GroupThe goals of the BioLabs 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. We are developing novel algorithms and methods for experimental data analysis, building scalable computational pipelines and tools, and working in collaboration with biologists on various ageing studies.
- Epigenetic changes in aging human monocytes - 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.
- Full projects list is available here.
- SPAN Peak Analyzer - semi-supervised peak analyzer
- JBR Genome Browser - fast and reliable genome browser with supervised peaks markup and analysis
- SnakeCharm - snakemake plugin for IntelliJ platform IDEs
- Pubtrends - publications analysis service
All the source code is available on GitHub.
Various presentations including journal club and talks are here.
- 2020, Anna Nikiforovskay, Bachelor Thesis "Extractive summarization for biomedical papers"
- 2019, Anna Vlasova, "Review generation for publications analysis service"
- 2019, Daria Chaplygina, "Noisy peak calling 2"
- 2019, Daria Likholetova and Nina Lukashina, "ARM using Fishbone diagram"
- 2019, Anna Vlasova and Nikolai Kapralov, "Publications analysis"
- 2019, Daria Sharkova and Nikita Nazarov, "Snakecharm plugin"
- 2019, Elena Kartysheva, "SPAN model improvement"
- 2019, Vladislav Kalinin, Master Thesis "Web server for accessing to human Chip-Seq data hosted in GEO and Chip-Atlas"
- 2019, Darya Sharkova, "SnakeCharm plugin code insight improvement"
- 2019, Alexander Petrovsky, Dmitry Belikov, "Detection of unique shared genomic sequences for the given group of organisms"
- 2019, Elena Kartysheva, "Improving SPAN data model with generalised linear regression"
- 2019, Daria Likholetova, Nina Lukashina, "Association Rule Mining on genome regions using fishbone diagrams"
- 2019, Daria Chaplygina, "Noisy peak calling"
- 2019, Daria Balashova, "ChIPSeq Rescue failures with Neural Networks"
- 2018, Nikolai Kapralov, "Publications analysis service"
- 2017, Eugene Bakin, “ChipQuery - Chipseq data comparison”
- 2016, Sergey Chernov, "A comprehensive comparison of tools for differential ChIP-seq analysis"
- 2016, Dmitriy Groshev, “Comparing the bisulphite sequencing data”
- 2015, Anna Atamanova, “Generalising data on bins for randomly sized genomic loci"
- 2014, Sergei Lebedev, Master Thesis “Bisulphite sequencing data modeling”
- 2013, Alexey Dievsky, Master Thesis “Modeling difference in ChIP-seq data”
- Snakemake advanced tutorial
- SPAN 0.12.0 and JBR 1.0.beta released
- Epigenetics module for ITMO masters students