The goals of our group are to uncover the mechanisms underlying epigenetic regulation in humans and other animals and to identify the role of these mechanisms in cell differentiation and aging. The projects topics cover effective Next Generation Sequencing data processing tools, scalable computational pipelines, visualization approaches and meta analysis of existing epigenomic databases.
The group is based at JetBrains. The group is actively collaborating with Maxim Artyomov’s laboratory at Washington University in St. Louis.
Main research project — Aging project in collaboration with Artyomov's Lab.
Aging is an inevitable biological process, consisting of a variety of physiological and molecular changes which occur at different rate across organism cells. It was shown that aging is associated with changes on both cell and the whole organism levels, including changes in DNA methylation (biomarkers known as “epigenetic clock”), histone post-translational modifications, expression profile changes, etc. It is known that aging is linked with low-grade inflammation, autophagy and metabolic changes on organism level. These are designated as a “hallmarks of aging”.
The goal of this project is to examine and describe system level changes between two groups of people: young and old in different tissues and cell lines.
The group provides bioinformatics analysis and develops computational pipelines for epigenetic analysis, novel methods and tools for NGS data processing, and analysis of public databases.
See projects page.
Possible students topics
- NEW What’s the buzz about / trends analysis in publications of Aging
- NEW Deep learning approaches for changes detection
If you are interested in working on these topics with us, please contact Oleg Shpynov.
- Eugene Bakin, “ChipQuery - Chipseq data comparison”
- Sergey Chernov, "A comprehensive comparison of tools for differential ChIP-seq analysis"
- Dmitriy Groshev, “Comparing the bisulphite sequencing data”
- Anna Atamanova, “Generalizing data on bins for randomly sized genomic loci"
- Alexey Dievsky, Master Thesis “Modeling difference in ChIP-seq data”
- Sergei Lebedev, Master Thesis “Bisulphite sequencing data modeling”