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Yana Safonova
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Year
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
R Akbar, PA Robert, M Pavlović, JR Jeliazkov, I Snapkov, A Slabodkin, ...
Cell Reports 34 (11), 2021
1482021
dipSPAdes: assembler for highly polymorphic diploid genomes
Y Safonova, A Bankevich, PA Pevzner
Journal of Computational Biology 22 (6), 528-545, 2015
1012015
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis
Y Safonova, S Bonissone, E Kurpilyansky, E Starostina, A Lapidus, ...
Bioinformatics 31 (12), i53-i61, 2015
572015
Diversity in immunogenomics: the value and the challenge
K Peng, Y Safonova, M Shugay, AB Popejoy, OL Rodriguez, F Breden, ...
Nature methods 18 (6), 588-591, 2021
482021
Reconstructing antibody repertoires from error-prone immunosequencing reads
A Shlemov, S Bankevich, A Bzikadze, MA Turchaninova, Y Safonova, ...
The Journal of Immunology 199 (9), 3369-3380, 2017
44*2017
Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells
JH Lee, L Toy, JT Kos, Y Safonova, WR Schief, C Havenar-Daughton, ...
NPJ vaccines 6 (1), 113, 2021
432021
Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease
P Zhou, G Song, H Liu, M Yuan, W He, N Beutler, X Zhu, VT Longping, ...
Immunity 56 (3), 669-686. e7, 2023
412023
Extraordinary genetic diversity in a wood decay mushroom
MA Baranova, MD Logacheva, AA Penin, VB Seplyarskiy, YY Safonova, ...
Molecular biology and evolution 32 (10), 2775-2783, 2015
402015
Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses
W He, R Musharrafieh, G Song, K Dueker, LV Tse, DR Martinez, ...
Nature immunology 23 (6), 960-970, 2022
392022
IgSimulator: a versatile immunosequencing simulator
Y Safonova, A Lapidus, J Lill
Bioinformatics 31 (19), 3213-3215, 2015
362015
De novo inference of diversity genes and analysis of non-canonical V (DD) J recombination in immunoglobulins
Y Safonova, PA Pevzner
Frontiers in immunology 10, 448987, 2019
292019
Trace reconstruction problems in computational biology
V Bhardwaj, PA Pevzner, C Rashtchian, Y Safonova
IEEE Transactions on Information Theory 67 (6), 3295-3314, 2020
252020
Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques
W He, M Yuan, S Callaghan, R Musharrafieh, G Song, M Silva, N Beutler, ...
Science translational medicine 14 (657), eabl9605, 2022
242022
Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease
P Zhou, G Song, W He, N Beutler, VT Longping, DR Martinez, A Schäfer, ...
bioRxiv, 2022
222022
Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire
OL Rodriguez, Y Safonova, CA Silver, K Shields, WS Gibson, JT Kos, ...
Nature communications 14 (1), 4419, 2023
20*2023
V (DD) J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s
Y Safonova, PA Pevzner
Genome research 30 (11), 1547-1558, 2020
152020
Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species
V Bhardwaj, M Franceschetti, R Rao, PA Pevzner, Y Safonova
PLoS computational biology 16 (4), e1007837, 2020
112020
Gene prediction in the immunoglobulin loci
V Sirupurapu, Y Safonova, PA Pevzner
Genome research 32 (6), 1152-1169, 2022
82022
Variations in antibody repertoires correlate with vaccine responses
Y Safonova, SB Shin, L Kramer, J Reecy, CT Watson, TPL Smith, ...
Genome research 32 (4), 791-804, 2022
82022
Tree-Guided Construction of Antibody Repertoires and Its Applications to CDR Annotation
Y Safonova, CT Watson, PA Pevzner
Available at SSRN 3728951, 0
7*
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