Published and accepted papers

1. Kalbfleisch T,  McKay S, Murdoch B, Adelson DL, Almansa D, Becker G, Beckett LM, Benítez-Galeano MJ, Biase F, Casey T, Chuong E, Clark E, Clarke S, Cockett N, Couldrey C, Davis BW, Elsik CG, Faraut T, Gao Y, Genet C, Grady P, Green J, Green R, Guan, D, Hagen D, Hartley GA, Heaton M, Hoyt SJ, Huang W, Jarvis E, Kalleberg J, Khatib H, Koepfi K, Koltes J, Koren S, Kuehn C, Leeb T, Leonard A, Liu GE, Low WY, McConnell H, McRae K, Miga K, Mousel M, Neibergs H, O'Neill R, Olagunju T, Pennell M, Petry B, Pewsner M, Phillippy AM, Pickett BD, Pineda P, Potapova T, Rachagani S, Rhie A, Rijnkels M, Robic A, Osorio NR, Safonova Y, Schettini G, Schnabel RD, Natesh NS, Stegemiller M, Storer J, Stothard P, Stull C, Tosser-Klopp G, Traglia GM, Tuggle C, Tassell CPV, Watson C, Weikard R, Wimmers K, Xie S, Yang L, Smith T, Rosen B. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics (AIP). 2024. [preprint]

2. Watson CT, Rodriguez OL, Engelbrecht E, Safonova Y, Marasco WA, Smith ML. Looking to the future of antibody genetics: resolving the roles of immunoglobulin diversity in gene regulation, function, and immunity. Genes & Immunity. 2023 Dec 14:1-3.

3. Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd S, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nature Communications. 2023. 14, 4419. [link]

4. Zhou P, Song G, He W, Beutler N, Tse LV, Martinez DR, Schäfer A, Anzanello F, Yong P , Peng L, Dueker K, Musharrafieh R, Callaghan S, Capozzola T, Yuan M, Liu H, Limbo O, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Jardine JG, Wilson IA, Safonova Y, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease. Immunity (in press). 2023. [link]

5. Zhang C, Bzikadze AV, Safonova Y, Mirarab S. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Frontiers in Immunology. 2022;13. [link]

6. Jenkins GW, Safonova Y, Smider VV. Germline-Encoded Positional Cysteine Polymorphisms Enhance Diversity in Antibody Ultralong CDR H3 Regions. Journal of Immunology. 2022 Oct 21. [link]

7. He W-T, Yuan M, Callaghan S, Musharrafieh R, Song G, Silva M, Beutler N, Lee W, Yong P, Torres J, Melo M, Zhou P, Zhao F, Zhu X, Peng L, Huang D, Anzanello F, Ricketts J, Parren M, Garcia E, Ferguson M, Rinaldi W, Rawlings SA, Nemazee D, Smith DM, Briney B, Safonova Y, Rogers TF, Crotty S, Darrell J, Irvine DJ, Ward AB, Wilson IA, Burton DR, Andrabi R. Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques. Science Translational Medicine. 2022. 14 (657): eabl9605. [link]

8. Sirupurapu V, Safonova Y, Pevzner PA. Gene prediction in immunoglobulin loci. Genome Research. 2022. 32:1152-1169. [link]

9. He WT, Musharrafieh R, Song G, Dueker K, Tse LV, Martinez DR, Schäfer A, Callaghan S, Yong P, Beutler N, Torres JL, Volk RM, Zhou P, Yuan M, Yuan M, Liu H, Anzanello F, Capozzola T, Parren M, Garcia E, Rawlings SA, Smith DM, Wilson IA, Safonova Y, Ward AB, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Targeted isolation of panels of diverse human broadly neutralizing antibodies against SARS-like viruses. Nature Immunology. 2022. 23:960–970. [link]

10. Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Research. 2022. 32:791-804. [link]

11. Lee JH, Toy L, Kos JT, Safonova Y, Schief WR, Havenar-Daughton C, Watson CT, Crotty S. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells. npj Vaccines. 2021. 6(1):1-12. [link]

12. Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Trace reconstruction problems in computational biology. IEEE Transactions on Information Theory (special issue). 2021. June 67(6):3295-314. [link]

13. Peng K, Safonova Y, Shugay M, Popejoy A, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau V-M, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, Jonsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT, Karlsson Hedestam GB, Mangul S. Diversity in immunogenomics: the value and the challenge. Nature Methods. 2021. 17:1-4. [link]

14. Akbar R, Jeliazkov JR, Robert PA, Snapkov I, Pavlović M, Slabodkin A, Weber CR, Safonova Y, Sandve GK, Greiff V. A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Cell Reports. 2021. 34(11): 108856. [link]

15. Safonova Y and Pevzner PA. V(DD)J recombination is an important and evolutionary conserved mechanism for generating antibodies with unusually long CDR3s. Genome Research. 2020. 30:1547–58. [link]

16. Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLOS Computational Biology. 2020. 16(4):e1007837. [link]

17. Safonova Y and Pevzner PA. De novo inference of diversity genes and analysis of non-canonical V(DD)J recombination in immunoglobulins. Frontiers in Immunology. 2019. 10:987 [link]

18. Shlemov A, Bankevich S, Bzikadze A, Turchaninova M, Safonova Y, Pevzner PA. Reconstructing antibody repertoires from error-prone immunosequencing datasets. Journal of Immunology. 2017. 199(9):3369-80. [link]

19. Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics. 2015. 31(12):i53-61. [link]

20. Safonova Y, Lapidus A, Lill J. IgSimulator: a versatile immunosequencing simulator. Bioinformatics. 2015. 31(19):3213-5. [link]

21. Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova Y, Naumenko SA, Klepikova AV, Gerasimov ES, Bazykin GA, James TY, Kondrashov AS. Extraordinary genetic diversity in a wood decay mushroom. Molecular Biology and Evolution. 2015. 32(10):2775-83. [link]

22. Safonova Y, Bankevich A, Pevzner PA. dipSPAdes: assembler for highly polymorphic diploid genomes. Journal of Computational Biology. 2015. 22(6):528-45. [link]