IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. - Yana Safonova; Stefano Bonissone; Eugene Kurpilyansky; Ekaterina Starostina; Alla L. Lapidus; Jeremy Stinson; Laura DePalatis; Wendy Sandoval; Jennie Lill; Pavel A. Pevzner (Bioinform., 2015)

IgSimulator: a versatile immunosequencing simulator. - Yana Safonova; Alla L. Lapidus; Jennie Lill (Bioinform., 2015)

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. - Yana Safonova; Anton Bankevich; Pavel A. Pevzner (J. Comput. Biol., 2015)

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Datasets. - Alexander Shlemov; Sergey Bankevich; Andrey V. Bzikadze; Yana Safonova; Pavel A. Pevzner (RECOMB, 2017)

Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. - Vinnu Bhardwaj; Massimo Franceschetti; Ramesh Rao; Pavel A. Pevzner; Yana Safonova (PLoS Comput. Biol., 2020)

Trace Reconstruction Problems in Computational Biology. - Vinnu Bhardwaj; Pavel A. Pevzner; Cyrus Rashtchian; Yana Safonova (IEEE Trans. Inf. Theory, 2021)