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Yana Safonova

Assistant Professor


  • School of Electrical Engineering and Computer Science
  • Computer Science and Engineering

W209 Westgate Building




  • B.Sc., Computer Science, Lobachevsky State University of Nizhny Novgorod, 2010
  • M.Sc., Computer Science, Lobachevsky State University of Nizhny Novgorod, 2012
  • Ph.D., BIoinformatics, Saint-Petersburg University, 2017


Journal Articles

  • C T Watson, O L Rodriguez, E Engelbrecht, Yana Safonova, W A Marasco and M L Smith, 2023, "Looking to the future of antibody genetics: resolving the roles of immunoglobulin diversity in gene regulation, function, and immunity.", Genes and immunity
  • O L Rodriguez, Yana Safonova, C A Silver, K Shields, W S Gibson, J T Kos, D Tieri, H Ke, Jackson KJL, S D Boyd, M L Smith, W A Marasco and C T Watson, 2023, "Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire.", Nature communications, 14, (1), pp. 4419
  • P Zhou, G Song, H Liu, M Yuan, W T He, N Beutler, X Zhu, L V Tse, D R Martinez, A Schäfer, F Anzanello, P Yong, L Peng, K Dueker, R Musharrafieh, S Callaghan, T Capozzola, O Limbo, M Parren, E Garcia, S A Rawlings, D M Smith, D Nemazee, J G Jardine, Yana Safonova, B Briney, T F Rogers, I A Wilson, R S Baric, L E Gralinski, D R Burton and R Andrabi, 2023, "Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.", Immunity, 56, (3), pp. 669-686.e7
  • C Zhang, A V Bzikadze, Yana Safonova and S Mirarab, 2022, "A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.", Frontiers in immunology, 13, pp. 1014439
  • G W Jenkins, Yana Safonova and V V Smider, 2022, "Germline-Encoded Positional Cysteine Polymorphisms Enhance Diversity in Antibody Ultralong CDR H3 Regions.", Journal of immunology (Baltimore, Md. : 1950), 209, (11), pp. 2141-2148
  • W T He, M Yuan, S Callaghan, R Musharrafieh, G Song, M Silva, N Beutler, W H Lee, P Yong, J L Torres, M Melo, P Zhou, F Zhao, X Zhu, L Peng, D Huang, F Anzanello, J Ricketts, M Parren, E Garcia, M Ferguson, W Rinaldi, S A Rawlings, D Nemazee, D M Smith, B Briney, Yana Safonova, T F Rogers, J M Dan, Z Zhang, D Weiskopf, A Sette, S Crotty, D J Irvine, A B Ward, I A Wilson, D R Burton and R Andrabi, 2022, "Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.", Science translational medicine, 14, (657), pp. eabl9605
  • V Sirupurapu, Yana Safonova and P A Pevzner, 2022, "Gene prediction in the immunoglobulin loci.", Genome research, 32, (6), pp. 1152-1169
  • W T He, R Musharrafieh, G Song, K Dueker, L V Tse, D R Martinez, A Schäfer, S Callaghan, P Yong, N Beutler, J L Torres, R M Volk, P Zhou, M Yuan, H Liu, F Anzanello, T Capozzola, M Parren, E Garcia, S A Rawlings, D M Smith, I A Wilson, Yana Safonova, A B Ward, T F Rogers, R S Baric, L E Gralinski, D R Burton and R Andrabi, 2022, "Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses.", Nature immunology, 23, (6), pp. 960-970
  • Yana Safonova, S B Shin, L Kramer, J Reecy, C T Watson, Smith TPL and P A Pevzner, 2022, "Variations in antibody repertoires correlate with vaccine responses.", Genome research, 32, (4), pp. 791-804
  • J H Lee, L Toy, J T Kos, Yana Safonova, W R Schief, C Havenar-Daughton, C T Watson and S Crotty, 2021, "Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells.", NPJ vaccines, 6, (1), pp. 113
