RESEARCH

Our group's main research area is NGS bioinformatics and its application towards systems biology and medicine. We are always looking for motivated students interested in learning systems biology and bioinformatics applied to genomic data.

Ongoing projects at Bioinformatics Institute are mostly focusing on:

1) medical and population genetics and bioinformatic approaches to variant discovery from whole-exome and whole-genome sequencing data;

2) systems biology of genome regulation, analysis of RNA-Seq and other genomic methods (such as ChIP-Seq and DNase-Seq), and their integration (using probabilistic and network methods).

The final goal of our research always lies in applied biological or medical problems, and we adhere to this principle in each of our active projects.
Collaborations
  1. St. Petersburg State University, Biobank
  2. Federal Almazov North-West Medical Research Centre, Renata Dmitrieva
  3. Washington University in St Louis, Maxim Artyomov laboratory
  4. Yale University, Vishwa Deep Dixit laboratory
  5. IFMO, Genome Assembly Algorithms Laboratory
Publications
1. Catching hidden variation: systematic correction of reference minor allele annotation in clinical varian calling. Genet Med, 2017. doi: 10.1038/gim.2017.168
2. Effect of gene-lifestyle interaction on gestational diabetes risk. Oncotarget, 2017. doi: 10.18632/oncotarget.22999
3. Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PLOS One, 2016, doi:10.1371/journal.pone.0154722
4. Ragout — a reference-assisted assembly tool for bacterial genomes. Bioinformatics, 2014, doi:10.1093/bioinformatics/btu280
5. C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison. F1000Research, 2013, doi:10.12688/f1000research.2-258.v1
Software
All of the code pertinent to our active and past projects can be found on our GitHub page.

We develop and maintain several program products that address a variety of issues arising when working with genomic and transcriptomic data.

This is the list of software or databases which is being developed or maintained in our group:

GeneQuery - a webserver for transcriptome-based hypothesis generation. Developed by Alexander Predeus under supervision of Maxim Artyomov. During his M.S. thesis work was improved by Ivan Arbuzov under supervision of Alexander Predeus.

SICER 2.0 - re-implementation of SICER algorithm for broad peak calling in appropriate ChIP-Seq experiments which was at different times developed by Yegor Prikaziuk, Dmitrii Krasheninnikov, Igor Bezdvornykh, and Evgenii Bakin under supervision of Alexander Predeus.

RMAHunter - a web-based tool to systematically analyze and correct reference minor alleles in variant calling data. The tool was developed by Yury Barbitoff and Igor Bezdvornykh under supervision of Alexander Predeus.

We also develop several tools for automation of whole-exome sequencing data analysis and interpretation for SPBU Biobank.
    If you have any questions or for potential collaborations please contact us at info@bioinf.me.