Yana Safonova

Assistant Professor of Electrical Engineering and Computer Science

Most Recent Publications

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Theodore S. Kalbfleisch, Stephanie D. McKay, Brenda M. Murdoch, David L. Adelson, Diego Almansa-Villa, Gabrielle Becker, Linda M. Beckett, María José Benítez-Galeano, Fernando Biase, Theresa Casey, Edward Chuong, Emily Clark, Shannon Clarke, Noelle Cockett, Christine Couldrey, Brian W. Davis, Christine G. Elsik, Thomas Faraut, Yahui Gao, Carine Genet, Patrick Grady, Jonathan Green, Richard Green, Dailu Guan, Darren Hagen, Gabrielle A. Hartley, Mike Heaton, Savannah J. Hoyt, Wen Huang, Erich Jarvis, Jenna Kalleberg, Hasan Khatib, Klaus Peter Koepfi, James Koltes, Sergey Koren, Christa Kuehn, Tosso Leeb, Alexander Leonard, George E. Liu, Wai Yee Low, Hunter McConnell, Kathryn McRae, Karen Miga, Michelle Mousel, Holly Neibergs, Temitayo Olagunju, Matt Pennell, Bruna Petry, Mirjam Pewsner, Adam M. Phillippy, Brandon D. Pickett, Paulene Pineda, Tamara Potapova, Satyanarayana Rachagani, Arang Rhie, Monique Rijnkels, Annie Robic, Nelida Rodriguez Osorio, Yana Safonova, Gustavo Schettini, Robert D. Schnabel, Nagabhishek Sirpu Natesh, Morgan Stegemiller, Jessica Storer, Paul Stothard, Caleb Stull, Gwenola Tosser-Klopp, Germán M. Traglia, Christopher K. Tuggle, Curtis P. Van Tassell, Corey Watson, Rosemarie Weikard, Klaus Wimmers, Shangqian Xie, Liu Yang, Timothy P.L. Smith, Rachel J. O’Neill, Benjamin D. Rosen, 2024, Nature Genetics on p. 1566-1573

Looking to the future of antibody genetics: resolving the roles of immunoglobulin diversity in gene regulation, function, and immunity

Corey T. Watson, Oscar L. Rodriguez, Eric Engelbrecht, Yana Safonova, Wayne A. Marasco, Melissa L. Smith, 2024, Genes and Immunity on p. 92-94

Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire

Oscar L. Rodriguez, Yana Safonova, Catherine A. Silver, Kaitlyn Shields, William S. Gibson, Justin T. Kos, David Tieri, Hanzhong Ke, Katherine J.L. Jackson, Scott D. Boyd, Melissa L. Smith, Wayne A. Marasco, Corey T. Watson, 2023, Nature Communications

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease

Panpan Zhou, Ge Song, Hejun Liu, Meng Yuan, Wan ting He, Nathan Beutler, Xueyong Zhu, Longping V. Tse, David R. Martinez, Alexandra Schäfer, Fabio Anzanello, Peter Yong, Linghang Peng, Katharina Dueker, Rami Musharrafieh, Sean Callaghan, Tazio Capozzola, Oliver Limbo, Mara Parren, Elijah Garcia, Stephen A. Rawlings, Davey M. Smith, David Nemazee, Joseph G. Jardine, Yana Safonova, Bryan Briney, Thomas F. Rogers, Ian A. Wilson, Ralph S. Baric, Lisa E. Gralinski, Dennis R. Burton, Raiees Andrabi, 2023, Immunity on p. 669-686.e7

A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods

Chao Zhang, Andrey V. Bzikadze, Yana Safonova, Siavash Mirarab, 2022, Frontiers in Immunology

Germline-Encoded Positional Cysteine Polymorphisms Enhance Diversity in Antibody Ultralong CDR H3 Regions

Gabrielle Warner Jenkins, Yana Safonova, Vaughn V. Smider, 2022, Journal of Immunology on p. 2141-2148

Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques

Wan Ting He, Meng Yuan, Sean Callaghan, Rami Musharrafieh, Ge Song, Murillo Silva, Nathan Beutler, Wen Hsin Lee, Peter Yong, Jonathan L. Torres, Mariane Melo, Panpan Zhou, Fangzhu Zhao, Xueyong Zhu, Linghang Peng, Deli Huang, Fabio Anzanello, James Ricketts, Mara Parren, Elijah Garcia, Melissa Ferguson, William Rinaldi, Stephen A. Rawlings, David Nemazee, Davey M. Smith, Bryan Briney, Yana Safonova, Thomas F. Rogers, Jennifer M. Dan, Zeli Zhang, Daniela Weiskopf, Alessandro Sette, Shane Crotty, Darrell J. Irvine, Andrew B. Ward, Ian A. Wilson, Dennis R. Burton, Raiees Andrabi, 2022, Science Translational Medicine

Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses

Wan ting He, Rami Musharrafieh, Ge Song, Katharina Dueker, Longping V. Tse, David R. Martinez, Alexandra Schäfer, Sean Callaghan, Peter Yong, Nathan Beutler, Jonathan L. Torres, Reid M. Volk, Panpan Zhou, Meng Yuan, Hejun Liu, Fabio Anzanello, Tazio Capozzola, Mara Parren, Elijah Garcia, Stephen A. Rawlings, Davey M. Smith, Ian A. Wilson, Yana Safonova, Andrew B. Ward, Thomas F. Rogers, Ralph S. Baric, Lisa E. Gralinski, Dennis R. Burton, Raiees Andrabi, 2022, Nature Immunology on p. 960-970

Gene prediction in the immunoglobulin loci

Vikram Sirupurapu, Yana Safonova, Pavel A. Pevzner, 2022, Genome Research on p. 1152-1169

Variations in antibody repertoires correlate with vaccine responses

Yana Safonova, Sung Bong Shin, Luke Kramer, James Reecy, Corey T. Watson, Timothy P.L. Smith, Pavel A. Pevzner, 2022, Genome Research on p. 791-804

Most-Cited Papers

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

Rahmad Akbar, Philippe A. Robert, Milena Pavlović, Jeliazko R. Jeliazkov, Igor Snapkov, Andrei Slabodkin, Cédric R. Weber, Lonneke Scheffer, Enkelejda Miho, Ingrid Hobæk Haff, Dag Trygve Tryslew Haug, Fridtjof Lund-Johansen, Yana Safonova, Geir K. Sandve, Victor Greiff, 2021, Cell Reports

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease

Panpan Zhou, Ge Song, Hejun Liu, Meng Yuan, Wan ting He, Nathan Beutler, Xueyong Zhu, Longping V. Tse, David R. Martinez, Alexandra Schäfer, Fabio Anzanello, Peter Yong, Linghang Peng, Katharina Dueker, Rami Musharrafieh, Sean Callaghan, Tazio Capozzola, Oliver Limbo, Mara Parren, Elijah Garcia, Stephen A. Rawlings, Davey M. Smith, David Nemazee, Joseph G. Jardine, Yana Safonova, Bryan Briney, Thomas F. Rogers, Ian A. Wilson, Ralph S. Baric, Lisa E. Gralinski, Dennis R. Burton, Raiees Andrabi, 2023, Immunity on p. 669-686.e7

DipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

Yana Safonova, Anton Bankevich, Pavel A. Pevzner, 2015, Journal of Computational Biology on p. 528-545

Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells

Jeong Hyun Lee, Laura Toy, Justin T. Kos, Yana Safonova, William R. Schief, Colin Havenar-Daughton, Corey T. Watson, Shane Crotty, 2021, npj Vaccines

Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses

Wan ting He, Rami Musharrafieh, Ge Song, Katharina Dueker, Longping V. Tse, David R. Martinez, Alexandra Schäfer, Sean Callaghan, Peter Yong, Nathan Beutler, Jonathan L. Torres, Reid M. Volk, Panpan Zhou, Meng Yuan, Hejun Liu, Fabio Anzanello, Tazio Capozzola, Mara Parren, Elijah Garcia, Stephen A. Rawlings, Davey M. Smith, Ian A. Wilson, Yana Safonova, Andrew B. Ward, Thomas F. Rogers, Ralph S. Baric, Lisa E. Gralinski, Dennis R. Burton, Raiees Andrabi, 2022, Nature Immunology on p. 960-970

Diversity in immunogenomics: the value and the challenge

Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jönsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid O. Adekoya, Rahaman A. Ahmed, Wei Chiao Chang, Clive Gray, Yusuke Nakamura, William D. Lees, Purvesh Khatri, Houda Alachkar, Cathrine Scheepers, Corey T. Watson, Gunilla B. Karlsson Hedestam, Serghei Mangul, 2021, Nature Methods on p. 588-591

Extraordinary genetic diversity in a wood decay mushroom

Maria A. Baranova, Maria D. Logacheva, Aleksey A. Penin, Vladimir B. Seplyarskiy, Yana Y. Safonova, Sergey A. Naumenko, Anna V. Klepikova, Evgeny S. Gerasimov, Georgii A. Bazykin, Timothy Y. James, Alexey S. Kondrashov, 2015, Molecular Biology and Evolution on p. 2775-2783

Ig Repertoire Constructor: 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 Sandoval, Jennie Lill, Pavel A. Pevzner, 2015, Bioinformatics on p. i53-i61

Reconstructing antibody repertoires from error-prone immunosequencing reads

Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze, Maria A. Turchaninova, Yana Safonova, Pavel A. Pevzner, 2017, Journal of Immunology on p. 3369-3380

IgSimulator: A versatile immunosequencing simulator

Yana Safonova, Alla Lapidus, Jennie Lill, 2015, Bioinformatics on p. 3213-3215