(* corresponding author, ✝ leading author, members of the lab are bolded)

2025

Safonova Y✝*, Collins A, Murdoch BM, Rosen BJ, Smith TPL, Watson CT. Immunogenomics Approaches to Studying Antibody Repertoires and Vaccine Responses in Ruminants. Annual Reviews of Animal Biosciences. 2025, 14. [early version]

Olagunju TA, Pospelova M, Schwartz SC, Mousel MR, Piel LMW, Grossman PC, Huyvaert KP, Kuhn KL, Raihan T, Stegemiller MR, Khilji SF, Murdoch GK, Tibary A, Waits LP, Rhie A, Koren S, Phillippy AM, McKay SD, Clarke SM, Clark EL, Brauning R, Cockett NE, Hammond JA, Highland M, Safonova Y, Smith TPL, Rosen BD, Murdoch BM. Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens. bioRxiv. [preprint]

Pospelova M✝, Safonova Y*. PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences. Bioinformatics. 2025. 41(10): btaf504. [link]

Song G, Yuan M, Liu H, Capozzola T, Lin RN, Torres JL, He WT, Musharrafieh R, Dueker K, Zhou P, Callaghan S, Mishra N, Yong P, Anzanello F, Avillion G, Vo AL, Li X, Makhdoomi M, Feng Z, Zhu X, Peng L, Nemazee D, Safonova Y, Briney B, Ward AB, Burton DR, Wilson IA, Andrabi R. Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift. Cell Reports. 2025 Jul 22;44(7). [link]

Kos JT, Safonova Y, Shields KM, Silver CA, Lees WD, Collins AM, Watson CT. Characterization of extensive diversity in immunoglobulin light chain variable germline genes across biomedically important mouse strains. ImmunoHorizons. 2025. 9(8):vlaf031. [link]

Collins AM, Watson CT, van den Hamc H-J, Teyton L, Rosati E*, Safonova Y*. Challenges for the Immunoglobulin and T cell receptor gene nomenclatures in the modern genomics era. ImmunoInformatics. 2025. [link]

Pospelova M✝, Voss K, Zamyatin A, Watson CT, Koepfli K-P, Bankevich A, Pennell M, Safonova Y*. Comparative analysis of mammalian adaptive immune loci revealed spectacular divergence and common genetic patterns. Molecular Biology and Evolution. 2025. msaf152. [link]

Zhu Y, Watson C, Safonova Y*, Pennell M*, Bankevich A*. CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies. Genome Biology. 2025. 26, 131. [link] 

Lin MJ✝, Langmead B*, Safonova Y*. IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads. Cell Reports Methods. 2025 May 1. [link]

Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. Nature. 2025. [link] 

2024

Kalbfleisch T,  McKay S, Murdoch B, Adelson DL, Almansa D, Becker G, Beckett LM, Benítez-Galeano MJ, Biase F, Casey T, Chuong E, Clark E, Clarke S, Cockett N, Couldrey C, Davis BW, Elsik CG, Faraut T, Gao Y, Genet C, Grady P, Green J, Green R, Guan, D, Hagen D, Hartley GA, Heaton M, Hoyt SJ, Huang W, Jarvis E, Kalleberg J, Khatib H, Koepfi K, Koltes J, Koren S, Kuehn C, Leeb T, Leonard A, Liu GE, Low WY, McConnell H, McRae K, Miga K, Mousel M, Neibergs H, O'Neill R, Olagunju T, Pennell M, Petry B, Pewsner M, Phillippy AM, Pickett BD, Pineda P, Potapova T, Rachagani S, Rhie A, Rijnkels M, Robic A, Osorio NR, Safonova Y, Schettini G, Schnabel RD, Natesh NS, Stegemiller M, Storer J, Stothard P, Stull C, Tosser-Klopp G, Traglia GM, Tuggle C, Tassell CPV, Watson C, Weikard R, Wimmers K, Xie S, Yang L, Smith T, Rosen B. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics. 2024. 5:1-8. [link]

