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Retreat Nov 2013

JOINT Retreat Dobzhansky Center and Algorhythmic Biology Laboratory

was held in Pushkin 21-23 November 2013

Agenda

Thursday November 21st
3-5PM Senior staff Workshop
Friday, November 22nd
9:15 AM Drs. OBrien and Pevzner Welcome and Introduction
CHAIR Alla Lapidus
09:30-09:50 Klaus 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)
09:50-10:10 Alexey 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
05:10-05:30 End of the retreat