Yana Safonova

Title(s)Postdoctoral Scholar, Qualcomm Institute
Address9500 Gilman Drive #0436
La Jolla CA 92093
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    2019AAI Intersect Fellowship for Computational Scientists and Immunologists

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Diversity in immunogenomics: the value and the challenge. Nat Methods. 2021 May 17. 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, Jönsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Abedalthagafi MS, Adekoya KO, Ahmed RA, Chang WC, Gray C, Nakamura Y, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT, Karlsson Hedestam GB, Mangul S. PMID: 34002093.
      View in: PubMed   Mentions: 1     Fields:    
    2. A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Cell Rep. 2021 Mar 16; 34(11):108856. Akbar R, Robert PA, Pavlovic M, Jeliazkov JR, Snapkov I, Slabodkin A, Weber CR, Scheffer L, Miho E, Haff IH, Haug DTT, Lund-Johansen F, Safonova Y, Sandve GK, Greiff V. PMID: 33730590.
      View in: PubMed   Mentions: 7     Fields:    
    3. Trace Reconstruction Problems in Computational Biology. IEEE Trans Inf Theory. 2021 Jun; 67(6):3295-3314. Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. PMID: 34176957.
      View in: PubMed   Mentions:
    4. V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s. Genome Res. 2020 11; 30(11):1547-1558. Safonova Y, Pevzner PA. PMID: 32948615.
      View in: PubMed   Mentions: 1     Fields:    
    5. Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLoS Comput Biol. 2020 04; 16(4):e1007837. Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. PMID: 32339161.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    6. De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins. Front Immunol. 2019; 10:987. Safonova Y, Pevzner PA. PMID: 31134072.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    7. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. J Immunol. 2017 11 01; 199(9):3369-3380. Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. PMID: 28978691.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimals
    8. Extraordinary Genetic Diversity in a Wood Decay Mushroom. Mol Biol Evol. 2015 Oct; 32(10):2775-83. Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova YY, Naumenko SA, Klepikova AV, Gerasimov ES, Bazykin GA, James TY, Kondrashov AS. PMID: 26163667.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    9. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics. 2015 Jun 15; 31(12):i53-61. Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. PMID: 26072509.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    10. IgSimulator: a versatile immunosequencing simulator. Bioinformatics. 2015 Oct 01; 31(19):3213-5. Safonova Y, Lapidus A, Lill J. PMID: 26007226.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    11. dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. J Comput Biol. 2015 Jun; 22(6):528-45. Safonova Y, Bankevich A, Pevzner PA. PMID: 25734602.
      View in: PubMed   Mentions: 23     Fields:    
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