Watson CT, Rodriguez OL, Engelbrecht E, Safonova Y, Marasco WA, Smith ML. Looking to the future of antibody genetics: resolving the roles of immunoglobulin diversity in gene regulation, function, and immunity. Genes & Immunity. 2024 Feb;25(1):92-4. [link] 

2023

Musharrafieh R, Safonova Y✝, Song G, Roark RS, Lee FH, Zhang S, Hurtado J, Yong P, Wang S, Russell RM, Ding W. Germline-targeting chimpanzee SIV Envelopes induce V2-apex broadly neutralizing-like B cell precursors in a rhesus macaque infection model. bioRxiv. 2023. [preprint]

Pospelova M✝, Safonova Y*. Analyzing patterns of tyrosine sulfation in naive antibody repertoires. bioRxiv. 2023. [preprint]

Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd S, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nature Communications. 2023. 14, 4419. [link]

Zhou P, Song G, He W, Beutler N, Tse LV, Martinez DR, Schäfer A, Anzanello F, Yong P , Peng L, Dueker K, Musharrafieh R, Callaghan S, Capozzola T, Yuan M, Liu H, Limbo O, Parren M, Garcia E, Rawlings SA, Smith DM, Nemazee D, Jardine JG, Wilson IA, Safonova Y, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease. Immunity. 2023. 56(3):669-86. [link]

2022

Zhang C, Bzikadze AV, Safonova Y, Mirarab S. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Frontiers in Immunology. 2022;13. [link]

Jenkins GW, Safonova Y, Smider VV. Germline-Encoded Positional Cysteine Polymorphisms Enhance Diversity in Antibody Ultralong CDR H3 Regions. Journal of Immunology. 2022 Oct 21. [link]

He W-T, Yuan M, Callaghan S, Musharrafieh R, Song G, Silva M, Beutler N, Lee W, Yong P, Torres J, Melo M, Zhou P, Zhao F, Zhu X, Peng L, Huang D, Anzanello F, Ricketts J, Parren M, Garcia E, Ferguson M, Rinaldi W, Rawlings SA, Nemazee D, Smith DM, Briney B, Safonova Y, Rogers TF, Crotty S, Darrell J, Irvine DJ, Ward AB, Wilson IA, Burton DR, Andrabi R. Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques. Science Translational Medicine. 2022. 14 (657): eabl9605. [link]

Sirupurapu V, Safonova Y, Pevzner PA. Gene prediction in immunoglobulin loci. Genome Research. 2022. 32:1152-1169. [link]

He WT, Musharrafieh R, Song G, Dueker K, Tse LV, Martinez DR, Schäfer A, Callaghan S, Yong P, Beutler N, Torres JL, Volk RM, Zhou P, Yuan M, Yuan M, Liu H, Anzanello F, Capozzola T, Parren M, Garcia E, Rawlings SA, Smith DM, Wilson IA, Safonova Y, Ward AB, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Targeted isolation of panels of diverse human broadly neutralizing antibodies against SARS-like viruses. Nature Immunology. 2022. 23:960–970. [link]

Safonova Y✝, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Research. 2022. 32:791-804. [link]

2021

Lee JH, Toy L, Kos JT, Safonova Y, Schief WR, Havenar-Daughton C, Watson CT, Crotty S. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells. npj Vaccines. 2021. 6(1):1-12. [link]

Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Trace reconstruction problems in computational biology. IEEE Transactions on Information Theory (special issue). 2021. June 67(6):3295-314. [link]

Peng K, Safonova Y, Shugay M, Popejoy A, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau V-M, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, Jonsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT, Karlsson Hedestam GB, Mangul S. Diversity in immunogenomics: the value and the challenge. Nature Methods. 2021. 17:1-4. [link]

Akbar R, Jeliazkov JR, Robert PA, Snapkov I, Pavlović M, Slabodkin A, Weber CR, Safonova Y, Sandve GK, Greiff V. A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Cell Reports. 2021. 34(11): 108856. [link]