Journal Articles
- C T Watson, O L Rodriguez, E Engelbrecht, Yana Safonova, W A Marasco and M L Smith, 2023, "Looking to the future of antibody genetics: resolving the roles of immunoglobulin diversity in gene regulation, function, and immunity.", Genes and immunity
- O L Rodriguez, Yana Safonova, C A Silver, K Shields, W S Gibson, J T Kos, D Tieri, H Ke, Jackson KJL, S D Boyd, M L Smith, W A Marasco and C T Watson, 2023, "Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire.", Nature communications, 14, (1), pp. 4419
- P Zhou, G Song, H Liu, M Yuan, W T He, N Beutler, X Zhu, L V Tse, D R Martinez, A Schäfer, F Anzanello, P Yong, L Peng, K Dueker, R Musharrafieh, S Callaghan, T Capozzola, O Limbo, M Parren, E Garcia, S A Rawlings, D M Smith, D Nemazee, J G Jardine, Yana Safonova, B Briney, T F Rogers, I A Wilson, R S Baric, L E Gralinski, D R Burton and R Andrabi, 2023, "Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.", Immunity, 56, (3), pp. 669-686.e7
- C Zhang, A V Bzikadze, Yana Safonova and S Mirarab, 2022, "A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.", Frontiers in immunology, 13, pp. 1014439
- G W Jenkins, Yana Safonova and V V Smider, 2022, "Germline-Encoded Positional Cysteine Polymorphisms Enhance Diversity in Antibody Ultralong CDR H3 Regions.", Journal of immunology (Baltimore, Md. : 1950), 209, (11), pp. 2141-2148
- W T He, M Yuan, S Callaghan, R Musharrafieh, G Song, M Silva, N Beutler, W H Lee, P Yong, J L Torres, M Melo, P Zhou, F Zhao, X Zhu, L Peng, D Huang, F Anzanello, J Ricketts, M Parren, E Garcia, M Ferguson, W Rinaldi, S A Rawlings, D Nemazee, D M Smith, B Briney, Yana Safonova, T F Rogers, J M Dan, Z Zhang, D Weiskopf, A Sette, S Crotty, D J Irvine, A B Ward, I A Wilson, D R Burton and R Andrabi, 2022, "Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.", Science translational medicine, 14, (657), pp. eabl9605
- V Sirupurapu, Yana Safonova and P A Pevzner, 2022, "Gene prediction in the immunoglobulin loci.", Genome research, 32, (6), pp. 1152-1169
- W T He, R Musharrafieh, G Song, K Dueker, L V Tse, D R Martinez, A Schäfer, S Callaghan, P Yong, N Beutler, J L Torres, R M Volk, P Zhou, M Yuan, H Liu, F Anzanello, T Capozzola, M Parren, E Garcia, S A Rawlings, D M Smith, I A Wilson, Yana Safonova, A B Ward, T F Rogers, R S Baric, L E Gralinski, D R Burton and R Andrabi, 2022, "Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses.", Nature immunology, 23, (6), pp. 960-970
- Yana Safonova, S B Shin, L Kramer, J Reecy, C T Watson, Smith TPL and P A Pevzner, 2022, "Variations in antibody repertoires correlate with vaccine responses.", Genome research, 32, (4), pp. 791-804
- J H Lee, L Toy, J T Kos, Yana Safonova, W R Schief, C Havenar-Daughton, C T Watson and S Crotty, 2021, "Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells.", NPJ vaccines, 6, (1), pp. 113
- K Peng, Yana Safonova, M Shugay, A B Popejoy, O L Rodriguez, F Breden, P Brodin, A M Burkhardt, C Bustamante, V M Cao-Lormeau, M M Corcoran, D Duffy, M Fuentes-Guajardo, R Fujita, V Greiff, V D Jönsson, X Liu, L Quintana-Murci, M Rossetti, J Xie, G Yaari, W Zhang, M S Abedalthagafi, K O Adekoya, R A Ahmed, W C Chang, C Gray, Y Nakamura, W D Lees, P Khatri, H Alachkar, C Scheepers, C T Watson, G B Karlsson Hedestam and S Mangul, 2021, "Diversity in immunogenomics: the value and the challenge.", Nature methods, 18, (6), pp. 588-591
- V Bhardwaj, P A Pevzner, C Rashtchian and Yana Safonova, 2021, "Trace Reconstruction Problems in Computational Biology.", IEEE transactions on information theory, 67, (6), pp. 3295-3314
- R Akbar, P A Robert, M Pavlovic, J R Jeliazkov, I Snapkov, A Slabodkin, C R Weber, L Scheffer, E Miho, I H Haff, Haug DTT, F Lund-Johansen, Yana Safonova, G K Sandve and V Greiff, 2021, "A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding.", Cell reports, 34, (11), pp. 108856
- Yana Safonova and P A Pevzner, 2020, "V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s.", Genome research, 30, (11), pp. 1547-1558
- V Bhardwaj, M Franceschetti, R Rao, P A Pevzner and Yana Safonova, 2020, "Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species.", PLoS computational biology, 16, (4), pp. e1007837
- Yana Safonova and P A Pevzner, 2019, "De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins.", Frontiers in immunology, 10, pp. 987
- A Shlemov, S Bankevich, A Bzikadze, M A Turchaninova, Yana Safonova and P A Pevzner, 2017, "Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.", Journal of immunology (Baltimore, Md. : 1950), 199, (9), pp. 3369-3380
- M A Baranova, M D Logacheva, A A Penin, V B Seplyarskiy, Yana Safonova, S A Naumenko, A V Klepikova, E S Gerasimov, G A Bazykin, T Y James and A S Kondrashov, 2015, "Extraordinary Genetic Diversity in a Wood Decay Mushroom.", Molecular biology and evolution, 32, (10), pp. 2775-83
- Yana Safonova, A Lapidus and J Lill, 2015, "IgSimulator: a versatile immunosequencing simulator.", Bioinformatics (Oxford, England), 31, (19), pp. 3213-5
- Yana Safonova, S Bonissone, E Kurpilyansky, E Starostina, A Lapidus, J Stinson, L DePalatis, W Sandoval, J Lill and P A Pevzner, 2015, "IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.", Bioinformatics (Oxford, England), 31, (12), pp. i53-61
- Yana Safonova, Anton Bankevich and P A Pevzner, 2015, "dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.", Journal of computational biology : a journal of computational molecular cell biology, 22, (6), pp. 528-45
