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In Cell Reports 22 July 2025 44(7)

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

In Cell Reports 16 March 2021 34(11)

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In ImmunoInformatics September 2025 19

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ImmunoHorizons; Aug2025, Vol. 9 Issue 8, p1-13, 13p

Pospelova, Mariia; Voss, Katalin; Zamyatin, Anton; Watson, Corey T; Koepfli, Klaus-Peter; Bankevich, Anton; Pennell, Matt; Safonova, Yana

Molecular Biology & Evolution; Jul2025, Vol. 42 Issue 7, p1-14, 14p

Zhu, Yixin; Watson, Corey; Safonova, Yana; Pennell, Matt; Bankevich, Anton

Genome Biology (Online Edition). May 20, 2025, Vol. 26 Issue 1

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Nature: International weekly journal of science. 641(8062):401-418

Bhardwaj, Vinnu; Franceschetti, Massimo; Rao, Ramesh; Pevzner, Pavel A.; Safonova, Yana

PLoS Computational Biology. 4/27/2020, Vol. 16 Issue 4, p1-28. 28p. 1 Color Photograph, 5 Charts, 16 Graphs.

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Nature Genetics. 56:1566-1573

Safonova, Yana; Pevzner, Pavel A.

Safonova Y; Computer Science and Engineering Department and Huck Institutes of Life Sciences, Pennsylvania State University, State College, Pennsylvania, USA; email: yana@psu.edu.; Collins A; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.; Murdoch BM; Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, Idaho, USA.; Rosen BD; Animal Genomics and Improvement Laboratory, USDA ARS, Beltsville, Maryland, USA.; Smith TPL; US Meat Animal Research Center, USDA ARS, Clay Center, Nebraska, USA.; Watson CT; Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA.

Publisher: Annual Reviews Country of Publication: United States NLM ID: 101614024 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2165-8110 (Electronic) Linking ISSN: 21658102 NLM ISO Abbreviation: Annu Rev Anim Biosci Subsets: MEDLINE

Dueker K; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Capozzola T; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.; Feng Z; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Lin RN; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Hurtado J; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Bangaru S; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Yuan M; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Beutler N; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Garcia E; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; He WT; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Callaghan S; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Avillion G; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Vo L; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.; Li X; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.; Torres JL; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Musharrafieh R; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Song G; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Mishra N; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Sharma P; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Yong P; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Anzanello F; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Kaczmarek-Michaels K; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Ben-Akiva E; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Silva M; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Melo M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.; Makhdoomi M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Westfall-Gomez E; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Rinaldi W; Alpha Genesis, Yemassee, SC 29945, USA.; Ferguson M; Alpha Genesis, Yemassee, SC 29945, USA.; Safonova Y; Computer Science and Engineering Department, Huck Institutes of the Life Sciences, Penn State University, State College, PA 16801, USA.; Crotty S; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.; Irvine DJ; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.; Rogers T; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.; Ward AB; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Briney B; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Wilson IA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.; Burton DR; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.; Andrabi R; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.; Lead Contact.

Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Shlemov, Alexander; Bankevich, Sergey; Bzikadze, Andrey; Turchaninova, Maria A.; Safonova, Yana; Pevzner, Pavel A.

Shlemov, Alexander; Bankevich, Sergey; Bzikadze, Andrey; Safonova, Yana

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

Nature Communications; 7/21/2023, Vol. 14 Issue 1, p1-18, 18p