ArticleScience (New York, N.Y.)2025
Disease diagnostics using machine learning of B cell and T cell receptor sequences.
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Article in Science (New York, N.Y.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61citing papers in PubMed
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Who cites it
61 citing papers in PubMed.
- Dynamic involvement of the core gut microbiome XNP_Guild1 in the evolution of gestational diabetes mellitus.Gut microbes · 2026Article
- How Big Data and AI are revolutionizing human immunology.Nature reviews. Immunology · 2026Article
- Article
- T Cell Thoughts.Immunological reviews · 2026Review
- Unsupervised identification of low-frequency antigen-specific TCRs using distance-based anomaly scoring.Briefings in bioinformatics · 2026Article
- Naïve adaptive immune receptor repertoires in celiac disease assessed by machine learning; impact of the HLA-DQ2.5 allotype on the TCR repertoire.Immunogenetics · 2026Article
- Machine Learning of Personal Repertoires From Public T Cell Receptors.Immunological reviews · 2026Review
- Integrating structurally defined DNA-carbon nanotube sensors with machine learning for cancer detection.Science advances · 2026Article
- Language Model Embedding Classifiers Enable Identification of Multiple Sclerosis-Associated BCRs and Repertoires.bioRxiv : the preprint server for biology · 2026Article
- A multi-fidelity tabular prior-data fitted network model for accurate prediction and uncertainty quantification.Nature communications · 2026Article
- Modeling TCR-Epitope Recognition Specificity: What We Should Learn to Succeed.Immunological reviews · 2026Review
- The T Cell Receptor: Molecular Sensor, Therapeutic Mediator and Probabilistic Driver of Adaptive Immunity.Immunological reviews · 2026Review
- Innovative strategies for diabetic peripheral neuropathy: From clinical management to emerging bioengineering solutions.Bioactive materials · 2026Review
- Biographical Feature: Benjamin A. Pinsky, MD, PhD.Journal of clinical microbiology · 2026Article
- Synthetic rewriting of the IGH locus.Cell genomics · 2026Article
- Pre-transplant TCR Network Topology Predicts Kidney Allograft Rejection Independent of HLA Mismatch.bioRxiv : the preprint server for biology · 2026Article
- T Cell Receptor Repertoires Across the Continuum of Vascular, Myocardial, and Age-Related Diseases.Immunological reviews · 2026Review
- Advances in predicting T cell epitope recognition for cancer immunotherapy.Nature cancer · 2026Review
- Protein foundation models: a comprehensive survey.Science China. Life sciences · 2026Review
- Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
37 authors.
Maxim E Zaslavsky *Department of Computer Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-4300-7854
Erin Craig *Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0002-4893-6671
Jackson K MichudaDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-0850-7693
Nidhi SehgalDepartment of Genetics, Stanford University, Stanford, CA, USA.
Nikhil Ram-MohanDepartment of Emergency Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0002-7761-2772
Ji-Yeun LeeDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID 0000-0002-0463-6802
Khoa D NguyenDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID 0000-0003-3149-3621
Ramona A HohDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID 0000-0002-5116-1942
Tho D PhamDepartment of Pathology, Stanford University, Stanford, CA, USA.
Katharina RöltgenDepartment of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland.ORCID 0000-0002-1582-1720
Brandon LamDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID 0000-0001-9737-2000
Ella S ParsonsSean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA.ORCID 0000-0002-9967-4173
Susan R MacwanaDepartment of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.ORCID 0009-0005-0007-0206
Wade DeJagerDepartment of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.ORCID 0009-0009-3333-5820
Elizabeth M DrapeauDepartment of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0002-8243-6478
Krishna M RoskinDepartment of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA.ORCID 0000-0002-5864-5093
Charlotte Cunningham-RundlesIcahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID 0000-0003-0725-0320
M Anthony MoodyDepartment of Pediatrics, Duke University, Durham, NC, USA.ORCID 0000-0002-3890-5855
Barton F HaynesDuke Human Vaccine Institute, Duke University, Durham, NC, USA.ORCID 0000-0002-7643-9023
Jason D GoldmanSwedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA.ORCID 0000-0002-3825-6832
James R HeathInstitute for Systems Biology, Seattle, WA, USA.ORCID 0000-0001-5356-4385
R Sharon ChinthrajahSean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA.
