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Retreat July 2014

THEODOSIUS DOBRZHANSKY CENTER FOR GENOME BIOINFORMATICS,

ST. PETERSBURG STATE UNIVERSITY & ACADEMIC UNIVERSITY RETREAT

7-8 JULY 2014, PETROVSKY HALL THE TWELVE COLLEGIA BUILDING

ABSTRACTS

AGENDA

MONDAY 7 July
9:00-9:20 Stephen J. O’Brien, Welcome and introduction
9:20-9:40 Gaik Tamazian, DC Annotating Felidae genomes
9:40-10:00 Anton Bankevich, AU Assembling short Moleculo reads into long Moleculo reads with SPAdes
10:00-10:20 Serguei Simonov, DC Evolution of the Genome Browser in Dobzhansky Center
10:20-10:40 Aleksey
Komissarov, DC
Aurelia aurita: Steps to assembly highly heterozygosity genomes. Advantage of PacBio long reads for assembly comples genomes regions
10:40-11:00 Sergey Nurk, AU SPAdes vs. jellyfish. Uncertain steps towards assembly of complex genomes
11:00-11:20 Coffee break
11:20-11:40 Anton Korobeynikov, AU New frontiers of genome assembly with SPAdes 3.1
11:40-12:00 Alexei Makunin, DC Assessing cat genome assembly with high-density genetic linkage map
12:00-12:20 Anton Svitin, DC GWATCH: Human genetic epidemiology in the user-friendly mode
12:20-12:40 Sergey Malov, DC Signal localization: a new way in signal discovery
12:40-13:00 Andrey Shevchenko, DC GWAS on Botswana cohort
13:00-14:30 Lunch by your own
14:30-14:50 Svetlana Limborska, DC guest Genome diversity of ethnic groups from European Russia and Sub-Arctic Transuralic region
14:50-15:10 Vladimir Brukhin, DC Whole genome C-methylation profiling in Felis catus
15:10-15:30 Ksenia Krahseninnikova, DC Application of the comparative genomics pipeline to mammalian genomes analysis
15:30-15:50 Alla Lapidus, DC/AU Educational initiatives in Bioinformatics
15:50 -16:40 Coffee break
16:40-17:00 Nikolai Vyakhi, DC/AU Education
17:00-17:20 Ekaterina, Chernyaeva, DC Genetic Diversity of the Russian Mycobacterium tuberculosis strains. Genome variation Database GMTV
17:20 -17:40 Mikhail Rotkevich, DC Genome-based Mycobacterium Tuberculosis Variation Database
19:00-22:00 DINNER: RESTAURANT “KARL & FRIEDRICH”
TUESDAY 8 July
9:40-10:00 Klaus Koepfli, DC The Genome 10K Project: An Update
10:00-10:20 Nikolay Cherkasov, DC Overview of Dobzhansky Center IT infrastructure and data
10:20-10:40 Yana Safonova, AU IgTools: toolkit analysis of antibody repertoires from sequencing data
10:40-11:00 Kira Vyatkina, AU Assessing the purity of a protein sample by means of de novo sequencing
11:00-11:40 Coffee break
11:40-12:00 Aleksey Gurevich, AU Variants QC tool
12:00-12:20 Pavel Dobrynin, DC Cheetah genome
12:20-12:40 Alexey Antonic DC Signal localization: simulations and efficiency estimations
12:40-13:00 Taras Oleksyk, DC guest Parrots of the Caribbean: from the community sponsored genome to the model of island evolution
13:00-14:30 Lunch by your own
14:30-14:50 Alexei Ryskov, DC guest Genomics of unisexual (parthenogenetic) lizard species of the genus Darevskia
14:50-15:10 Mike Rayko, DC RNA-Seq analysis of marine sponge Cinachyrella — model organism for oil and dispersant ecotoxicology
15:10-15:30 Andrey Yurchenko, DC Analysis of selection and genetic load in the cat lineage
15:30-15:50 Nesli Avgan, DC Genetic Screening of Southern Africans for Known Diseases
15:50 -16:30 Coffee break
16:30-16:50 Anna Gorbunova, DC TCGA data analysis for cancer research
16:50-17:10 Anton Logachev, DC Repeats in genome sequences
17:10-17:30 Igor Evsyukov, DC Comparative transcriptome analysis of colon cancer metastatic cell lines using RNA-sequencing
17:30-17:50 Stephen J. O’Brien, DC Genes
17:50-18:00 Stephen J. O’Brien, DC Closing

 

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