SynthesisNature communications2021
Interpretation of T cell states from single-cell transcriptomics data using reference atlases.
Synthesis in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 372 papers.
What it found
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Who cites it
372 citing papers in PubMed.
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- Immune dysregulation in the prostates of C57BL/6The Journal of pathology · 2026Article
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- Trustworthy Agentic AI in Bioinformatics: From Workflow Automation to Traceable and Validated Biological Inference.Biology · 2026Review
- Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma.Nature communications · 2026Article
- A Tumor-Microenvironment-Responsive Chemically Masked IL‑2 Prodrug Potentiates PD‑1 Checkpoint Blockade and Elicits Robust Antitumor Efficacy.ACS central science · 2026Article
- Single-cell transcriptomics reveals bladder microenvironment dynamics in Hunner type interstitial cystitis.iScience · 2026Article
- Targeting ABL kinases overcomes melanoma immune evasion following resistance to MAPK inhibition.Nature communications · 2026Article
- Peripheral CD4 T-Cell State Remodeling in Migraine Revealed by Single-Cell RNA Sequencing.Journal of molecular neuroscience : MN · 2026Article
- Immune Circuit Rewiring by HDAC Inhibition Enables Response to Dual Checkpoint Blockade in Metastatic Breast Cancer.Cancer research · 2026Article
- The transcription factor IRF8 drives tumor-specific exhaustion in CD8+ T cells.The Journal of experimental medicine · 2026Article
- Efficacious suppression of primary and metastasized liver tumors by polyIC-loaded lipid nanoparticles.Hepatology (Baltimore, Md.) · 2026Article
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- A scalable, low-cost, sample hashing workflow for multiomic single-cell analysis using the Seq-Well SNature protocols · 2026Review
- Integrated Single-Cell and TCR Profiling Reveals Protection-Associated CD8Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Differential T cell clonal dynamics underlie outcomes to frontline chemoimmunotherapy in advanced gastric cancer.Cell reports. Medicine · 2026Article
312 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing (scRNA-seq) has revealed an unprecedented degree of immune cell diversity. However, consistent definition of cell subtypes and cell states across studies and diseases remains a major challenge. Here we generate reference T cell atlases for cancer and viral infection by multi-study integration, and develop ProjecTILs, an algorithm for reference atlas projection. In contrast to other methods, ProjecTILs allows not only accurate embedding of new scRNA-seq data into a reference without altering its structure, but also characterizing previously unknown cell states that "deviate" from the reference. ProjecTILs accurately predicts the effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. A meta-analysis of tumor-infiltrating T cells from several cohorts reveals a strong conservation of T cell subtypes between human and mouse, providing a consistent basis to describe T cell heterogeneity across studies, diseases, and species.
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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 Socratic graph.