Kari C NadeauDepartment of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.ORCID 0000-0002-2146-2955
Benjamin A PinskyDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID 0000-0001-8751-4810
Catherine A BlishDepartment of Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0001-6946-7627
Scott E HensleyDepartment of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0002-2928-7506
Kent JensenDepartment of Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0001-9721-4379
Everett MeyerDepartment of Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0001-7953-853X
Imelda BalboniDepartment of Pediatrics, Stanford University, Stanford, CA, USA.ORCID 0000-0001-8231-1352
Paul J UtzDepartment of Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1181-1565
Joan T MerrillDepartment of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.ORCID 0000-0002-4514-2382
Joel M GuthridgeDepartment of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.ORCID 0000-0002-9308-237X
Judith A JamesDepartment of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.ORCID 0000-0002-9574-7355
Samuel YangDepartment of Emergency Medicine, Stanford University, Stanford, CA, USA.ORCID 0000-0003-1123-9036
Robert TibshiraniDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-0553-5090
Anshul Kundaje *Department of Computer Science, Stanford University, Stanford, CA, USA.ORCID 0000-0003-3084-2287
Scott D Boyd *Department of Pathology, Stanford University, Stanford, CA, USA.ORCID 0000-0003-0963-044X
Funding
Virus biology scientific research support componentUM1AI100645 · NIAID · DUKE UNIVERSITY · PI HAYNES, BARTON F. · 2012 to 2018
$204.7MNonhuman primate studies for development of a prototype HIV vaccine that induces broadly neutralizing antibodiesUM1AI144371 · NIAID · DUKE UNIVERSITY · PI HAYNES, BARTON F. · 2019 to 2025
$190.4MUsing a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5MNIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00015 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HENSLEY, SCOTT · 2021 to 2025
$50.7MStanford Islet Research CoreP30DK116074 · NIDDK · STANFORD UNIVERSITY · PI Seung K Kim · 2017 to 2026
$19.5MSystems biological assessment of T cell responses to vaccinationU19AI167903 · NIAID · STANFORD UNIVERSITY · PI BALI PULENDRAN · 2022 to 2026
$13.2MProject 3: T CellsU54CA260517 · NCI · STANFORD UNIVERSITY · PI DAVIS, MARK MORRIS · 2020 to 2024
$10.4MOklahoma Rheumatic Disease Research Cores Center (Overall Application)P30AR073750 · NIAMS · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI JUDITH A JAMES · 2018 to 2026
$8.5MResources to Assist Investigations in Primary Immunodeficiency Diseases (U24)U24AI086037 · NIAID · IMMUNE DEFICIENCY FOUNDATION · PI CUNNINGHAM-RUNDLES, CHARLOTTE · 2010 to 2019
$6.5MTARGETING PRIMARY IMMUNODEFICIENCY AMONG MINORITIESR18AI048693 · NIAID · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI CUNNINGHAM-RUNDLES, CHARLOTTE · 2000 to 2016
$6.2MNew Statistical Methods for Medical Signals and ImagesR01EB001988 · NIBIB · STANFORD UNIVERSITY · PI JOHNSTONE, IAIN M · 2003 to 2018
$6.1MAutoimmune Drivers and Protectors Team Science (ADAPTS)U01AI176244 · NIAID · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI JUDITH A JAMES, Jeffrey C Rathmell · 2023 to 2026
$5.1MNCI NIH HHS R01 CA264090NCI NIH HHS U54 CA260517NIAID NIH HHS 75N93021C00015NIAID NIH HHS R01 AI127877NIAID NIH HHS R01 AI130398NIAID NIH HHS R01 AI137272NIAID NIH HHS R01 AI153133NIAID NIH HHS R01 AI175771NIAID NIH HHS R18 AI048693NIAID NIH HHS R21 AI101093NIAID NIH HHS U01 AI176244NIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI167903NIAID NIH HHS U24 AI086037NIAID NIH HHS UM1 AI100645NIAID NIH HHS UM1 AI144292NIAID NIH HHS UM1 AI144371NIAMS NIH HHS P30 AR073750NIBIB NIH HHS R01 EB001988NIDDK NIH HHS P30 DK116074NIGMS NIH HHS R01 GM134483
Abstract
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system's own record of antigen exposures encoded by receptors on B cells and T cells. We analyzed immune receptor datasets from 593 individuals to develop MAchine Learning for Immunological Diagnosis, an interpretive framework to screen for multiple illnesses simultaneously or precisely test for one condition. This approach detects specific infections, autoimmune disorders, vaccine responses, and disease severity differences. Human-interpretable features of the model recapitulate known immune responses to severe acute respiratory syndrome
Indexed as
Autoimmune DiseasesB-LymphocytesInfectionsMachine LearningReceptors, Antigen, B-CellReceptors, Antigen, T-CellCOVID-19Diabetes Mellitus, Type 1HIV InfectionsHumansInfluenza, HumanLupus Erythematosus, SystemicSARS-CoV-2Receptors, Antigen, B-CellReceptors, Antigen, T-Cell
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