Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response

Cell2location maps fine-grained cell types in spatial transcriptomics

(2022) Vitalii Kleshchevnikov et al.   NATURE BIOTECHNOLOGY

Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer

(2022) Maxime Meylan et al.   IMMUNITY

Landscape of helper and regulatory antitumour CD4+ T cells in melanoma

(2022) Giacomo Oliveira et al.   NATURE

Cell type-specific inference of differential expression in spatial transcriptomics

(2022) Dylan M. Cable et al.   NATURE METHODS

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma

(2021) David A. Braun et al.   CANCER CELL

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

(2021) Kevin Bi et al.   CANCER CELL

Dynamic regulation of TFH selection during the germinal centre reaction

(2021) Julia Merkenschlager et al.   NATURE

Robust decomposition of cell type mixtures in spatial transcriptomics

(2021) Dylan M. Cable et al.   NATURE BIOTECHNOLOGY

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

(2021) Chirag Krishna et al.   CANCER CELL

Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

(2021) Sunny Z. Wu et al.   Genome Medicine

Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

(2021) Giacomo Oliveira et al.   NATURE

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

A cell atlas of human thymic development defines T cell repertoire formation

(2020) Jong-Eun Park et al.   SCIENCE

Immune gene signatures for predicting durable clinical benefit of anti-PD-1 immunotherapy in patients with non-small cell lung cancer

(2020) Sohyun Hwang et al.   Scientific Reports

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

(2020) Pierre Bost et al.   CELL

A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy

(2020) Satyen H. Gohil et al.   Nature Reviews Clinical Oncology

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

Intratumoral Activity of the CXCR3 Chemokine System Is Required for the Efficacy of Anti-PD-1 Therapy

(2019) Melvyn T. Chow et al.   IMMUNITY

CD8+ T cells regulate tumour ferroptosis during cancer immunotherapy

(2019) Weimin Wang et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

RNase H–dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis

(2019) Shuqiang Li et al.   Nature Protocols

Comparison of Biomarker Modalities for Predicting Response to PD-1/PD-L1 Checkpoint Blockade

(2019) Steve Lu et al.   JAMA Oncology

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

(2019) Matthew L. Bendall et al.   PLoS Computational Biology

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

(2019) Jacob C. Kimmel et al.   GENOME RESEARCH

TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

(2019) Ang A. Tu et al.   NATURE IMMUNOLOGY

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

(2019) Kroopa Joshi et al.   NATURE MEDICINE

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR

(2018) David Zemmour et al.   NATURE IMMUNOLOGY

The epigenetic control of stemness in CD8+T cell fate commitment

(2018) Luigia Pace et al.   SCIENCE

Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells

(2018) Monica Golumbeanu et al.   Cell Reports

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

(2017) Theres Oakes et al.   Frontiers in Immunology

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

T Follicular Helper Cells Have Distinct Modes of Migration and Molecular Signatures in Naive and Memory Immune Responses

(2015) Dan Suan et al.   IMMUNITY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life

(2014) Joseph J.C. Thome et al.   CELL

STAT3 Regulates Proliferation and Survival of CD8+T Cells: Enhances Effector Responses to HSV-1 Infection, and Inhibits IL-10+Regulatory CD8+T Cells in Autoimmune Uveitis

(2013) Cheng-Rong Yu et al.   MEDIATORS OF INFLAMMATION

T Follicular Helper Cell Dynamics in Germinal Centers

(2013) Z. Shulman et al.   SCIENCE

RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers

(2011) Joseph R Dobosy et al.   BMC BIOTECHNOLOGY

The Transcriptional Repressor Bcl-6 Directs T Follicular Helper Cell Lineage Commitment

(2009) Di Yu et al.   IMMUNITY

Bcl6 and Blimp-1 Are Reciprocal and Antagonistic Regulators of T Follicular Helper Cell Differentiation

(2009) R. J. Johnston et al.   SCIENCE