Tuesday, May 8th at 2pm. Alex Zelikovsky (Atlanta) : “Scalable Reconstruction of Intra-Host Viral Population from NGS Reads”

Highly mutable RNA viruses such as influenza A virus, human immunodeficiency virus and hepatitis C virus exist in infected hosts as highly heterogeneous populations of closely related genomic variants. The presence of low-frequency variants with few mutations with respect to major strains may result in an immune escape, emergence of drug resistance, and an increase of virulence and infectivity. Next-generation sequencing technologies permit detection of sample intra-host viral population at extremely great depth, thus providing an opportunity to access low-frequency variants. Long read lengths offered by single-molecule sequencing technologies allow all viral variants to be sequenced in a single pass. However, high sequencing error rates limit the ability to study heterogeneous viral populations composed of rare, closely related variants. This talk present sCliqueSNV, a novel reference-based method for reconstruction of viral variants from NGS data. It efficiently constructs an allele graph based on linkage between single nucleotide variations and identifies true viral variants by merging cliques of that graph using combinatorial optimization techniques. The new method outperforms existing methods in both accuracy and running time on experimental and simulated NGS data for titrated levels of known viral variants. For PacBio and Illumina reads, it accurately reconstructs variants with frequency as low as 0.1\% even a couple of mutations away from each other.


Wednesday, August 23. at 2:00om. Anna Kukekova (University of Illinois) Genome analyses of tame and aggressive SILver Foxes; The Baleyev experiment revisited

Retreat 2017

Traditional Miniconference (retreat) for the lab’s staff and for guests on August 20-22 2017 in Druzhba hotel (Vyborg).

New Journal club meeting will be on Thursday, July 13 at 3:00pm. Anna Gorbunova will present the article “A global reference for human genetic variation” Nature 526, 68-74, 2015

Journal club will held on Thursday, June 22, at 3:00pm. Sergey Kliver talk about an article: “An integrated map of structural variation in 2,504 human genomes” Nature 526, 75-81 (2015).

Journal club will held on Friday, Jube 9-th at 2:00pm. Sergey Malov will present article A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe 2013

New Journal club meeting will on June 1 at 2:00pm. Igor Evsukov discuss an article Reconstructing genetic history of Siberian and Northeastern European populations. Genome Research CSHL 2016 http://www.genome.org/cgi/doi/10.1101/gr.202945.115

Thursday, May 25 at 3:00pm. Journal club: Anton Logachev: Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics. 2014. doi: 10.1038/ng.3021

Wednesday, April 19 at 2:00pm. Dasha Zherakova discuss the article Genomic analyses inform on migration events during the peopling of Eurasia. 238 NATURE VOL 538, 13 OcTObER 2016 doi:10.1038/nature19792

Thursday, April 6 at 2:00pm Lab’s journal club Gaik Tamazian Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. 2015, Nature Communications DOI: 10.1038/ncomms9018 www.nature.com/naturecommunications

Thursday, March 23 at 2:00pm Lab’s journal club, Vladimir Brukhin by article “Swedish Population Substructure Revealed by GenomeWide Single Nucleotide Polymorphism Data”, PLoS One, 2011, 6(2).

Wednesday Dec. 14 2016 at 2:00pm. Alexandros Triantafyllidis (Aristotle University of Thessaloniki, Macedonia, Greece) “Phylogenetic investigations of animals in Greece”.

Monday, October 31 at 1:00 Jose Horacio Grau Museum für Naturkunde Berlin Current genomic projects at the Museum für Naturkunde Berlin

Tuesrday, October 25 at 11:30AM at Dobzhansky Center

Denis Larkin.

New approaches to vertebrate genome assembly at the chromosome level

Lab’s retreat in October 2016

Traditional laboratory’s retreat held twice a year this year has a specific. The invited guests of the retreat this year were representatives of rectorate of the University, including Scientific rector-deputy S. Aplonov, the first rector-deputy I.Dementiev, and also director of the scienepark S.Mikushev and director of biobank A. Glotov.
So the retreat became extended presentation for rectorate the project, implementing by T. Dobzhansky Centre called Genome Russia.
With restriction of time of Rectorate members the presentation was short and the total duration of the retreat was less than 4 hours.


