Safonova YY - Search Results

1

Extraordinary Genetic Diversity in a Wood Decay Mushroom.

Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova YY, Naumenko SA, Klepikova AV, Gerasimov ES, Bazykin GA, James TY, Kondrashov AS. Baranova MA, et al. Among authors: safonova yy. Mol Biol Evol. 2015 Oct;32(10):2775-83. doi: 10.1093/molbev/msv153. Epub 2015 Jul 10. Mol Biol Evol. 2015. PMID: 26163667 Free PMC article.

2

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.

Safonova Y, Bankevich A, Pevzner PA. Safonova Y, et al. J Comput Biol. 2015 Jun;22(6):528-45. doi: 10.1089/cmb.2014.0153. Epub 2015 Mar 3. J Comput Biol. 2015. PMID: 25734602 Free PMC article.

3

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. Safonova Y, et al. Bioinformatics. 2015 Jun 15;31(12):i53-61. doi: 10.1093/bioinformatics/btv238. Bioinformatics. 2015. PMID: 26072509 Free PMC article.

4

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.

Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. Shlemov A, et al. J Immunol. 2017 Nov 1;199(9):3369-3380. doi: 10.4049/jimmunol.1700485. Epub 2017 Oct 4. J Immunol. 2017. PMID: 28978691 Free PMC article.

5

Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species.

Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. Bhardwaj V, et al. PLoS Comput Biol. 2020 Apr 27;16(4):e1007837. doi: 10.1371/journal.pcbi.1007837. eCollection 2020 Apr. PLoS Comput Biol. 2020. PMID: 32339161 Free PMC article.

6

V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s.

Safonova Y, Pevzner PA. Safonova Y, et al. Genome Res. 2020 Nov;30(11):1547-1558. doi: 10.1101/gr.259598.119. Epub 2020 Sep 18. Genome Res. 2020. PMID: 32948615 Free PMC article.

7

De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins.

Safonova Y, Pevzner PA. Safonova Y, et al. Front Immunol. 2019 May 3;10:987. doi: 10.3389/fimmu.2019.00987. eCollection 2019. Front Immunol. 2019. PMID: 31134072 Free PMC article.

8

Gene prediction in the immunoglobulin loci.

Sirupurapu V, Safonova Y, Pevzner PA. Sirupurapu V, et al. Genome Res. 2022 Jun;32(6):1152-1169. doi: 10.1101/gr.276676.122. Epub 2022 May 11. Genome Res. 2022. PMID: 35545447 Free PMC article.

9

Trace Reconstruction Problems in Computational Biology.

Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Bhardwaj V, et al. IEEE Trans Inf Theory. 2021 Jun;67(6):3295-3314. doi: 10.1109/tit.2020.3030569. Epub 2020 Oct 13. IEEE Trans Inf Theory. 2021. PMID: 34176957 Free PMC article.

10

Variations in antibody repertoires correlate with vaccine responses.

Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Safonova Y, et al. Genome Res. 2022 Apr;32(4):791-804. doi: 10.1101/gr.276027.121. Epub 2022 Mar 31. Genome Res. 2022. PMID: 35361626 Free PMC article.

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