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Yana Safonova
Yana Safonova
Johns Hopkins University
Подтвержден адрес электронной почты в домене cs.jhu.edu - Главная страница
Название
Процитировано
Процитировано
Год
dipSPAdes: assembler for highly polymorphic diploid genomes
Y Safonova, A Bankevich, PA Pevzner
Journal of Computational Biology 22 (6), 528-545, 2015
912015
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
512015
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), 108856, 2021
482021
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
332015
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
32*2017
IgSimulator: a versatile immunosequencing simulator
Y Safonova, A Lapidus, J Lill
Bioinformatics 31 (19), 3213-3215, 2015
302015
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, 987, 2019
222019
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
152021
Trace reconstruction problems in computational biology
V Bhardwaj, PA Pevzner, C Rashtchian, Y Safonova
IEEE Transactions on Information Theory 67 (6), 3295-3314, 2020
152020
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), 1-12, 2021
112021
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, ...
biorxiv, 2021
112021
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
72020
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
72020
Tree-Guided Construction of Antibody Repertoires and Its Applications to CDR Annotation
Y Safonova, CT Watson, PA Pevzner
Available at SSRN 3728951, 0
4*
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, 1-11, 2022
3*2022
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
32022
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
12022
Gene prediction in the immunoglobulin loci
V Sirupurapu, Y Safonova, P Pevzner
Genome Research, gr. 276676.122, 2022
2022
Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains
JT Kos, Y Safonova, KM Shields, CA Silver, WD Lees, AM Collins, ...
bioRxiv, 2022
2022
Scalable Models of Antibody Evolution and Benchmarking of Clonal Tree Reconstruction Methods
C Zhang, AV Bzikadze, Y Safonova, S Mirarab
bioRxiv, 2020
2020
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Статьи 1–20