Research Project Portals

I welcome you to the Site of the brand new Center of Genome Informatics at St Petersburg State University. The Center is named to honor the seminal research and mentorring contributions of Professor Theodosius Dobzhansky who is considered the father of empirical populations genetics.

Dobzhansky began his studies of genetics as a young faculty member at St Petersburg State University in the 1920s before immigrating to Columbia University in New York to study with Thomas Hunt Morgan and the amazing “Drosophila fly “ group. His voluminous and insightful work has been an inspiration to a generation of gene and genome scientists who have embraced his appreciation for the value natural population assessment. His legacy includes a plethora of productive students (notably Richard Lewontin, Bruce Wallace, Francisco Ayala, Wyatt Anderson, Jeff Powell and many more innovators of population genetic theory and practice). In step with (actually at times in conflict with) the giants of theoretical population genetics of his day (Sewell Wright, Jim Crow, Motoo Kimura), Dobzhansky’s team set the stage for applications in today’s genome wide association studies (GWAS) in human and model species, forensic identifications in capitol crime scenes, and conservation genetics, three fields to which I have been honored to have contributed.

The Dobzhansky Center is dedicated to building a strong forward-thinking group of genome and computer scientists to generate and interpret the massive datasets of our genomic era. At first, we will act as a training center dedicated to producing capable and innovation junior investigators in genome informatics. Their applications shall complement and perhaps invigorate research discoveries in human and comparative medicine as well as in evolutionary and conservation genomics. I had the privilege to have learned in my youth so much from Professor Dobzhansky and his students, that I am hoping that the faculty and fellows that make us the Dobzhansky Center would give back to the Russian students of genetics a taste of the honey that Dobzhansky and his contemporaries have seeded.

Stephen J O'Brien
April 2, 2012

RESEARCH PROJECTS OF THE CENTER

Genome Russia Project

Genes are the basic “instruction book” for the cells that make up our bodies, and are made out of DNA. The DNA of a person is more than 99% the same as the DNA of any other unrelated person. But no two people have exactly the same DNA except identical twins. Differences in DNA are called genetic variations. They explain some of the physical differences among people, and partly explain why some people get diseases like cancer, diabetes, asthma, and depression, while others do not. Such diseases may also be affected by factors like diet, exercise, smoking, and pollution in the environment, which makes it hard to figure out which genes affect the diseases.

GWATCH - web-based genome browser for genome-wide association studies

GWATCH is a web-based genome browser designed to automate analysis, visualization and release of data from genome-wide association studies (GWAS) and whole genome sequence association studies of genetic epidemiological cohorts. For any association study, GWATCH allows cataloging and viewing of significant statistical results of association tests (p-values, odds ratios, hazard ratios and others) for single or multiple variants (SNP, indels, CNV), for single or multiple tests.

Genome-based Mycobacterium Tuberculosis Variation Database

Comparative genomics of Mycobacterium tuberculosis clinical strains spread in Russia – is one of the research projects conducted at Theodosius Dobzhansky Center for Genome Bioinformatics. We are studying genomic signatures associated with M. tuberculosis clinical and microbiological features. A Database of M. tuberculosis Genome Variations (GMTV) developed by our team, integrates clinical, epidemiological and microbiological information with genome variations based on whole genome sequencing data. This research is conducted in collaboration with St. Petersburg Research institute of Phthisiopulmonology and St. Petersburg Pasteur Institute, and supported by St. Petersburg State University and Russian Foundation for Basic Research (RFBR) grants.

Single-cell analysis of tumor-microenvironment interactions in follicular lymphoma

Follicular lymphoma

Follicular Lymphoma (FL) is a slow-growing cancer of the lymphatic system, which affects one in every three thousand individuals. While existing frontline therapies are effective at suppressing FL, it remains an incurable disease with a median survival of 8-10 years. A fifth of the patients develop resistance to the standard treatment within the first two years. Understanding the mechanisms facilitating resistance and identifying early molecular prognostic indicators remains a high priority.

Assembly, Annotation, and Comparative Analysis of Apomictic Boechera Species Genome

Principal investigator of the project Vladimir Brukhin

Apomixis is asexual way of plant reproduction through seeds, which could be found in more than 400 plant species representing almost 40 families. It is believed that apomixis evolved independently in several taxa from sexual ancestors. Apomixis could be considered as a developmental variation of sexual reproduction in which some steps are lost, reduced, deregulated or desynchronized (Fig.1). The main features of gametophytic apomixis are:

  • Avoidance of meiosis (apomeiosis);
  • Embryo formation via parthenogenesis;
  • Functional endosperm develops either autonomously or pseudogamously (central cell fertilized by sperm cell).

Theodosius Dobzhansky

Geneticist & Evolutionary Biologist
 
Theodosius Dobzhansky American geneticist and evolutionary biologist and a central figure in the field of evolutionary biology is recognized for...

Stephen J O'Brien

Chief Scientific Officer
 
I welcome you to the Site of the brand new Center of Genome Informatics at St Petersburg State University. The...

Vladimir Brukhin

Leading researcher, Deputy Director 
 
Vladimir Brukhin    Leading researcher, Deputy Director  Joined the Theodosius Dobzhansky Center for Genome Bioinformatics in February 2013 right after returning...

Lab's news

SPBU on web site published an article about achievement of the Center and published article.

September, 27 2019 ( Friday at 2pm: Dr. Kirill Vinnikov from Hawaii University (USA) and head of the lab at the Far Eastern Federal University (Vladivostok) "Exome sequencing of non-model species"