Evidence map›Paper›PMID 40027781›Full record

ArticlebioRxiv : the preprint server for biology2025

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

Perry T Wasdin, Nicole V Johnson, Alexis K Janke, Sofia Held, Toma M Marinov, Gwen Jordaan, Léna Vandenabeele, Fani Pantouli, Rebecca A Gillespie, Matthew J Vukovich and 13 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

23 authors.

Perry T WasdinProgram in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.ORCID 0000-0001-7351-2048
Nicole V JohnsonDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA.
Alexis K JankeVanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Sofia HeldDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Toma M MarinovCenter for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN, 37232, USA.
Gwen JordaanVanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Léna VandenabeeleDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Fani PantouliFlorida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA.
Rebecca A GillespieVaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
Matthew J VukovichVanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Clinton M HoltProgram in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.
Jeongryeol KimDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA.
Grant HansmanInstitute for Biomedicine and Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, Australia.
Jennifer LogueDivision of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA.
Helen Y ChuDivision of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA.
Sarah F AndrewsVaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
Masaru KanekiyoVaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
Giuseppe A SauttoFlorida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA.
Ted M RossFlorida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, 34987 FL, USA.
Daniel J ShewardDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Jason S McLellanDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712 USA.
Alexandra A Abu-ShmaisVanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Ivelin S GeorgievProgram in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN, USA.

Funding

VANDERBILT UNIVERSITY CTSA FOR PEDIATRIC RESEARCHUL1RR024975 · NCRR · VANDERBILT UNIVERSITY · PI BERNARD, GORDON RAPHAEL · 2007 to 2011
$45.7M
High-throughput mapping of antigen specificity to B-cell-receptor sequence for characterizing antibody responses in HIV-vaccinated and infected individualsR01AI152693 · NIAID · VANDERBILT UNIVERSITY MEDICAL CENTER · PI GEORGIEV, IVELIN · 2020 to 2023
$3.4M
Technologies for High-Throughput Mapping of Antigen Specificity to B-Cell-Receptor SequenceR01AI175245 · NIAID · VANDERBILT UNIVERSITY MEDICAL CENTER · PI Ivelin Georgiev · 2023 to 2026
$3.4M
NCRR NIH HHS UL1 RR024975NIAID NIH HHS R01 AI152693NIAID NIH HHS R01 AI175245
6 · The paper itself

Abstract

The traditional process of antibody discovery is limited by inefficiency, high costs, and low success rates. Recent approaches employing artificial intelligence (AI) have been developed to optimize existing antibodies and generate antibody sequences in a target-agnostic manner. In this work, we present MAGE (Monoclonal Antibody GEnerator), a sequence-based Protein Language Model (PLM) fine-tuned for the task of generating paired human variable heavy and light chain antibody sequences against targets of interest. We show that MAGE can generate novel and diverse antibody sequences with experimentally validated binding specificity against SARS-CoV-2, an emerging avian influenza H5N1, and respiratory syncytial virus A (RSV-A). MAGE represents a first-in-class model capable of designing human antibodies against multiple targets with no starting template.

Identifiers

PMID40027781
PMCPMC11870394

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.