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 novel data analysis algorithms, effective Next Generation Sequencing data processing tools, scalable computational pipelines, visualization approaches, and meta-analysis of existing epigenomic databases.
- 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
All the source code is available on GitHub.
Various presentations including journal club and talks are here.
- 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”
- BioLabs summer student internships 2019
- Bioinformatics Institute Summer School 2019
- Epigenetics data analysis tutorial
Bioinformatics Institute 2018/19 project abstractsSaint-Petersburg, ISBN 978-5-6043094-2-1,