ArticleNucleic acids research2022
Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 45 citations in OpenAlex.
- Structure-based TCR-pMHC binding prediction and generalization to unseen peptides.npj drug discovery · 2026Article
- Systematic analysis of CDR contacts and pairing constraints between T cell receptor αβ chains.Bioinformatics (Oxford, England) · 2026Article
- Ensembles ofbioRxiv : the preprint server for biology · 2026Article
- Coincident epithelial signals restrain commensal-specific CD8αβbioRxiv : the preprint server for biology · 2026Article
- Healthy donor T cell receptors expand functional neoantigen recognition beyond patient vaccination.Science advances · 2026Article
- TCR Repertoire Analysis Unveils the Link Between Kawasaki Disease and Viral Infection.Biomedicines · 2026Article
- Article
- Mutant KRAS vaccine with dual checkpoint blockade in resected pancreatic cancer: a phase I trial.Nature communications · 2026Article
- Peptide-driven identification of TCRs reveals dynamics and phenotypes of CD4 T cells in tuberculosis.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- DecoderTCR: Compositional Pretraining and Entropy-Guided Decoding for TCR-pMHC Interactions.bioRxiv : the preprint server for biology · 2026Article
- Structural quality-tier assessment for TCR-pMHC functional enrichment.Frontiers in immunology · 2026Article
- Benchmarking of T cell receptor-epitope predictors with ePytope-TCR.Cell genomics · 2025Article
- nuTCRacker: Predicting the Recognition of HLA-I-Peptide Complexes by αβTCRs for Unseen Peptides.European journal of immunology · 2025Article
- Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction.bioRxiv : the preprint server for biology · 2025Article
- TCRCluster: a novel approach to T-cell receptor latent featurization and clustering using contrastive learning-guided two-stage variational autoencoders.NAR genomics and bioinformatics · 2025Article
- Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.Nucleic acids research · 2025Article
- STAG-LLM: Predicting TCR-pHLA binding with protein language models and computationally generated 3D structures.Computational and structural biotechnology journal · 2025Article
- Exploring the potential of structure-based deep learning approaches for T cell receptor design.PLoS computational biology · 2024Article
- Influenza vaccination stimulates maturation of the human T follicular helper cell response.Nature immunology · 2024Article
- Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
The study and manipulation of T cell receptors (TCRs) is central to multiple fields across basic and translational immunology research. Produced by V(D)J recombination, TCRs are often only recorded in the literature and data repositories as a combination of their V and J gene symbols, plus their hypervariable CDR3 amino acid sequence. However, numerous applications require full-length coding nucleotide sequences. Here we present Stitchr, a software tool developed to specifically address this limitation. Given minimal V/J/CDR3 information, Stitchr produces complete coding sequences representing a fully spliced TCR cDNA. Due to its modular design, Stitchr can be used for TCR engineering using either published germline or novel/modified variable and constant region sequences. Sequences produced by Stitchr were validated by synthesizing and transducing TCR sequences into Jurkat cells, recapitulating the expected antigen specificity of the parental TCR. Using a companion script, Thimble, we demonstrate that Stitchr can process a million TCRs in under ten minutes using a standard desktop personal computer. By systematizing the production and modification of TCR sequences, we propose that Stitchr will increase the speed, repeatability, and reproducibility of TCR research. Stitchr is available on GitHub.
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Registered trials
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.