Evidence map›Paper›PMID 41126882›Full record

ArticleiScience2025

Integrated antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy.

Hannah F Almubarak, Wuwei Tan, Andrew D Hoffmann, Yuanfei Sun, Juncheng Wei, Lamiaa El-Shennawy, Joshua R Squires, Nurmaa K Dashzeveg, Brooke Simonton, Yuzhi Jia and 11 more

Abstract read
In one paragraph

Article in iScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Hannah F AlmubarakDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Wuwei TanDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
Andrew D HoffmannDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Yuanfei SunDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
Juncheng WeiDepartment of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Lamiaa El-ShennawyDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Joshua R SquiresDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Nurmaa K DashzevegDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Brooke SimontonDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Yuzhi JiaDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Radhika IyerDepartment of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Yanan XuDepartment of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Vlad NicolaescuHoward T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637, USA.
Derek ElliHoward T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637, USA.
Glenn C RandallHoward T. Ricketts Laboratory and Department of Microbiology, the University of Chicago, Chicago, IL 60637, USA.
Matthew J SchipmaNUseq Core Facility, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Suchitra SwaminathanRobert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Michael G IsonRockville, MD 20892, USA.
Huiping LiuDepartment of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Deyu FangDepartment of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Yang ShenDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.

Funding

Tumor Environment and Metastasis (TEAM) Research ProgramP30CA060553 · NCI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Devalingam Mahalingam · 1993 to 2026
$153.9M
Univ.of Calif., Irvine Cancer Center Support GrantP30CA062203 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Melanie Funes · 1994 to 2026
$57.9M
Northwestern University Clinical and Translational Science Institute (NUCATS)UL1TR001422 · NCATS · NORTHWESTERN UNIVERSITY AT CHICAGO · PI D'AQUILA, RICHARD · 2015 to 2023
$56.8M
Facility Management, Maintenance and Operations CoreUC7AI180312 · NIAID · UNIVERSITY OF CHICAGO · PI Dominique Missiakas · 2023 to 2026
$12.4M
Clinical analysis and therapeutic development of exosomal ACE2R01AI167272 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Deyu Fang, Huiping Liu · 2022 to 2026
$3.6M
Unraveling molecular and system-level mechanisms of human disease-associated protein mutationsR35GM124952 · NIGMS · TEXAS ENGINEERING EXPERIMENT STATION · PI Yang Shen · 2017 to 2026
$2.9M
Develop a novel therapy with immuno- and onco-targeting dual efficacies to treat the triple negative breast cancerR01CA288387 · NCI · NORTHWESTERN UNIVERSITY · PI Deyu Fang, Huiping Liu · 2025 to 2026
$1.3M
A streamlined platform for phosphoproteome mapping of human tissuesUH3CA256967 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI LIU, HUIPING, SHI, TUJIN · 2022 to 2023
$1.2M
Novel functions of PlexinB2 in circulating tumor cell clustersR01CA298232 · NCI · NORTHWESTERN UNIVERSITY · PI Huiping Liu · 2025 to 2026
$1.1M
5-laser 30-parameter FACSymphony-S6 SORP Cell Sorter from BD BiosciencesS10OD026814 · OD · NORTHWESTERN UNIVERSITY AT CHICAGO · PI PERLMAN, HARRIS R · 2019 to 2019
$904k
A streamlined platform for phosphoproteome mapping of human tissuesUG3CA256967 · NCI · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI LIU, HUIPING, SHI, TUJIN · 2020 to 2021
$800k
FACSAria SORP Cell SorterS10OD011996 · OD · NORTHWESTERN UNIVERSITY AT CHICAGO · PI GOOLSBY, CHARLES L. · 2012 to 2012
$482k
NCATS NIH HHS UL1 TR001422NCI NIH HHS F31 CA287701NCI NIH HHS P30 CA060553NCI NIH HHS P30 CA062203NCI NIH HHS R01 CA288387NCI NIH HHS R01 CA298232NCI NIH HHS UG3 CA256967NCI NIH HHS UH3 CA256967NIAID NIH HHS R01 AI167272NIAID NIH HHS UC7 AI180312NIGMS NIH HHS R35 GM124952NIH HHS S10 OD011996NIH HHS S10 OD026814
6 · The paper itself

Abstract

Identifying highly efficacious, broad-spectrum antibodies against fast-mutating viral variants remains a major challenge in therapeutic development. Here, we developed AbGen, a machine learning-assisted antibody generation pipeline powered by an antibody language model (AbLM), to accelerate antibody screening and re-design. AbLM, pretrained on protein domain sequences and fine-tuned on paired VH-VL sequences, enables the analysis and prediction of neutralization activity against viruses (specifically SARS-CoV-2 in this study), targeting both wild-type (through antigen interaction prediction [docking]) and emerging variants (through Gaussian process regression [Kriging]). Screening over 1300 RBD-binding IgG sequences from convalescent patients, AbGen efficiently prioritized candidates for experimental validation and/or redesign against wild-type, Delta, and Omicron variants, preventing viral infections

Indexed as

BioinformaticsImmunological methodsImmunology

Identifiers

PMID41126882
PMCPMC12539245

What OpenQuestion holds

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Read underepoch 390

Registered trials

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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.