Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy

Neoadjuvant Nivolumab plus Chemotherapy in Resectable Lung Cancer

(2022) Patrick M. Forde et al.   NEW ENGLAND JOURNAL OF MEDICINE

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

(2021) Nathan D. Mathewson et al.   CELL

Pathological response and survival with neoadjuvant therapy in melanoma: a pooled analysis from the International Neoadjuvant Melanoma Consortium (INMC)

(2021) Alexander M. Menzies et al.   NATURE MEDICINE

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

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

(2021) Paul Gueguen et al.   Science Immunology

Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer

(2021) Milena Hornburg et al.   CANCER CELL

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

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

(2021) Ayse Bassez et al.   NATURE MEDICINE

Intratumoral CD103+ CD8+ T cells predict response to PD-L1 blockade

(2021) Romain Banchereau et al.   Journal for ImmunoTherapy of Cancer

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

(2021) Justina X. Caushi et al.   NATURE

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

(2021) Giacomo Oliveira et al.   NATURE

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

(2021) Massimo Andreatta et al.   Nature Communications

Neoadjuvant nivolumab for patients with resectable HPV-positive and HPV-negative squamous cell carcinomas of the head and neck in the CheckMate 358 trial

(2021) Robert L Ferris et al.   Journal for ImmunoTherapy of Cancer

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

(2020) Benjamin P. Fairfax et al.   NATURE MEDICINE

Neoadjuvant checkpoint blockade for cancer immunotherapy

(2020) Suzanne L. Topalian et al.   SCIENCE

Trajectory-based differential expression analysis for single-cell sequencing data

(2020) Koen Van den Berge et al.   Nature Communications

Impact of Neoadjuvant Durvalumab with or without Tremelimumab on CD8+ Tumor Lymphocyte Density, Safety, and Efficacy in Patients with Oropharynx Cancer: CIAO Trial Results

(2020) Renata Ferrarotto et al.   CLINICAL CANCER RESEARCH

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

Learning from clinical trials of neoadjuvant checkpoint blockade

(2020) Judith M. Versluis et al.   NATURE MEDICINE

Neoadjuvant immunotherapy leads to pathological responses in MMR-proficient and MMR-deficient early-stage colon cancers

(2020) Myriam Chalabi et al.   NATURE MEDICINE

Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy

(2020) Adrienne M. Luoma et al.   CELL

Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase 2 Trial

(2020) Ravindra Uppaluri et al.   CLINICAL CANCER RESEARCH

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

(2020) Bo Li et al.   NATURE METHODS

Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein

(2020) Andrew P. Ferretti et al.   IMMUNITY

Neoadjuvant immunotherapy for melanoma

(2020) Ann Y. Lee et al.   JOURNAL OF SURGICAL ONCOLOGY

Neoadjuvant Nivolumab or Nivolumab Plus Ipilimumab in Untreated Oral Cavity Squamous Cell Carcinoma

(2020) Jonathan D. Schoenfeld et al.   JAMA Oncology

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Model to improve specificity for identification of clinically-relevant expanded T cells in peripheral blood

(2019) Julie Rytlewski et al.   PLoS One

A single dose of neoadjuvant PD-1 blockade predicts clinical outcomes in resectable melanoma

(2019) Alexander C. Huang et al.   NATURE MEDICINE

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer

(2019) James Clarke et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

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

Location, location, location: Tissue resident memory T cells in mice and humans

(2019) Peter A. Szabo et al.   Science Immunology

T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes

(2019) Tomasz Kula et al.   CELL

Tissue-Resident Memory T Cells in Cancer Immunosurveillance

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

The impact of CTLA-4 blockade and interferon-α on clonality of T-cell repertoire in the tumor microenvironment and peripheral blood of metastatic melanoma patients

(2019) Arjun Khunger et al.   OncoImmunology

Neoadjuvant PD-1 Immune Checkpoint Blockade Reverses Functional Immunodominance among Tumor Antigen–Specific T Cells

(2019) Jay Friedman et al.   CLINICAL CANCER RESEARCH

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

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

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

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

DeTiN: overcoming tumor-in-normal contamination

(2018) Amaro Taylor-Weiner et al.   NATURE METHODS

Neoadjuvant PD-1 Blockade in Resectable Lung Cancer

(2018) Patrick M. Forde et al.   NEW ENGLAND JOURNAL OF MEDICINE

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors

(2018) Thomas Duhen et al.   Nature Communications

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors

(2018) Diana Miao et al.   NATURE GENETICS

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

Resident memory T cells, critical components in tumor immunology

(2018) Fathia Mami-Chouaib et al.   Journal for ImmunoTherapy of Cancer

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Neoadjuvant immune checkpoint blockade in high-risk resectable melanoma

(2018) Rodabe N. Amaria et al.   NATURE MEDICINE

Neoadjuvant versus adjuvant ipilimumab plus nivolumab in macroscopic stage III melanoma

(2018) Christian U. Blank et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Proliferation of PD-1+ CD8 T cells in peripheral blood after PD-1–targeted therapy in lung cancer patients

(2017) Alice O. Kamphorst et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

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

(2016) I. Tirosh et al.   SCIENCE

Improved Efficacy of Neoadjuvant Compared to Adjuvant Immunotherapy to Eradicate Metastatic Disease

(2016) J. Liu et al.   Cancer Discovery

The future of immune checkpoint therapy

(2015) P. Sharma et al.   SCIENCE

A comparative review of methods for comparing means using partially paired data

(2015) Beibei Guo et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression

(2015) Jelle Scholtalbers et al.   Genome Medicine

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Anti-CTLA-4 therapy broadens the melanoma-reactive CD8+ T cell response

(2014) P. Kvistborg et al.   Science Translational Medicine

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

(2013) Laura K Mackay et al.   NATURE IMMUNOLOGY

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH