Circulating immune cell phenotype dynamics reflect the strength of tumor–immune cell interactions in patients during immunotherapy

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

(2019) Robert M. Samstein et al.   NATURE GENETICS

Mathematical modeling of tumor-immune cell interactions

(2019) Grace E. Mahlbacher et al.   JOURNAL OF THEORETICAL BIOLOGY

PD-L1 and Emerging Biomarkers in Immune Checkpoint Blockade Therapy

(2018) Tricia R. Cottrell et al.   CANCER JOURNAL

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

(2018) Carsten Krieg et al.   NATURE MEDICINE

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

PD-1/PD-L1 pathway: an adaptive immune resistance mechanism to immunogenic chemotherapy in colorectal cancer

(2018) Magalie Dosset et al.   OncoImmunology

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow

(2018) Jonathan Ozik et al.   BMC BIOINFORMATICS

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

(2018) Moshe Sade-Feldman et al.   CELL

Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-γ and IL-12

(2018) Christopher S. Garris et al.   IMMUNITY

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

Increased abundance of myeloid-derived suppressor cells and Th17 cells in peripheral blood of newly-diagnosed Parkinson’s disease patients

(2017) Siyuan Chen et al.   NEUROSCIENCE LETTERS

First-Line Nivolumab in Stage IV or Recurrent Non–Small-Cell Lung Cancer

(2017) David P. Carbone et al.   NEW ENGLAND JOURNAL OF MEDICINE

Protein Expression of Programmed Death 1 Ligand 1 and HER2 in Gastric Carcinoma

(2017) Eiji Oki et al.   ONCOLOGY

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

(2017) Dung T. Le et al.   SCIENCE

Peripheral CD4+ naïve/memory ratio is an independent predictor of survival in non-small cell lung cancer

(2017) Peng Yang et al.   Oncotarget

T cells in chronic lymphocytic leukemia display dysregulated expression of immune checkpoints and activation markers

(2016) Marzia Palma et al.   HAEMATOLOGICA

Too Much of a Good Thing? Chronic IFN Fuels Resistance to Cancer Immunotherapy

(2016) James L. Reading et al.   IMMUNITY

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells

(2016) Marco De Simone et al.   IMMUNITY

Mathematical model of tumor–immune surveillance

(2016) Khaphetsi Joseph Mahasa et al.   JOURNAL OF THEORETICAL BIOLOGY

PD-1 Blockade with Pembrolizumab in Advanced Merkel-Cell Carcinoma

(2016) Paul T. Nghiem et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2016) I. Tirosh et al.   SCIENCE

T cells in chronic lymphocytic leukemia display dysregulated expression of immune checkpoints and activation markers

(2016) Marzia Palma et al.   HAEMATOLOGICA

IL-17-producing γδ T cells and neutrophils conspire to promote breast cancer metastasis

(2015) Seth B. Coffelt et al.   NATURE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Pembrolizumab for the Treatment of Non–Small-Cell Lung Cancer

(2015) Edward B. Garon et al.   NEW ENGLAND JOURNAL OF MEDICINE

PD-1 Blockade with Nivolumab in Relapsed or Refractory Hodgkin's Lymphoma

(2015) Stephen M. Ansell et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

High Numbers of Differentiated Effector CD4 T Cells Are Found in Patients with Cancer and Correlate with Clinical Response after Neoadjuvant Therapy of Breast Cancer

(2014) Isabelle Péguillet et al.   CANCER RESEARCH

MPDL3280A (anti-PD-L1) treatment leads to clinical activity in metastatic bladder cancer

(2014) Thomas Powles et al.   NATURE

The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints

(2014) Nicolas J. Llosa et al.   Cancer Discovery

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Safety and Tumor Responses with Lambrolizumab (Anti–PD-1) in Melanoma

(2013) Omid Hamid et al.   NEW ENGLAND JOURNAL OF MEDICINE

PTEN Loss Increases PD-L1 Protein Expression and Affects the Correlation between PD-L1 Expression and Clinical Parameters in Colorectal Cancer

(2013) Minmin Song et al.   PLoS One

Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity

(2013) Adria Carbo et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer

(2012) Suzanne L. Topalian et al.   NEW ENGLAND JOURNAL OF MEDICINE

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

A mathematical model of tumor–immune interactions

(2011) Mark Robertson-Tessi et al.   JOURNAL OF THEORETICAL BIOLOGY

Interactions Between the Immune System and Cancer: A Brief Review of Non-spatial Mathematical Models

(2010) Raluca Eftimie et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Clinical Significance of B7-H1 and B7-1 Expressions in Pancreatic Carcinoma

(2010) Liancai Wang et al.   WORLD JOURNAL OF SURGERY

Interaction of B7-H1 on intrahepatic cholangiocarcinoma cells with PD-1 on tumor-infiltrating T cells as a mechanism of immune evasion

(2009) Yufu Ye et al.   JOURNAL OF SURGICAL ONCOLOGY

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

(2009) Alexander R. Abbas et al.   PLoS One

Clinical significance and regulation of the costimulatory molecule B7-H1 in pancreatic cancer

(2008) Martin Loos et al.   CANCER LETTERS