Theodosius Dobzhansky Center for Genome Bioinformatics
St. Petersburg State University

9:00AM-1:00PM October 6

  • I. Intro, Goals and collecting specimens
    • S.O’Brien Introduction Goals and datasets
    • V.Brukhin Genome Russia samples
  • II. Lab protocols+ tracking
    • Anna Gorbunova Lab protocols for specimen processing
    • A.Logachov/A.Shevchenko /I.Evsyukov
  • III. Data and IT organization
    • N.Cherkasov IT capacity and needs
    • S.Simonov Websites
    • V.Rotkevich Databases
  • IV. Sequencing production and Platform Bake Off
    • D.Polev Peterhof sequencing to date
    • A.Yurchenko Bake-off description , analysis, findings
  • V. Analysis for Gene mutation discovery -new and known
    • A.Komissarov Overview of analytical findings
    • S.Kliver QC of sequence and SNV calls
    • S.Sidorov Multi sample alignment and SNV calls
    • K.Krasheninnikova Copy number variation
    • G.Tamazian Known mutations
    • D.Zhernakova Novel mutations
  • VI. Natural History
    • P.Dobrynin Population and demographic analysis
  • VII. Phenotypes
    • A.Shevchenko GWATCH gene association Application
    • S.Malov Statistics & mutations
    • Katya Chernyaeva TB Russia
  • VII. Closing
    • S.OBrien Summation

Wednesday Sept 28 2016 at 2:00pm Chupov Vladimir (Komarov Botanical Institute RAS): New elements of macro evolutionary process in angiosperms


Wednesday Sept. 7 2016 at 2:00pm. Gaik Tamazian Benchmarking R implementations of multiple Pearson’s chi-square test


Monday, 29.08.2016 в 14-00. Prof. Baskar Rammamurthy (Indian Institute of Technology Madras (IITM)) “Hybridization and parental age affects somatic mutation rates in Arabidopsis”.


Wednesday 27.07.2016 в 3:00pm Irina Karpova (LLC Roche Diagnostics Rus). Expectation turned into Reality: single molecular sequencing from Roche


Friday, July 7 at 2:00pm Andrey Yurchenko The search for pathogenic mutations in the genomes of patients with autoimmune hepatitis).


Thursday, June 16 at 2pm we are having a guest seminar by Dr. Sasha Kagansky from the University of Edinburg.
Topic: “Metabolo-Epigenetics and Cancer”


26 of April 4:30pm Lev V. Utkin (Telematics Department, Peter the Great Saint-Petersburg Polytechnic University). A simple and fast GWAS algorithm by means of analysis of pairs of individuals


April 22 at 2:00pm Florence Haseltine (President of Haseltine Systems; Founder – Society for Women’s Health Research (SWHR); Emerita Scientist NIH) Global Virus Network – Planning for the Future


April 20 2016 at 2:00pm Oleg Glotov: Molecular-genetic analysis of mutations in children with rare endocrine diseases in North -West Russia by NGS technology

The Lab’s seminar will be on Wednesday, April 13

April 13 at 2:00pm Anton Logachev: Interconnection of cytoskeletal components and detergent-resistance membranes during hyphal growth in basidiomycete Schizophyllum commune


06.04.2016 at 2pm Alexey Meshkov (Head of the Laboratory of Molicular Genetics in Federal State Institution National Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation)
ATHEROGEN-IVANOVO study «The study of the development and progression ofATHEROsclerosis, including taking into account the GENetic and epigenetic factors of cardiovascular risk – a substudy of the ESSE-RF» – design, main results so far and plans.


March 30 2016 at 2pm Vladimir Brukhin: Sequencing, Assembly, and Annotation of the Highly Heterozygous Genome of the Apomictic Plant Boechera divaricarpa