Yana Safonova

• 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

• 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

• 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.