Research Project Portals

JOINT Retreat Dobzhansky Center and Algorhythmic Biology Laboratory

was held in Pushkin 21-23 November 2013


Thursday November 21st
3-5PM Senior staff Workshop
Friday, November 22nd
9:15 AMDrs. OBrien and PevznerWelcome and Introduction
CHAIR Alla Lapidus
09:30-09:50Klaus P. Koepfli A tale of two canids: Uncovering the history of genomic divergence in populations of golden jackals (Canis aureus) and black-backed jackals (Canis mesomelas)
09:50-10:10Alexey Gurevich Evaluation of leading genome assemblers on modern Illumina data.
10:10-10:30 Aleksey Komissarov Troubleshooting poor Illumina data
10:30-10:50 Nikolay Cherkasov Dobzansky Center IT infrastructure
10:50-11:10 Pavel Pevzner Algorhytmic Biology A New Frontier
11:10-11:40 coffee-break
CHAIR Ekaterina Chernyaeva
11:40-12:00 Ekaterina Chernyaeva Whole genome sequencing of Mycobacterium tuberculosis isolates
12:00-12:20 Mikhail Rotkevich Genome-based Mycobacterium Tuberculosis Variation (GMTV) Database
12:20-12:40 Andrey Yurchenko Rhino forensic project and other directions
12:40-01:00 Pavel Dobrynin Cheetah whole genome sequence annotation
01:00-02:00 Lunch, check-in
CHAIR Alla Lapidus
02:00-02:20 Anton Svitin GWATCH: genome-wide associations in action
02:20-02:40 Sergey Malov Recent prospective in GWATCH-software development
02:40-03:00 Alexey Antonik Selection of the regions with small p-value
03:00-03:20 Stephen J. O'Brien GWATCH The future is Now!
03:20-03:40 Olga Bajenova Development of Molecular Diagnostics of Metastasis by Comparative Cancer Cell Gene Expression Profiling using RNA-Sequencing technology
03:40-04:10 coffee-break
CHAIR Kira Vyatkina
04:10-04:30 Irina Vasilinec Improved algorithm for repeat resolution using paired-end and mate-pair libraries
04:30-04:50 Andrey Prjibelski Scaffolding using mate-pairs and de Bruijng graph
04:50-05:10 Sergey Nurk Analysis of Mosaic Structures of Segmental Duplications
05:10-05:30 Anton Bankevich Using perfect hashing for de Bruijn graph construction
05:30-07:00 free time
7:00 PM Dinner celebration of our visions
Saturday, November 23rd
07:30-09:30 Breakfast, check out
CHAIR Anton Svitin
09:30-09:50 Sergey Simonov Garfield2-New JBrowser for cat genome: experiences, results, and lessons learned
09:50-10:10 Alexey Makunin Cat genome reference-assisted assembly and synteny analysis
10:10-10:30 Gaik Tamazyan Cat genome annotation: problems and solutions
10:30-10:50 Anton Logachev New advances in repeats annotation in Felis catus genome
10:50-11:10 Vladimir Brukhin Epigenetics-Second Genome Code: Whole Genome Cmethylation in Domestic Cat
11:10-11:40 coffee-break, check out
CHAIR Valdimir Brukhin
11:40-12:00 Andrey Shevchenko ERVs in cat's genome (6.2)
12:00-12:20 Stephen J. O'Brien New Horizons in Compartaive Genome Analyses
12:20-12:40 Dmitry Antipov PacBio reads in SPAdes 3.0.
12:40-01:00 Yana Safonova Improvement of S. commune assembly using assemblies of a number of individuals
01:00-02:00 Lunch
CHAIR Sergey Malov
02:00-02:20 Ricardo Godinez Comparative genomics and evolution of the Major Histocompatibility Complex in Birds, Mammals and Reptiles
02:20-02:40 Ksenia Krasheninnikova Educational Projects Perspective
02:40-03:00 Nikolay Vyahhi Bioinformatics Education in St. Petersburg and Worldwide
03:00-03:20 Alla Lapidus Coursera speaks Russian:Bioinformatics applications
03:20-03:40 Kira Vyatkina А top-down approach to de novo antibody sequencing
03:40-04:10 coffee-break
04:10-04:30 Anton Korobeynikov HammerIT: Error Correction for IonTorrent data
04:30-04:50 Aleskey Pyshkin Ion Torrent data research
04:50-05:10 Mikhail Rayko Gluconacetobacter genome assembly and annotation
05:10-05:30End of the retreat


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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"

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