Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma

Epidemiology and surveillance for hepatocellular carcinoma: New trends

(2020) Amit G. Singal et al.   JOURNAL OF HEPATOLOGY

Challenges of combination therapy with immune checkpoint inhibitors for hepatocellular carcinoma

(2020) Ann-Lii Cheng et al.   JOURNAL OF HEPATOLOGY

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

(2019) Johanna Wagner et al.   CELL

Nivolumab in patients with advanced hepatocellular carcinoma and Child‐Pugh class B cirrhosis: Safety and clinical outcomes in a retrospective case series

(2019) Swetha Kambhampati et al.   CANCER

Nivolumab in advanced hepatocellular carcinoma: Sorafenib-experienced Asian cohort analysis

(2019) Thomas Yau et al.   JOURNAL OF HEPATOLOGY

Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas

(2019) Xiaofan Ding et al.   GASTROENTEROLOGY

Neoantigen vaccine: an emerging tumor immunotherapy

(2019) Miao Peng et al.   Molecular Cancer

Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer

(2019) Lichun Ma et al.   CANCER CELL

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade

(2019) Imran G. House et al.   CLINICAL CANCER RESEARCH

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

(2018) Elham Azizi et al.   CELL

Multidimensional analyses reveal distinct immune microenvironment in hepatitis B virus-related hepatocellular carcinoma

(2018) Chun Jye Lim et al.   GUT

The function and dysfunction of memory CD8+ T cells in tumor immunity

(2018) James L. Reading et al.   IMMUNOLOGICAL REVIEWS

EASL Clinical Practice Guidelines: Management of hepatocellular carcinoma

(2018) Peter R. Galle et al.   JOURNAL OF HEPATOLOGY

Pembrolizumab in patients with advanced hepatocellular carcinoma previously treated with sorafenib (KEYNOTE-224): a non-randomised, open-label phase 2 trial

(2018) Andrew X Zhu et al.   LANCET ONCOLOGY

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

(2018) Derk Amsen et al.   NATURE IMMUNOLOGY

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

(2018) Xinyi Guo et al.   NATURE MEDICINE

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

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Metabolic Control of CD8 + T Cell Fate Decisions and Antitumor Immunity

(2018) Lianjun Zhang et al.   TRENDS IN MOLECULAR MEDICINE

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2018) Freddie Bray et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Exosomal PD-L1 contributes to immunosuppression and is associated with anti-PD-1 response

(2018) Gang Chen et al.   NATURE

Evolution of Metastases in Space and Time under Immune Selection

(2018) Mihaela Angelova et al.   CELL

Feasibility and safety of nivolumab in advanced hepatocellular carcinoma: real-life experience from three German centers

(2018) Fabian Finkelmeier et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

Dendritic Cells but Not Macrophages Sense Tumor Mitochondrial DNA for Cross-priming through Signal Regulatory Protein α Signaling

(2017) Meng Michelle Xu et al.   IMMUNITY

Nivolumab in patients with advanced hepatocellular carcinoma (CheckMate 040): an open-label, non-comparative, phase 1/2 dose escalation and expansion trial

(2017) Anthony B El-Khoueiry et al.   LANCET

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

CTLA-4 positive breast cancer cells suppress dendritic cells maturation and function

(2017) Xi Chen et al.   Oncotarget

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

Human intrahepatic ILC2 are IL-13positive amphiregulinpositive and their frequency correlates with model of end stage liver disease score

(2017) Hannah C. Jeffery et al.   PLoS One

Actual 10-Year Survivors After Resection of Hepatocellular Carcinoma

(2016) Jian Zheng et al.   ANNALS OF SURGICAL ONCOLOGY

Voluntary Running Suppresses Tumor Growth through Epinephrine- and IL-6-Dependent NK Cell Mobilization and Redistribution

(2016) Line Pedersen et al.   Cell Metabolism

Cutting Edge: Foxp1 Controls Naive CD8+T Cell Quiescence by Simultaneously Repressing Key Pathways in Cellular Metabolism and Cell Cycle Progression

(2016) Hairong Wei et al.   JOURNAL OF IMMUNOLOGY

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

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

(2016) I. Tirosh et al.   SCIENCE

Krüppel-like factor KLF10 regulates transforming growth factor receptor II expression and TGF-β signaling in CD8+ T lymphocytes

(2015) Konstantinos A. Papadakis et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Antibody mediated therapy targeting CD47 inhibits tumor progression of hepatocellular carcinoma

(2015) Zhenyu Xiao et al.   CANCER LETTERS

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

(2015) Wei Zhang et al.   GENETICS

Anti-CD47 antibody suppresses tumour growth and augments the effect of chemotherapy treatment in hepatocellular carcinoma

(2015) Jessica Lo et al.   LIVER INTERNATIONAL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis

(2015) Wei Zhang et al.   GENETICS

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

(2015) Liang Wu et al.   GigaScience

Transforming Growth Factor β-Mediated Suppression of Antitumor T Cells Requires FoxP1 Transcription Factor Expression

(2014) Tom L. Stephen et al.   IMMUNITY

Memory CD8+ T Cells Use Cell-Intrinsic Lipolysis to Support the Metabolic Programming Necessary for Development

(2014) David O’Sullivan et al.   IMMUNITY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

The Chemokine Receptor CCR7 Expressed by Dendritic Cells: A Key Player in Corneal and Ocular Surface Inflammation

(2014) Daniel R. Saban   Ocular Surface

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

NK1.1+ CD8+ T cells escape TGF-β control and contribute to early microbial pathogen response

(2014) Anne L. Ruiz et al.   Nature Communications

Regulation of T cell proliferation by JMJD6 and PDGF-BB during chronic hepatitis B infection

(2014) Cai-Feng Chen et al.   Scientific Reports

CD161 Defines a Transcriptional and Functional Phenotype across Distinct Human T Cell Lineages

(2014) Joannah R. Fergusson et al.   Cell Reports

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Cell-extrinsic CTLA4-mediated regulation of dendritic cell maturation depends on STAT3

(2013) Aleksandra Kowalczyk et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

On the armament and appearances of human myeloid-derived suppressor cells

(2012) Isabel Poschke et al.   CLINICAL IMMUNOLOGY

Discrete nature of EpCAM+and CD90+cancer stem cells in human hepatocellular carcinoma

(2012) Taro Yamashita et al.   HEPATOLOGY

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Hepatocellular Carcinoma

(2011) Nuh N. Rahbari et al.   ANNALS OF SURGERY

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Increased killer immunoglobulin-like receptor expression and functional defects in natural killer cells in lung cancer

(2011) Suliman Y. Al Omar et al.   IMMUNOLOGY

Circulating and tumor-infiltrating myeloid cell subsets in patients with bladder cancer

(2011) Evgeniy Eruslanov et al.   INTERNATIONAL JOURNAL OF CANCER

Pathogen-Induced Inflammatory Environment Controls Effector and Memory CD8 + T Cell Differentiation

(2011) Joshua J. Obar et al.   JOURNAL OF IMMUNOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Chemokine Expression in Melanoma Metastases Associated with CD8+ T-Cell Recruitment

(2009) H. Harlin et al.   CANCER RESEARCH

Inhibition of “self” engulfment through deactivation of myosin-II at the phagocytic synapse between human cells

(2008) Richard K. Tsai et al.   JOURNAL OF CELL BIOLOGY