Public

Yana Safonova

Email: safonova (dot) yana@gmail.com

Education:

2012 - present. St. Petersburg University of the Russian Academy of Sciences, Department of Mathematics and Information Technology, PhD student
2010 - 2012. Lobachevsky State University of Nizhny Novgorod, Computational Mathematics and Cybernetics Faculty, Department of Computer Aided Research, MSc in Applied Informatics
2006 - 2010. Lobachevsky State University of Nizhny Novgorod, Computational Mathematics and Cybernetics Faculty, Department of Computer Aided Research, BSc in Applied Informatics

Teaching experience:

2014. Genome Assembly. Saint Petersburg Academic University, Department of Mathematics and Information Technology

2013. Algorithms in Bioinformatics. Lobachevsky State University of Nizhny Novgorod, Computational Mathematics and Cybernetics Faculty, Department of Bioinformatics.
Supervision of student projects in Bioinformatics Institute

Projects:

dipSPAdes: an assembler for highly polymorphic diploid genomes (including collaboration with Laboratory of Evolutionary Genomics in Moscow). dipSPAdes is available as a part of SPAdes genome assembler.
Immunoproteogenomics
- IgRepertoireConstructor, an algorithm for construction of antibody repertoire and immunoproteogenomics analysis
- IgSimulator, a versatile immunosequencing simulator
- IgQUAST, a quality assessment tool for of antibody repertoire(s)
- AntEvolo, an algorithm for evolutionary analysis of antibody repertoires

Publications & Talks:

Important papers:

Yana Safonova, Stefano Bonissone, Eugene Kurpilyansky, Ekaterina Starostina, Alla Lapidus, Jeremy Stinson, Laura DePalatis, Wendy Sandoval, Jennie Lill and Pavel A. Pevzner. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics, June 2015, 31(12), pp. i53-i61 [online]
M.A. Baranova, M.D. Logacheva, A.A. Penin, V.B. Seplyarskiy, Y.Y. Safonova, S.A. Naumenko, A.V. Klepikova, E.S. Gerasimov, G.A. Bazykin, T.Y. James, A.S. Kondrashov. Extraordinary genetic diversity in a wood decay mushroom. Mol Biol Evol. 2015 Jul 10. pii: msv153 [online]
Yana Safonova, Alla Lapidus, and Jennie Lill. IgSimulator: a versatile immunosequencing simulator. doi:10.1093/bioinformatics/btv326. Bioinformatics. 2015 [online]
Yana Safonova, Anton Bankevich, Pavel A. Pevzner. dipSPAdes: an assembler for highly polymorphic diploid genomes (extended version). Journal of Computational Biology, June 2015, 22(6). pp. 528-45 [online]
Yana Safonova, Anton Bankevich, Pavel A. Pevzner. dipSPAdes: an assembler for highly polymorphic diploid genomes. In Sharan, Roded (eds.) RECOMB 2014, LNCS (8394). pp. 265-279. Springer, Heidelberg (2014) [online]

Posters and talks:

Yana Safonova, Alexander Shlemov, Ekaterina Starostina, Andrey Bzikadze, Alla Lapidus, Pavel A. Pevzner. IgTools: a toolkit for analysis of antibody repertoire from immunosequencing and mass spectra data. Poster on Immunogenomics 2015. Huntsville, USA [pdf]
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Talk on ISMB/ECCB 2015. Dublin, Ireland.
Yana Safonova, Ekaterina Starostina, Alexander Shlemov. IgTools: a toolkit for construction of antibody repertoire using immunosequencing data. Poster on ISMB/ECCB 2015. Dublin, Ireland [pdf]
dipSPAdes: assembler for highly polymorphic diploid genomes. Talk on RECOMB 2014. Pittsburgh, USA.
Alla Lapidus, Dmitry Antipov, Anton Bankevich, Alexey Gurevich, Anton Korobeynikov, Sergey Nurk, Andrey D. Prjibelski, Yana Safonova, Irina Vasilinetc, and Pavel Pevzner. New Frontiers of Genome Assembly with SPAdes 3.0. Poster on JGI User Meeting 2014, Walnut Creek, USA [pdf]
Yana Safonova, Alexey Kondrashov, Maria Logacheva, Aleksey Penin and Anton Bankevich. NGS assembly of highly polymorphic diploid genomes. Poster on RECOMB 2013. Beijing, China [pdf]

Books:

Gergel V.P., Barkalov K.A., Meerov I.B., Sysoev A.V., Bastrakov S.I., Bogolepov D.K., Donchenko R.V., Kozinov E.A., Kustikova V.D., Malova A.Y., Safonova Y.Y., Sidnev A.A.. Parallel calculus. Technologies and numerical analysis. Tutorial. 2013. NNSU Publ.

Scientific interests:

bioinformatics, immunoinformatics, computational genomics, graph theory, software engineering

My detailed CV is available here.

Стажировки 2013

Прием заявок завершен, но он вновь откроется следующей весной!

Мы ищем талантливых и мотивированных кандидатов для прохождения летней стажировки.

В настоящее время биоинформатика является одним из наиболее интенсивно развивающихся научных направлений.

Эта тенденция в полной мере находит отражение и в Санкт-Петербурге: появляется все больше лабораторий, стартапов и филиалов международных компаний, деятельность которых неразрывно связана с биоинформатикой.

Если Вы:

Разбираетесь в алгоритмах.
Умеете и любите программировать.
Имеете хорошую математическую подготовку.
Хотите заниматься интересными прикладными задачами.

То мы готовы предложить:

Достойную стипендию.
Дружный молодой коллектив.
Общежитие для иногородних.

Занятость — полная, продолжительность — 2 месяца.

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Success Stories

Administrative support

The lab couldn't even exist without administrative and moral support of the university administration:

Member of the Academy

Zhores Alferov

president

Corresponding member of the Academy

Michail Dubina

vice-president

Doctor of science

Alexander Omelchenko

vice-president (education)

Русский

RECOMB 2013

RECOMB 2013 is an international conference on research in computational biology, that has been held in Beijing, China, April 7-19, 2013.

At the conference, we have presented

a talk on genome assembly from highly chimeric reads:

Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott Clingenpeel, Tanja Woyke, Glenn Tesler, Max Alekseyev, and Pavel Pevzner. Assembling Genomes and Multigenomes from Highly Chimeric Reads. Lecture Notes in Computer Science 7821, 2013.

posters on different topics: