ArticleNature methods2025
Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions.
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Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28citing papers in PubMed
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Who cites it
28 citing papers in PubMed.
- SpatialZoomer: multi-scale feature analysis of spatial transcriptomics.Nature biomedical engineering · 2026Article
- Spatial multi-omics uncovers an invasive-desmoplastic cellular community with prognostic and therapeutic implications in pancreatic ductal adenocarcinoma.Advanced biotechnology · 2026Article
- A Gene-Program Architecture of Mouse T cells.bioRxiv : the preprint server for biology · 2026Article
- Scalable context-dependent single-cell eQTL mapping reveals disease-relevant regulatory variation beyond static models.medRxiv : the preprint server for health sciences · 2026Article
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- The Role of the T Cell Receptor Sequence in Shaping T Cell Functional Fate.Immunological reviews · 2026Review
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.Nature communications · 2026Article
- Perturbation of genes linked to common schizophrenia risk variants identifies cilia programs.bioRxiv : the preprint server for biology · 2026Article
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.bioRxiv : the preprint server for biology · 2026Article
- Aging disrupts spatiotemporal coordination in the cycling murine ovary.Nature aging · 2026Article
- Intestinal resident effector-memory CD4 T cells on the adaptive-innate spectrum comprise IL-18 reactivity and adaptive CMV specificity.Science advances · 2026Article
- A Perturb-seq screen guided by species divergence uncovers pathways for collateral artery formation.bioRxiv : the preprint server for biology · 2026Article
- sigNATURE maps cohort-specific T-cell states to reproducible programs of ICI response.bioRxiv : the preprint server for biology · 2026Article
- A population-scale atlas of blood and tissue in lupus nephritis.bioRxiv : the preprint server for biology · 2026Article
- Olfactory cleft biopsy analysis of Alzheimer's disease pathobiology across disease stages.Nature communications · 2026Article
- Redefining the immune microenvironment of gliomas in the era of single-cell genomics.Neuro-oncology advances · 2026Review
- Diverse Microbial Exposure Enhances CD8bioRxiv : the preprint server for biology · 2026Article
- An inflammatory and quiescent HSC subpopulation expands with age in humans.Genome biology · 2026Article
- Symptomatic SARS-CoV-2 breakthrough infections broaden the repertoire of Spike-reactive CD4 T cells.mBio · 2026Article
- CD4/CD8 ratio is associated with structural reorganization of vaccine-induced immune responses in people living with HIV.Frontiers in immunology · 2026Article
Corrections and comments
- Update of
Authors and funding
11 authors.
Dylan Kotliar *Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-7968-645X
Michelle Curtis *Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Ryan AgnewCenter for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Kathryn WeinandCenter for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-8491-7251
Aparna NathanCenter for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Yuriy BaglaenkoCenter for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Kamil SlowikowskiBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Yu ZhaoCenter for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2632-7530
Pardis C SabetiBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-9843-1890
Deepak A RaoDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-9672-7746
Soumya RaychaudhuriCenter for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. soumya@broadinstitute.org.ORCID http://orcid.org/0000-0002-1901-8265
Funding
Role of fibroblastic stromal cells and notch signaling in tissue inflammation in RA and SLEP01AI148102 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI Michael B. Brenner, Nir Hacohen · 2021 to 2026
$17.3MTraining Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8MMECHANISMS OF ARTHRITIC &DERMATOLOGY DISORDERST32AR007530 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Michael B. Brenner, Ellen M Gravallese · 1986 to 2026
$10.4MJoint Biology Consortium Resource-based CenterP30AR070253 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Peter A Nigrovic, Jeffrey Andrew Sparks · 2016 to 2026
$9.4MDiscovery and Functional Impact of Common and Rare Variants in RAR01AR063759 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Soumya Raychaudhuri · 2013 to 2026
$5.4MIntegrative analysis of high dimensional tissue molecular data to define key biological systems in autoimmune diseases (SBC)UC2AR081023 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Soumya Raychaudhuri · 2022 to 2026
$4.8MPredicting the impact of genetic variants, genes and pathways on human DiseaseU01HG012009 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ALKES L PRICE, Soumya Raychaudhuri · 2021 to 2026
$4.2MIntegrative modelling of single-cell data to elucidate the genetic architecture of complex diseaseR56HG013083 · NHGRI · DANA-FARBER CANCER INST · PI GUSEV, ALEXANDER, PRICE, ALKES L · 2023 to 2023
$400kNHGRI NIH HHS R56 HG013083NHGRI NIH HHS T32 HG002295NHGRI NIH HHS U01 HG012009NIAID NIH HHS P01 AI148102NIAMS NIH HHS P30 AR070253NIAMS NIH HHS R01 AR063759NIAMS NIH HHS T32 AR007530NIAMS NIH HHS UC2 AR081023U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R56HG013083U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) T32HG002295U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U01HG012009U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) P01AI148102U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) R01AR063759U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) T32AR007530U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) UC2AR081023
Abstract
T cells recognize antigens and induce specialized gene expression programs (GEPs), enabling functions like proliferation, cytotoxicity and cytokine production. Traditionally, different T cell classes are thought to exhibit mutually exclusive responses, including T
Indexed as
Lymphocyte ActivationSingle-Cell AnalysisT-Lymphocyte SubsetsGene Expression ProfilingHumansNeoplasmsReproducibility of ResultsSequence Analysis, RNASoftware
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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 OpenQuestion graph.