.2026 [online] Role of cancer-associated fibroblasts (CAFs) in glioblastoma pathogenesis
Zoom
Speaker: Ismailov Aly Mehti Ogly, Research Assistant
CAFs play a central role in glioblastoma by shaping the tumor microenvironment via ECM remodeling, immune suppression (TAM recruitment, PD-L1, TIGIT, IL-6, TGF-β), and pro-angiogenic signaling (VEGF, CXCL12), thereby promoting hypoxia and invasiveness; priority is given to ligand–receptor interaction analysis (IGFBP6, IL-6) to identify therapeutic targets.
08.04.2026 [online] Methodological approaches of glioblastoma cells classification using chromosomal expression distribution
Zoom
Speaker: Ismailov Aly Mehti Ogly, Research Assistant
Glioblastoma cell classification is based on chromosomal expression profiles (CNVs, e.g., +7/−10) using ML; scRNA-seq is transformed into genomic signals via smoothing and HMM, with models including L1-logistic regression, ensembles (Random Forest, XGBoost), and 1D-CNN; results will be integrated with CAF spatial data to link tumor genetics with stromal context.
22.04.2026 [online] Analysis of the honeybee metagenome
Zoom
Speaker: Alexandra Kozlova, Research Assistant
The report included a presentation on the study of the bee microbiome. It examined the composition of microorganisms living in bees and their role in maintaining health. Particular attention was paid to the influence of environmental factors on the microbial community. Examples were given of how environmental conditions can alter the composition and activity of microorganisms. The significance of these changes for the resilience of bees and ecosystems as a whole was also discussed.
13.05.2026 [online] Prediction of miRNA expression in single cell data
Zoom
Speaker: Ismailov Aly Mehti Ogly, Research Assistant
miRNA levels in GBM single-cell data are predicted via ML-based imputation from mRNA profiles (target genes, TFs), using ensembles (Random Forest, Gradient Boosting) and GNNs; performance is evaluated by correlation and MSE, with links to EMT and invasiveness; cross-validation on TCGA/GTEx followed by transfer to scRNA-seq is planned.
27.05.2026 [online] Non-homological recombination in acrocentric short arms
Zoom
Speaker: Fedor Ryabov, Junior Research Fellow
The talk examined the phenomenon of non-homologous recombination, in which different acrocentric chromosomes exchange their short arms. Studying this phenomenon became possible after the emergence of technologies for assembling complete T2T genomes. The speaker showed that these recombination events can also involve centromeric regions, and discussed the evolutionary significance of such events.
10.06.2026 [online] ClusterSourMash — a tool for rapid clustering of DNA sequences
Zoom
Speaker: Fedor Ryabov, Junior Research Fellow
The talk presented a study of centromeric regions in complete T2T genomes of five individuals from the same family. This made it possible to compare the centromeres of parents and their child and determine whether any changes had occurred within a single generation. The inheritance analysis showed that in approximately half of the chromosomes, centromeres were transmitted without changes, while in the remaining cases specific events were described: rare single-nucleotide substitutions, as well as more frequent duplications and deletions of centromeric repeats.
24.06.2026 [online] Analysis of the microbiomes of highly divergent amphipods in Lake Baikal
Zoom
Speaker: Alexandra Kozlova, Research Assistant
The report included a presentation on the analysis of the microbiomes of highly divergent amphipods in Lake Baikal. Amphipods are an important part of the Baikal ecosystem and play a key role in nutrient cycling. The study examined the composition of their microbiomes and differences between species. Particular attention was paid to the coevolution of hosts and their microbial communities, as well as the relationships between them. It was shown that changes in the microbiome may reflect evolutionary processes and the adaptation of amphipods to different environmental conditions.
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