Publications

1. Bzikadze A. , Shlemov A., Bankevich S. , Safonova Y., Pevzner P. A. AntEvolo: a novel approach for clonal analysis of antibody repertoires (poster), 2017
2. Shlemov A., Bankevich S. , Safonova Y., Bzikadze A. , Pevzner P. A. Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017
3. Bankevich S. , Shlemov A., Safonova Y., Bzikadze A. , Pevzner P. A. Reconstructing antibody repertoires from error-prone immunosequencing datasets (talk), 2017
4. Alexander Shlemov , Sergey Bankevich , Andrey Bzikadze , Maria A. Turchaninova, Yana Safonova , and Pavel A. Pevzner Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. The Journal of Immunology, 2017
5. 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
6. Shlemov A., Bzikadze A., Bankevich S., Safonova Y. IgReC 2.0: New algorithmic challenges of adaptive immune repertoire construction. Proceedings of RECOMB­Seq, 2016
7. Safonova Y., Bonissone S., Kurpilyansky E., Starostina E., Lapidus A., Stinson J., DePalatis L., Sandoval W., Lill J., Pevzner P. A. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics, 2015
8. Safonova Y., Shlemov A., Starostina E., Bzikadze A., Lapidus A., Pevzner P. A. IgTools: a toolkit for analysis of antibody repertoire from immunosequencing and mass spectra data. Poster on Immunogenomics 2015. Huntsville, USA, 2015
9. Safonova Y. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Talk on ISMB/ECCB 2015. Dublin, Ireland., 2015
10. Safonova Y., Starostina E., Shlemov A. IgTools: a toolkit for construction of antibody repertoire using immunosequencing data. Poster on ISMB/ECCB 2015. Dublin, Ireland, 2015
11. Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. Journal of Computational Biology, 2015
12. Baranova M., Logacheva M., Penin A., Seplyarskiy V., Safonova Y., Naumenko S., Klepikova A., Gerasimov E., Bazykin G., James T. Y., Kondrashov A. Extraordinary Genetic Diversity in a Wood Decay Mushroom. Mol Biol Evol., 2015
13. Safonova Y., Lapidus A., Lill J. IgSimulator: a versatile immunosequencing simulator. Bioinformatics, 2015
14. 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
15. Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. Talk., 2014
16. 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
17. Safonova Y., Kondrashov A., Logacheva M., Penin A., Bankevich A. NGS assembly of highly polymorphic diploid genomes. , 2013