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Generation of antigen-specific paired chain antibody sequences using large language models.

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Title: Generation of antigen-specific paired chain antibody sequences using large language models.
Authors: Wasdin PT; Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA., Johnson NV; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA., Janke AK; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA., Held S; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden., Marinov TM; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA., Jordaan G; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA., Vandenabeele L; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden., Pantouli F; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA., Gillespie RA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA., Vukovich MJ; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA., Holt CM; Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA., Kim J; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA., Hansman G; Institute for Biomedicine and Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, Australia., Logue J; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA., Chu HY; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA., Andrews SF; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA., Kanekiyo M; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA., Sautto GA; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA., Ross TM; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA., Sheward DJ; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden., McLellan JS; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA., Abu-Shmais AA; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA., Georgiev IS; Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN.; Department of Computer Science, Vanderbilt University, Nashville, TN.; Center for Structural Biology, Vanderbilt University, Nashville, TN.; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237 USA.
Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Mar 26. Date of Electronic Publication: 2025 Mar 26.
Publication Type: Journal Article; Preprint
Journal Info: 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
Database: MEDLINE Ultimate
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PubType: Academic Journal
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  Data: Generation of antigen-specific paired chain antibody sequences using large language models.
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  Data: <searchLink fieldCode="AU" term="%22Wasdin+PT%22">Wasdin PT</searchLink>; Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.<br /><searchLink fieldCode="AU" term="%22Johnson+NV%22">Johnson NV</searchLink>; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA.<br /><searchLink fieldCode="AU" term="%22Janke+AK%22">Janke AK</searchLink>; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.<br /><searchLink fieldCode="AU" term="%22Held+S%22">Held S</searchLink>; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.<br /><searchLink fieldCode="AU" term="%22Marinov+TM%22">Marinov TM</searchLink>; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.<br /><searchLink fieldCode="AU" term="%22Jordaan+G%22">Jordaan G</searchLink>; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.<br /><searchLink fieldCode="AU" term="%22Vandenabeele+L%22">Vandenabeele L</searchLink>; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.<br /><searchLink fieldCode="AU" term="%22Pantouli+F%22">Pantouli F</searchLink>; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA.<br /><searchLink fieldCode="AU" term="%22Gillespie+RA%22">Gillespie RA</searchLink>; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.<br /><searchLink fieldCode="AU" term="%22Vukovich+MJ%22">Vukovich MJ</searchLink>; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.<br /><searchLink fieldCode="AU" term="%22Holt+CM%22">Holt CM</searchLink>; Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.<br /><searchLink fieldCode="AU" term="%22Kim+J%22">Kim J</searchLink>; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA.<br /><searchLink fieldCode="AU" term="%22Hansman+G%22">Hansman G</searchLink>; Institute for Biomedicine and Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, Australia.<br /><searchLink fieldCode="AU" term="%22Logue+J%22">Logue J</searchLink>; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA.<br /><searchLink fieldCode="AU" term="%22Chu+HY%22">Chu HY</searchLink>; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA.<br /><searchLink fieldCode="AU" term="%22Andrews+SF%22">Andrews SF</searchLink>; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.<br /><searchLink fieldCode="AU" term="%22Kanekiyo+M%22">Kanekiyo M</searchLink>; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.<br /><searchLink fieldCode="AU" term="%22Sautto+GA%22">Sautto GA</searchLink>; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA.<br /><searchLink fieldCode="AU" term="%22Ross+TM%22">Ross TM</searchLink>; Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA.<br /><searchLink fieldCode="AU" term="%22Sheward+DJ%22">Sheward DJ</searchLink>; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.<br /><searchLink fieldCode="AU" term="%22McLellan+JS%22">McLellan JS</searchLink>; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA.<br /><searchLink fieldCode="AU" term="%22Abu-Shmais+AA%22">Abu-Shmais AA</searchLink>; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.<br /><searchLink fieldCode="AU" term="%22Georgiev+IS%22">Georgiev IS</searchLink>; Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.; Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.; Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN.; Department of Computer Science, Vanderbilt University, Nashville, TN.; Center for Structural Biology, Vanderbilt University, Nashville, TN.; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237 USA.
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  Data: <searchLink fieldCode="JN" term="%22101680187%22">BioRxiv : the preprint server for biology</searchLink> [bioRxiv] 2025 Mar 26. <i>Date of Electronic Publication: </i>2025 Mar 26.
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