  • K Peng, Yana Safonova, M Shugay, A B Popejoy, O L Rodriguez, F Breden, P Brodin, A M Burkhardt, C Bustamante, V M Cao-Lormeau, M M Corcoran, D Duffy, M Fuentes-Guajardo, R Fujita, V Greiff, V D Jönsson, X Liu, L Quintana-Murci, M Rossetti, J Xie, G Yaari, W Zhang, M S Abedalthagafi, K O Adekoya, R A Ahmed, W C Chang, C Gray, Y Nakamura, W D Lees, P Khatri, H Alachkar, C Scheepers, C T Watson, G B Karlsson Hedestam and S Mangul, 2021, "Diversity in immunogenomics: the value and the challenge.", Nature methods, 18, (6), pp. 588-591
  • V Bhardwaj, P A Pevzner, C Rashtchian and Yana Safonova, 2021, "Trace Reconstruction Problems in Computational Biology.", IEEE transactions on information theory, 67, (6), pp. 3295-3314
  • R Akbar, P A Robert, M Pavlovic, J R Jeliazkov, I Snapkov, A Slabodkin, C R Weber, L Scheffer, E Miho, I H Haff, Haug DTT, F Lund-Johansen, Yana Safonova, G K Sandve and V Greiff, 2021, "A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding.", Cell reports, 34, (11), pp. 108856
  • Yana Safonova and P A Pevzner, 2020, "V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s.", Genome research, 30, (11), pp. 1547-1558
  • V Bhardwaj, M Franceschetti, R Rao, P A Pevzner and Yana Safonova, 2020, "Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species.", PLoS computational biology, 16, (4), pp. e1007837
  • Yana Safonova and P A Pevzner, 2019, "De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins.", Frontiers in immunology, 10, pp. 987
  • A Shlemov, S Bankevich, A Bzikadze, M A Turchaninova, Yana Safonova and P A Pevzner, 2017, "Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.", Journal of immunology (Baltimore, Md. : 1950), 199, (9), pp. 3369-3380
  • M A Baranova, M D Logacheva, A A Penin, V B Seplyarskiy, Yana Safonova, S A Naumenko, A V Klepikova, E S Gerasimov, G A Bazykin, T Y James and A S Kondrashov, 2015, "Extraordinary Genetic Diversity in a Wood Decay Mushroom.", Molecular biology and evolution, 32, (10), pp. 2775-83
  • Yana Safonova, A Lapidus and J Lill, 2015, "IgSimulator: a versatile immunosequencing simulator.", Bioinformatics (Oxford, England), 31, (19), pp. 3213-5
  • Yana Safonova, S Bonissone, E Kurpilyansky, E Starostina, A Lapidus, J Stinson, L DePalatis, W Sandoval, J Lill and P A Pevzner, 2015, "IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.", Bioinformatics (Oxford, England), 31, (12), pp. i53-61
  • Yana Safonova, Anton Bankevich and P A Pevzner, 2015, "dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.", Journal of computational biology : a journal of computational molecular cell biology, 22, (6), pp. 528-45

Research Projects

Honors and Awards

  • AAI Intersect Fellowship for Computational Scientists and Immunologists, American Association of Immunologists, January 2019 - January 2020


Service to Penn State:

Service to External Organizations:




The School of Electrical Engineering and Computer Science was created in the spring of 2015 to allow greater access to courses offered by both departments for undergraduate and graduate students in exciting collaborative research fields.

We offer B.S. degrees in electrical engineering, computer science, computer engineering and data science and graduate degrees (master's degrees and Ph.D.'s) in electrical engineering and computer science and engineering. EECS focuses on the convergence of technologies and disciplines to meet today’s industrial demands.

School of Electrical Engineering and Computer Science

The Pennsylvania State University

207 Electrical Engineering West

University Park, PA 16802


Department of Computer Science and Engineering


Department of Electrical Engineering