Научно-исследовательское направление Института биоинформатики занимается решением прикладных биологических или медицинских проблем.
Our group's main research area is NGS bioinformatics and its application towards systems biology and medicine. Our research group is lead by Alexander Predeus. We are always looking for motivated students interested in learning systems biology and bioinformatics applied to genomic data.

Existing projects can be divided into two categories:

  1. projects related to transcriptomics, that rely on analysis of RNA-Seq, microarrays, and other methods of expression profiling;
  2. projects studying mechanisms of biological processes via genomic methods (such as ChIP-Seq and DNase-Seq), and their integration (using probabilistic and network methods) for genome annotation and better understanding of biological regulation.
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.

If you have any questions contact us at predeus@bioinf.me.
Group Meetings
Our group meetings are held biweekly at Bioinformatics Institute (Kantemirovskaya St. 2A, "Times" business center, 4th floor). Everybody is welcome. Preliminary schedule is available here. Information and group meeting discussions are available via our Google group.
  1. Washington University in St Louis, Maxim Artyomov laboratory
  2. Yale University, Vishwa Deep Dixit laboratory
  3. IFMO, Genome Assembly Algorithms Laboratory
  4. Federal Almazov North-West Medical Research Centre
  5. Institute of Cytology of RAS (SPb), Dmitry Tentler laboratory
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:

  1. GeneQuery - a webserver for transcriptome-based hypothesis generation. Developed by Alexander Predeus under supervision of Maxim Artyomov. Currently Ivan Arbuzov works under supervision of Alexander Predeus on making a more efficient web-server and better statistical algorithms for enrichment evaluation.
  2. ClusDec - an R package, developed by Konstantin Zaytsev, Pavel Fedotov and Alexander Predeus under supervision of Maxim Artyomov. Currently is an active project of Konstantin Zaytsev.
  3. BroadPeaks - re-implementation of SICER algorithm for broad peak calling in appropriate ChIP-Seq experiments.
If you have any questions contact predeus@bioinf.me.