Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors

Conventional type I dendritic cells maintain a reservoir of proliferative tumor-antigen specific TCF-1+ CD8+ T cells in tumor-draining lymph nodes

(2021) Jason M. Schenkel et al.   IMMUNITY

Interpretation of T cell states from single-cell transcriptomics data using reference atlases

(2021) Massimo Andreatta et al.   Nature Communications

T Cell Epitope Predictions

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Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

The CCL20-CCR6 Axis in Cancer Progression

(2020) Suguru Kadomoto et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

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A Phase Ib Trial of Personalized Neoantigen Therapy Plus Anti-PD-1 in Patients with Advanced Melanoma, Non-small Cell Lung Cancer, or Bladder Cancer

(2020) Patrick A. Ott et al.   CELL

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(2020) Charles R. Harris et al.   NATURE

The mouse Gene Expression Database (GXD): 2021 update

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

(2019) Moshe Sade-Feldman et al.   CELL

Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1−CD8+ Tumor-Infiltrating T Cells

(2019) Sema Kurtulus et al.   IMMUNITY

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

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Turning the corner on therapeutic cancer vaccines

(2019) Robert E. Hollingsworth et al.   npj Vaccines

Genomic correlates of response to immune checkpoint blockade

(2019) Tanya E. Keenan et al.   NATURE MEDICINE

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

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

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Commensal Microbiota Promote Lung Cancer Development via γδ T Cells

(2019) Chengcheng Jin et al.   CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

TOX is a critical regulator of tumour-specific T cell differentiation

(2019) Andrew C. Scott et al.   NATURE

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

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

Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells

(2019) Sunil Kumar Saini et al.   Science Immunology

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging

(2019) Ziming Du et al.   Nature Protocols

The role of interleukin-17 in tumor development and progression

(2019) Junjie Zhao et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigens

(2019) Gerald P. Linette et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Proliferating Transitory T Cells with an Effector-like Transcriptional Signature Emerge from PD-1+ Stem-like CD8+ T Cells during Chronic Infection

(2019) William H. Hudson et al.   IMMUNITY

CD4+ T Cell Help Is Required for the Formation of a Cytolytic CD8+ T Cell Subset that Protects against Chronic Infection and Cancer

(2019) Ryan Zander et al.   IMMUNITY

Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer

(2019) Rumana Rashid et al.   Scientific Data

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair

(2018) Jonathan L. Linehan et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer

(2018) Nikolaos Zacharakis et al.   NATURE MEDICINE

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

Cancer Neoantigens

(2018) Ton N. Schumacher et al.   Annual Review of Immunology

Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

(2018) Wouter Scheper et al.   NATURE MEDICINE

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

A BaSiC tool for background and shading correction of optical microscopy images

(2017) Tingying Peng et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

T Cell Factor 1-Expressing Memory-like CD8 + T Cells Sustain the Immune Response to Chronic Viral Infections

(2016) Daniel T. Utzschneider et al.   IMMUNITY

IL-17+ CD8+ T cells: Differentiation, phenotype and role in inflammatory disease

(2016) Ushani Srenathan et al.   IMMUNOLOGY LETTERS

Neoantigen landscape dynamics during human melanoma–T cell interactions

(2016) Els M. E. Verdegaal et al.   NATURE

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

(2016) E. Stronen et al.   SCIENCE

Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

(2016) Valsamo Anagnostou et al.   Cancer Discovery

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

γδT17 Cells Promote the Accumulation and Expansion of Myeloid-Derived Suppressor Cells in Human Colorectal Cancer

(2014) Pin Wu et al.   IMMUNITY

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Rapid modelling of cooperating genetic events in cancer through somatic genome editing

(2014) Francisco J. Sánchez-Rivera et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Intravascular staining for discrimination of vascular and tissue leukocytes

(2014) Kristin G Anderson et al.   Nature Protocols

T helper 17 cells play a critical pathogenic role in lung cancer

(2014) S. H. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism of tumor rejection with doublets of CTLA-4, PD-1/PD-L1, or IDO blockade involves restored IL-2 production and proliferation of CD8+ T cells directly within the tumor microenvironment

(2014) Stefani Spranger et al.   Journal for ImmunoTherapy of Cancer

Relapse or Eradication of Cancer Is Predicted by Peptide-Major Histocompatibility Complex Affinity

(2013) Boris Engels et al.   CANCER CELL

CD8+ T Cells That Produce Interleukin-17 Regulate Myeloid-Derived Suppressor Cells and Are Associated With Survival Time of Patients With Gastric Cancer

(2012) Yuan Zhuang et al.   GASTROENTEROLOGY

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

(2012) Hirokazu Matsushita et al.   NATURE

Expression of tumour-specific antigens underlies cancer immunoediting

(2012) Michel DuPage et al.   NATURE

Promiscuous binding of extracellular peptides to cell surface class I MHC protein

(2012) H. N. Eisen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Endogenous T Cell Responses to Antigens Expressed in Lung Adenocarcinomas Delay Malignant Tumor Progression

(2011) Michel DuPage et al.   CANCER CELL

Fate mapping of IL-17-producing T cells in inflammatory responses

(2011) Keiji Hirota et al.   NATURE IMMUNOLOGY

The molecular signature of CD8+T cells undergoing deletional tolerance

(2009) Ian A. Parish et al.   BLOOD

Comparing Measures of Sparsity

(2009) Niall Hurley et al.   IEEE TRANSACTIONS ON INFORMATION THEORY

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

(2009) Linda Madisen et al.   NATURE NEUROSCIENCE

Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase

(2009) Michel DuPage et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY