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Yana Safonova
Researcher at University of California, San Diego
Publications - 40
Citations - 700
Yana Safonova is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Biology & Medicine. The author has an hindex of 10, co-authored 27 publications receiving 324 citations. Previous affiliations of Yana Safonova include Saint Petersburg State University & University of Louisville.
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Journal ArticleDOI
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
TL;DR: The first de Bruijn graph assembler, dipSPAdes, for HP genomes is developed that significantly improves on the state-of-the-art assemblers for HP diploid genomes.
Journal ArticleDOI
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding.
Rahmad Akbar,Philippe Robert,Milena Pavlović,Jeliazko R. Jeliazkov,Igor Snapkov,Andrei Slabodkin,Cédric R. Weber,Lonneke Scheffer,Enkelejda Miho,Ingrid Hobæk Haff,Dag Haug,Fridtjof Lund-Johansen,Yana Safonova,Geir Kjetil Sandve,Victor Greiff +14 more
TL;DR: In this paper, the authors identify structural interaction motifs, which together compose a commonly shared structure-based vocabulary of paratope-epitope interactions, and show that this vocabulary enables the machine learnability of antibody-antigen binding using generative machine learning.
Journal ArticleDOI
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis
Yana Safonova,Stefano Bonissone,Eugene Kurpilyansky,Ekaterina Starostina,Alla Lapidus,Jeremy Stinson,Laura DePalatis,Wendy N. Sandoval,Jennie R. Lill,Pavel A. Pevzner +9 more
TL;DR: The IgRepertoireConstructor algorithm is presented, that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires.
Journal ArticleDOI
Extraordinary Genetic Diversity in a Wood Decay Mushroom
Maria A. Baranova,Maria A. Baranova,Maria A. Baranova,Maria D. Logacheva,Maria D. Logacheva,Maria D. Logacheva,Aleksey A. Penin,Aleksey A. Penin,Vladimir B. Seplyarskiy,Vladimir B. Seplyarskiy,Vladimir B. Seplyarskiy,Yana Safonova,Sergey Naumenko,Anna V. Klepikova,Anna V. Klepikova,Evgeniy S. Gerasimov,Evgeniy S. Gerasimov,Georgii A. Bazykin,Timothy Y. James,Alexey S. Kondrashov,Alexey S. Kondrashov +20 more
TL;DR: The results of a comparative analysis of 24 haploid genotypes of a split-gill fungus Schizophyllum commune show that the mutation rate in S. commune is high, and this exceptionally high level of nucleotide diversity leads to extreme amino acid diversity of protein-coding genes.
Posted ContentDOI
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
Rahmad Akbar,Philippe Robert,Milena Pavlović,Jeliazko R. Jeliazkov,Igor Snapkov,Andrei Slabodkin,Cédric R. Weber,Lonneke Scheffer,Enkelejda Miho,Ingrid Hobæk Haff,Dag Haug,Fridtjof Lund-Johansen,Yana Safonova,Geir Kjetil Sandve,Victor Greiff +14 more
TL;DR: The largest available set of non-redundant antibody-antigen structures are screened for binding patterns and identified structural interaction motifs are identified, which together compose a vocabulary of paratope-epitope interactions that is universally shared among investigated antibody-antsigen structures.