Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: paired ✕ Assay: tcr ✕ Clear

Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

PMID 41820396 · PMC13121706 · Nature communications · 2026 · 8 claims · 7 setups

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TRIM, a conditional multi-modal variational autoencoder integrating paired scRNAseq and scTCRseq data, predicts T cell clonality and transcriptional states at unmeasured tissue sites/timepoints.

hnscc colorectal pan-cancer tcr paired umap convolutional
Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

PMID 41794040 · PMC13006398 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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CSF exhibits distinct, disease-specific immune landscapes across CNSL, BrMs, and GB-associated LMD

csf peripheral brain cell-free single-cell deep spatial
Novel approaches for identifying target antigens of autoreactive human B and T cells.

PMID 19763575 · PMC2845891 · Seminars in immunopathology · 2009 · 8 claims · 8 setups

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CD8+ T cells infiltrating MS brain and IM muscle tissue show clonal expansions consistent with antigen-driven selection

muscle brain morphologically autopsy cdr3-spectratyping single-cell immunohistochemistry
Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

PMID 41782826 · PMC12955150 · iScience · 2026 · 8 claims · 6 setups

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Tet2-deficient NOD mice transplanted with WT bone marrow show fewer islet-infiltrating lymphocytes beginning 8–10 weeks post-transplant, primarily among CD4+ T cells

islets islet islet-infiltrating cadaveric flow single-cell single-nucleus
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies.

PMID 41503158 · PMC12770963 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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A comprehensive comparison of seven 3'/whole-transcriptome single-cell platforms and two 5' whole-transcriptome + TCR platforms was performed using PBMCs from multiple donors.

pbmcs sorted scrna-seq evercode
Unique phenotypic and T cell receptor characteristics of CD8(+) T cells accumulated in the brains of Alzheimer's disease mice.

PMID 41794902 · PMC13087195 · Scientific reports · 2026 · 8 claims · 5 setups

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Brain CD8+ T cells segregate into two major, mutually exclusive Trm populations: a CXCR6-related immunosuppressive cluster (cd8_c0) present in both aged non-Tg and 5xFAD_WT mice, and an AD-associated stem-like cluster (cd8_c1) present only in 5xFAD mice.

brain-derived brain cd8+ clonally scrna-seq paired cellchat
Clonal CD8(+) T cells populate the leptomeninges and coordinate with immune cells in human degenerative brain diseases.

PMID 41593242 · PMC12864034 · Nature immunology · 2026 · 8 claims · 6 setups

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The human leptomeninges harbor substantial numbers of clonally expanded, tissue-resident memory CD8 T cells (ZNF683-high, CXCR6+, PD-1+)

postmortem leptomeninges scrna-seq-derived leptomeningeal single-cell flow imaging
Antigen specificity of clonally enriched CD8(+) T cells in multiple sclerosis.

PMID 41644766 · PMC12956596 · Nature immunology · 2026 · 8 claims · 7 setups

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A subset of 23 highly expanded, CSF-enriched CD8+ T cell clonotypes exists predominantly in the CSF of the MS/CIS cohort.

paired cd8+ cd4+ csf single-cell differential pseudotime
Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

PMID 18312668 · PMC2275272 · BMC genomics · 2008 · 8 claims · 5 setups

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The conventional TCR loci (TRA/D, TRB, TRG) in opossum are highly conserved in organization and complexity with those of eutherian mammals.

monodelphis 23-day-old trav trbv comparative rt-pcr phylogenetic
RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction.

PMID 41734278 · PMC12975283 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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RUMINA improves detection accuracy of ultra-low frequency SNVs (0.01%-1%) compared to UMI-tools and UMICollapse

hiv simulated empirical clinical simulated umi iclip
Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.

PMID 41680899 · PMC12903587 · Genome medicine · 2026 · 7 claims · 6 setups

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A novel batch-effect correction method (log-normal gene usage modeling, Z-score normalization, and roulette-wheel resampling) allows combining AIRR-seq data from different batches and protocols.

blood peripheral batch-corrected airr-seq airr-seq hla tcrβ
Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma.

PMID 41519381 · PMC12983186 · Mucosal immunology · 2026 · 8 claims · 6 setups

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BAL and endobronchial brush sampling capture phenotypically and clonally distinct T cell populations

sorted paired bal subjects single-cell fluorescence-activated methacholine
Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

PMID 41526347 · PMC12852879 · Nature communications · 2026 · 8 claims · 8 setups

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SELENOP+ macrophages co-occur and spatially co-localize with precursor exhausted (GZMH+) CD8+ T cells and activate these T cells via selenoprotein P in vitro and in vivo.

hgsoc million pseudo-bulk hgsoc-derived scrna-seq sctcr-seq spatial
Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

Has reproduction · 88

CD39+CD8+ TILs constitute a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells

memory sorted caix-specific cd39+pd-1bright scrna-seq bulk mhc
Multi-modal skin atlas identifies a multicellular immune-stromal community associated with disrupted cornification and specific T cell expansion in atopic dermatitis.

PMID 41741455 · PMC13057205 · Nature communications · 2026 · 8 claims · 8 setups

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Generated a multi-modal single-cell atlas of 280,518 cells from 27 samples/17 adults (healthy, AD non-lesional/lesional, scleroderma), integrated with 430,186 cells from four prior studies into a 710,704-cell human skin atlas with 86 annotated granular cell subsets.

skin healthy keratinocytes re-annotated droplet-based scrna-seq bulk

Experiments

Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

Novel approaches for identifying target antigens of autoreactive human B and T cells.

Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies.

Unique phenotypic and T cell receptor characteristics of CD8(+) T cells accumulated in the brains of Alzheimer's disease mice.

Clonal CD8(+) T cells populate the leptomeninges and coordinate with immune cells in human degenerative brain diseases.

Antigen specificity of clonally enriched CD8(+) T cells in multiple sclerosis.

Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction.

Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.

Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma.

Hypoxia-driven remodeling of SELENOP(+) macrophages shapes T cell dynamics and promotes ovarian cancer metastasis.

Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

Multi-modal skin atlas identifies a multicellular immune-stromal community associated with disrupted cornification and specific T cell expansion in atopic dermatitis.