The goals of our group are to uncover the mechanisms underlying epigenetic regulation in humans and animals and to identify the role of these mechanisms in cell differentiation and aging. The project topics cover effective Next Generation Sequencing data processing tools, scalable computational pipelines, visualization approaches, and meta-analysis of existing epigenomic databases.
Project topics cover:
- Effective Next Generation Sequencing data analysis tools
- Scalable and reproducible computational pipelines
- Visualization approaches
- Data mining algorithms
- Meta-analysis of existing epigenomic databases
The group is based at JetBrains.
Contact person: Oleg Shpynov.
- Multiomics dissection of healthy human aging - joint research project of Healthy Aging in collaboration with Maxim Artyomov’s laboratory at Washington University in St. Louis. The group provides bioinformatic analysis and develops novel algorithms and approaches for epigenetic data analysis.
- SPAN Peak Analyzer - semi-supervised peak analyzer
- JBR Genome Browser - fast and reliable genome browser with supervised peaks markup and analysis
Full projects list is available here.
Github page - all the source code is here.
Journal Club - here you can find different materials including internal presentations, journal club and talks.
- 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”