Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T cells

Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets

(2021) Michael E.B. FitzPatrick et al.   Cell Reports

Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer

(2021) Paul Gueguen et al.   Science Immunology

Hobit identifies tissue-resident memory T cell precursors that are regulated by Eomes

(2021) Loreto Parga-Vidal et al.   Science Immunology

Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation

(2021) Jaikumar Duraiswamy et al.   CANCER CELL

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

T Cell Factor 1 Suppresses CD103+ Lung Tissue-Resident Memory T Cell Development

(2020) Jingxia Wu et al.   Cell Reports

Transcriptional and Functional Analysis of CD1c+ Human Dendritic Cells Identifies a CD163+ Subset Priming CD8+CD103+ T Cells

(2020) Pierre Bourdely 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

(2019) Imran Siddiqui et al.   IMMUNITY

A transcriptionally distinct CXCL13+CD103+CD8+ T-cell population is associated with B-cell recruitment and neoantigen load in human cancer

(2019) Hagma H Workel et al.   Cancer Immunology Research

ER stress-induced mediator C/EBP homologous protein thwarts effector T cell activity in tumors through T-bet repression

(2019) Yu Cao et al.   Nature Communications

Tissue-Resident T Cells and Other Resident Leukocytes

(2019) David Masopust et al.   Annual Review of Immunology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade

(2019) Rohit R. Jadhav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tissue-Resident Memory T Cells in Cancer Immunosurveillance

(2019) Simone L. Park et al.   TRENDS IN IMMUNOLOGY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Tissue-resident memory CD8+ T cells amplify anti-tumor immunity by triggering antigen spreading through dendritic cells

(2019) Evelyn Menares et al.   Nature Communications

Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

(2019) Peter A. Szabo et al.   Nature Communications

The art of using t-SNE for single-cell transcriptomics

(2019) Dmitry Kobak 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

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells

(2019) Caroline S. Jansen et al.   NATURE

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Tissue-resident memory T cells are epigenetically cytotoxic with signs of exhaustion in human urinary bladder cancer

(2018) Ciputra Adijaya Hartana et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Tissue-resident memory T cells at the center of immunity to solid tumors

(2018) Derk Amsen et al.   NATURE IMMUNOLOGY

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

The Emerging Role of CD8+ Tissue Resident Memory T (TRM) Cells in Antitumor Immunity: A Unique Functional Contribution of the CD103 Integrin

(2018) Stéphanie Corgnac et al.   Frontiers in Immunology

Tumor Resident Memory T Cells: New Players in Immune Surveillance and Therapy

(2018) Nina Dumauthioz et al.   Frontiers in Immunology

IRE1α–XBP1 controls T cell function in ovarian cancer by regulating mitochondrial activity

(2018) Minkyung Song et al.   NATURE

Tissue Resident CD8 Memory T Cell Responses in Cancer and Autoimmunity

(2018) Aleksey Molodtsov et al.   Frontiers in Immunology

Trigger-happy resident memory CD4+ T cells inhabit the human lungs

(2017) A E Oja et al.   Mucosal Immunology

Survival of tissue-resident memory T cells requires exogenous lipid uptake and metabolism

(2017) Youdong Pan et al.   NATURE

Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours

(2017) J. Justin Milner et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

Coinhibitory Pathways in Immunotherapy for Cancer

(2016) Susanne H. Baumeister et al.   Annual Review of Immunology

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

(2016) Ge Tan et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation

(2016) Jernej Godec et al.   IMMUNITY

Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes

(2016) L. K. Mackay et al.   SCIENCE

Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade

(2016) K. E. Pauken et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

BET Bromodomain Inhibition Promotes Anti-tumor Immunity by Suppressing PD-L1 Expression

(2016) Hengrui Zhu et al.   Cell Reports

Microbially Driven TLR5-Dependent Signaling Governs Distal Malignant Progression through Tumor-Promoting Inflammation

(2015) Melanie R. Rutkowski et al.   CANCER CELL

The Ovarian Cancer Chemokine Landscape Is Conducive to Homing of Vaccine-Primed and CD3/CD28-Costimulated T Cells Prepared for Adoptive Therapy

(2015) E. Zsiros et al.   CLINICAL CANCER RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

The T Cell Receptor's  -Chain Connecting Peptide Motif Promotes Close Approximation of the CD8 Coreceptor Allowing Efficient Signal Initiation

(2014) M. Mallaun et al.   JOURNAL OF IMMUNOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Tumor-Infiltrating Lymphocytes Expressing the Tissue Resident Memory Marker CD103 Are Associated with Increased Survival in High-Grade Serous Ovarian Cancer

(2013) J. R. Webb et al.   CLINICAL CANCER RESEARCH

The developmental pathway for CD103+CD8+ tissue-resident memory T cells of skin

(2013) Laura K Mackay et al.   NATURE IMMUNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Ovarian cancer progression is controlled by phenotypic changes in dendritic cells

(2012) Uciane K. Scarlett et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Molecular Signature of Tissue Resident Memory CD8 T Cells Isolated from the Brain

(2012) L. M. Wakim et al.   JOURNAL OF IMMUNOLOGY

Methods for diversity and overlap analysis in T-cell receptor populations

(2012) Grzegorz A. Rempala et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Community Structure in Time-Dependent, Multiscale, and Multiplex Networks

(2010) P. J. Mucha et al.   SCIENCE

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT