γδ T cells are effectors of immunotherapy in cancers with HLA class I defects

CD4 T cell dependent rejection of beta 2 microglobulin null mismatch repair deficient tumors

(2021) Giovanni Germano et al.   Cancer Discovery

Determinants of Response and Intrinsic Resistance to PD-1 Blockade in Microsatellite Instability-High Gastric Cancer

(2021) Minsuk Kwon et al.   Cancer Discovery

Semi‐automated background removal limits data loss and normalizes imaging mass cytometry data

(2021) Marieke E. Ijsselsteijn et al.   CYTOMETRY PART A

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

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

(2020) Myriam Chalabi et al.   NATURE MEDICINE

A peripheral immune signature of responsiveness to PD-1 blockade in patients with classical Hodgkin lymphoma

(2020) Fathima Zumla Cader et al.   NATURE MEDICINE

Revisiting immune escape in colorectal cancer in the era of immunotherapy

(2019) Marieke Erica Ijsselsteijn et al.   BRITISH JOURNAL OF CANCER

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity

(2019) Natasja L de Vries et al.   GUT

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

The Immune Landscape of Cancer

(2019) Vésteinn Thorsson et al.   IMMUNITY

The Drug Rediscovery protocol facilitates the expanded use of existing anticancer drugs

(2019) D. L. van der Velden et al.   NATURE

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

An innate-like Vδ1+ γδ T cell compartment in the human breast is associated with remission in triple-negative breast cancer

(2019) Yin Wu et al.   Science Translational Medicine

A 40-Marker Panel for High Dimensional Characterization of Cancer Immune Microenvironments by Imaging Mass Cytometry

(2019) Marieke E. Ijsselsteijn et al.   Frontiers in Immunology

Tumor organoid–T-cell coculture systems

(2019) Chiara M. Cattaneo et al.   Nature Protocols

ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data

(2019) Antonios Somarakis et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Durable Clinical Benefit With Nivolumab Plus Ipilimumab in DNA Mismatch Repair–Deficient/Microsatellite Instability–High Metastatic Colorectal Cancer

(2018) Michael J. Overman et al.   JOURNAL OF CLINICAL ONCOLOGY

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Thomas Duhen et al.   Nature Communications

Generation of Tumor-Reactive T Cells by Co-culture of Peripheral Blood Lymphocytes and Tumor Organoids

(2018) Krijn K. Dijkstra et al.   CELL

Nivolumab in patients with metastatic DNA mismatch repair-deficient or microsatellite instability-high colorectal cancer (CheckMate 142): an open-label, multicentre, phase 2 study

(2017) Michael J Overman et al.   LANCET ONCOLOGY

Inactivation of DNA repair triggers neoantigen generation and impairs tumour growth

(2017) Giovanni Germano et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

(2017) Moshe Sade-Feldman et al.   Nature Communications

Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer

(2017) Scott Gettinger et al.   Cancer Discovery

Apoptosis Induced via Gamma Delta T Cell Antigen Receptor “Blocking” Antibodies: A Cautionary Tale

(2017) Indrani Dutta et al.   Frontiers in Immunology

Gene expression markers of Tumor Infiltrating Leukocytes

(2017) Patrick Danaher et al.   Journal for ImmunoTherapy of Cancer

Delta One T Cells for Immunotherapy of Chronic Lymphocytic Leukemia: Clinical-Grade Expansion/Differentiation and Preclinical Proof of Concept

(2016) A. R. Almeida et al.   CLINICAL CANCER RESEARCH

Cytosplore: Interactive Immune Cell Phenotyping for Large Single-Cell Datasets

(2016) T. Höllt et al.   COMPUTER GRAPHICS FORUM

Classification and characterization of microsatellite instability across 18 cancer types

(2016) Ronald J Hause et al.   NATURE MEDICINE

Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma

(2016) Jesse M. Zaretsky et al.   NEW ENGLAND JOURNAL OF MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations

(2015) Mi Ni Huang et al.   Scientific Reports

Ex vivoexpanded human circulating Vδ1 γδT cells exhibit favorable therapeutic potential for colon cancer

(2015) Dang Wu et al.   OncoImmunology

Association of PD-1, PD-1 Ligands, and Other Features of the Tumor Immune Microenvironment with Response to Anti-PD-1 Therapy

(2014) J. M. Taube et al.   CLINICAL CANCER RESEARCH

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Extensive expansion of primary human gamma delta T cells generates cytotoxic effector memory cells that can be labeled with Feraheme for cellular MRI

(2012) Gabrielle M. Siegers et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Immunohistochemistry for PMS2 and MSH6 alone can replace a four antibody panel for mismatch repair deficiency screening in colorectal adenocarcinoma

(2010) Geoffrey Hall et al.   PATHOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS