Yana Safonova

Junior Research Fellow

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.

Immunoinformatics:

  • 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

Scientific interests:

Bioinformatics, Immunoinformatics, Computational Genomics, Graph Theory, Software Engineering

Detailed CV is available here.

Books:

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

Software

Publications

  1. Shlemov A., Bzikadze A., Bankevich S., Safonova Y. IgReC 2.0: New algorithmic challenges of adaptive immune repertoire construction. Proceedings of RECOMB­Seq, 2016
  2. Safonova Y., Shlemov A., Bzikadze A., Bankevich S., Pevzner P. A. A novel toolkit for analysis of adaptive immune repertoires using immunosequencing and mass spectra data. Poster., 2016
  3. Safonova Y. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Talk on ISMB/ECCB 2015. Dublin, Ireland., 2015
  4. Lapidus A., Antipov D., Bankevich A., Gurevich A., Korobeynikov A., Nurk S., Prjibelski A., Safonova Y., Vasilinetc I., Pevzner P. A. New Frontiers of Genome Assembly with SPAdes 3.0. (poster), 2014
  5. Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. In Sharan, Roded (eds.) RECOMB 2014, LNCS (8394). pp. 265-279. Springer, Heidelberg, 2014
  6. Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. Talk., 2014
  7. Safonova Y., Kondrashov A., Logacheva M., Penin A., Bankevich A. NGS assembly of highly polymorphic diploid genomes. , 2013