| Year |
Citation |
Score |
| 2024 |
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, et al. Complete sequencing of ape genomes. Biorxiv : the Preprint Server For Biology. PMID 39131277 DOI: 10.1101/2024.07.31.605654 |
0.622 |
|
| 2024 |
Kalbfleisch TS, McKay SD, Murdoch BM, Adelson DL, Almansa-Villa D, Becker G, Beckett LM, Benítez-Galeano MJ, Biase F, Casey T, Chuong E, Clark E, Clarke S, Cockett N, Couldrey C, ... ... Safonova Y, et al. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics. PMID 39103649 DOI: 10.1038/s41588-024-01835-2 |
0.554 |
|
| 2024 |
Lin MJ, Langmead B, Safonova Y. IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads. Biorxiv : the Preprint Server For Biology. PMID 39091872 DOI: 10.1101/2024.07.20.604421 |
0.345 |
|
| 2024 |
Zhu Y, Watson C, Safonova Y, Pennell M, Bankevich A. Assessing Assembly Errors in Immunoglobulin Loci: A Comprehensive Evaluation of Long-read Genome Assemblies Across Vertebrates. Biorxiv : the Preprint Server For Biology. PMID 39091785 DOI: 10.1101/2024.07.19.604360 |
0.581 |
|
| 2023 |
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 and Immunity. PMID 38097744 DOI: 10.1038/s41435-023-00238-3 |
0.574 |
|
| 2023 |
Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd SD, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nature Communications. 14: 4419. PMID 37479682 DOI: 10.1038/s41467-023-40070-x |
0.598 |
|
| 2022 |
Sirupurapu V, Safonova Y, Pevzner PA. Gene prediction in the immunoglobulin loci. Genome Research. 32: 1152-1169. PMID 35545447 DOI: 10.1101/gr.276676.122 |
0.558 |
|
| 2022 |
Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Research. PMID 35361626 DOI: 10.1101/gr.276027.121 |
0.623 |
|
| 2021 |
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. 6: 113. PMID 34489473 DOI: 10.1038/s41541-021-00376-7 |
0.546 |
|
| 2021 |
Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Trace Reconstruction Problems in Computational Biology. Ieee Transactions On Information Theory. 67: 3295-3314. PMID 34176957 DOI: 10.1109/tit.2020.3030569 |
0.436 |
|
| 2021 |
Peng K, Safonova Y, Shugay M, Popejoy AB, Rodriguez OL, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau VM, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, et al. Diversity in immunogenomics: the value and the challenge. Nature Methods. PMID 34002093 DOI: 10.1038/s41592-021-01169-5 |
0.585 |
|
| 2020 |
Safonova Y, Pevzner PA. V(DD)J recombination is an important and evolutionary conserved mechanism for generating antibodies with unusually long CDR3s. Genome Research. PMID 32948615 DOI: 10.1101/Gr.259598.119 |
0.56 |
|
| 2020 |
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. 16: e1007837. PMID 32339161 DOI: 10.1371/Journal.Pcbi.1007837 |
0.523 |
|
| 2019 |
Safonova Y, Pevzner PA. Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins. Frontiers in Immunology. 10: 987. PMID 31134072 DOI: 10.3389/Fimmu.2019.00987 |
0.537 |
|
| 2017 |
Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. Journal of Immunology (Baltimore, Md. : 1950). PMID 28978691 DOI: 10.4049/Jimmunol.1700485 |
0.481 |
|
| 2015 |
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 (Oxford, England). 31: i53-61. PMID 26072509 DOI: 10.1093/Bioinformatics/Btv238 |
0.512 |
|
| 2015 |
Safonova Y, Bankevich A, Pevzner PA. dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 528-45. PMID 25734602 DOI: 10.1089/Cmb.2014.0153 |
0.486 |
|
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