The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Benchmarking unsupervised methods for inferring TCR specificity
Open accessPreprint — published as 10.1093/nargab/lqaf150
Abstract
Identifying T cell receptor (TCR) specificity is crucial for advancing the understanding of adaptive immunity. Despite the development of computational methods to infer TCR specificity, their performance has not been thoroughly compared. We addressed this by curating a unified database of 190,670 human TCRs with known specificities for 2,313 epitopes across 121 organisms, combining data from IEDB, McPAS-TCR, and VDJdb. Nine methods for clustering TCRs based on similarity were benchmarked against this dataset. DeepTCR demonstrated the best retention, while ClusTCR, TCRMatch, and GLIPH2 excelled in cluster purity but had lower retention. DeepTCR, Levenshtein distance, and TCRdist3 generated large clusters, with DeepTCR showing high purity. Smaller, antigen-specific clusters were produced by Hamming distance, GIANA, and iSMART. GLIPH2 and DeepTCR were the most sensitive in capturing antigen-specific TCRs. This study offers a unified TCR database and a benchmark of specificity inference methods, guiding researchers in selecting appropriate tools.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Varadi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1011 · Cited by 2,052
Flagged first, then by citations
Research works printed but not linked: 35
- 10.1038/309322a0 · DOI
- 10.1038/334395a0 · DOI · Paper page
- 10.1016/S0167-5699(98)01299-7 · DOI
- V. Levenshtein , ‘Binary codes capable of correcting deletions, insertions, and reversals’, Sov. Phys. Dokl., 1965, Accessed: May 09, 2024. [Online]. Available: https://www.semanticscholar.org/paper/Binary-codes-capable-of-correcting-deletions%2C-and-Levenshtein/b2f8876482c97e804bb50a5e2433881ae31d0cdd
- 10.7554/eLife.22057 · DOI
- 10.1016/S1074-7613(02)00427-2 · DOI · Paper page
- 10.1101/2020.12.11.418426 · DOI
- 10.7554/eLife.68605 · DOI
- 10.1101/2021.02.22.432291 · DOI
- 10.1158/1078-0432.CCR-19-3249 · DOI
- 10.1038/s41467-021-25006-7 · DOI
- 10.1038/s41587-020-0505-4 · DOI · Paper page
- 10.1038/s41467-021-21879-w · DOI
- 10.1038/s41577-023-00835-3 · DOI
- 10.1093/nar/gky1006 · DOI
- 10.1093/nar/gkx760 · DOI
- 10.1093/bioinformatics/btx286 · DOI
- 10.1101/gr.1239303 · DOI · Paper page
- 10.1038/s41592-022-01578-0 · DOI
- 10.7554/eLife.81274 · DOI
- 10.1074/jbc.M111.289488 · DOI
- 10.1038/nmeth.1345 · DOI · Paper page
- 10.3389/fimmu.2021.664514 · DOI
- 10.1016/j.cell.2023.06.020 · DOI · Paper page
- 10.1016/j.cell.2014.03.047 · DOI
- 10.1016/j.celrep.2017.03.072 · DOI
- 10.4049/jimmunol.2300141 · DOI
- 10.4049/immunohorizons.2200062 · DOI
- 10.3389/fimmu.2023.1116906 · DOI
- 10.1016/j.molimm.2021.07.020 · DOI
- 10.1093/nar/gkad356 · DOI
- 10.1111/imm.13641 · DOI
- 10.1073/pnas.89.22.10915 · DOI · Paper page
- 10.1038/nature22383 · DOI
- 10.1038/nature22976 · DOI · Paper page
Metadata
- Authors
- Jouannet, C., Vantomme, H., Klatzmann, D., & Mariotti-Ferrandiz, E.
- Affiliations
- Inserm (FR)
- Venue
- NAR Genomics and Bioinformatics
- Publisher
- openRxiv
- Published
- 2024-10-29
- Volume
- 7
- Issue
- 4
- Pages
- lqaf150-lqaf150
- ISSN
- 2631-9268 (ISSN-L)
- PMC
- PMC12629845
- OpenAlex
- W4416380430
- Cited by
- 15
- References
- 2
- Citations by year
- 2026: 12 · 2025: 3
- FWCI
- 1.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- NAR Genomics and Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Agence Nationale de la Recherche (ANR-16-RHUS-0001, ANR-23-CE17-0039, ANR-21-CO12-0005, ANR-18-ECVD-0001)
- Institut Universitaire de France
- Sorbonne Université
- H2020 European Research Council (322856)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Physical Sciences › Computer Science › Artificial Intelligence › Artificial Immune Systems Applications
- Keywords
- T cell receptor, TCR clustering, benchmarking, CDR3 motifs, adaptive immunity
- MeSH terms
- Algorithms, Humans, Receptors, Antigen, T-Cell, Cluster Analysis, Computational Biology, Benchmarking
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
