The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy

The landscape of viral associations in human cancers

(2020) Marc Zapatka et al.   NATURE GENETICS

Current status of immune checkpoint inhibitors for gastric cancer

(2020) Koji Kono et al.   Gastric Cancer

Anti–PD-1/PD-L1 Blockade Immunotherapy Employed in Treating Hepatitis B Virus Infection–Related Advanced Hepatocellular Carcinoma: A Literature Review

(2020) Bin Li et al.   Frontiers in Immunology

New advances in the diagnosis and management of hepatocellular carcinoma

(2020) Ju Dong Yang et al.   BMJ-British Medical Journal

Anti-viral therapy is associated with improved survival but is underutilised in patients with hepatitis B virus-related hepatocellular carcinoma: real-world east and west experience

(2018) V. L. Chen et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Understanding the tumor immune microenvironment (TIME) for effective therapy

(2018) Mikhail Binnewies et al.   NATURE MEDICINE

Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden

(2018) Matthew D. Hellmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Epstein–Barr Virus and Cancer

(2018) Paul J. Farrell   Annual Review of Pathology-Mechanisms of Disease

Genomic characterization of six virus-associated cancers identifies changes in the tumor immune microenvironment and altered genetic programs

(2018) Frederick S. Varn et al.   CANCER RESEARCH

Immunotherapy for Merkel Cell Carcinoma

(2018) Kotaro Nagase et al.   CURRENT TREATMENT OPTIONS IN ONCOLOGY

Screening for Cervical Cancer With High-Risk Human Papillomavirus Testing

(2018) Joy Melnikow et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

A Paradigm Shift in Cancer Immunotherapy: From Enhancement to Normalization

(2018) Miguel F. Sanmamed et al.   CELL

Immune Activation and Benefit From Avelumab in EBV-Positive Gastric Cancer

(2017) Anshuman Panda et al.   JNCI-Journal of the National Cancer Institute

Tumour virology in the era of high-throughput genomics

(2017) Ka-Wei Tang et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Immune Activation and Benefit From Avelumab in EBV-Positive Gastric Cancer

(2017) Anshuman Panda et al.   JNCI-Journal of the National Cancer Institute

Epigenetics and Genetics of Viral Latency

(2016) Paul M. Lieberman   Cell Host & Microbe

Safety and clinical activity of pembrolizumab for treatment of recurrent or metastatic squamous cell carcinoma of the head and neck (KEYNOTE-012): an open-label, multicentre, phase 1b trial

(2016) Tanguy Y Seiwert et al.   LANCET ONCOLOGY

Predictive biomarkers for checkpoint inhibitor-based immunotherapy

(2016) Geoffrey T Gibney et al.   LANCET ONCOLOGY

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

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

Divergent viral presentation among human tumors and adjacent normal tissues

(2016) Song Cao et al.   Scientific Reports

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association

(2016) Michael J. Strong et al.   Acta Neuropathologica Communications

The tumor virus landscape of AIDS-related lymphomas

(2015) A. Arvey et al.   BLOOD

Classifying Cancers Based on T-cell Infiltration and PD-L1

(2015) Michele W.L. Teng et al.   CANCER RESEARCH

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Human Viral Oncogenesis: A Cancer Hallmarks Analysis

(2014) Enrique A. Mesri et al.   Cell Host & Microbe

Dendritic Cell-Derived Exosomes as Immunotherapies in the Fight against Cancer

(2014) J. M. Pitt et al.   JOURNAL OF IMMUNOLOGY

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

(2013) J. D. Khoury et al.   JOURNAL OF VIROLOGY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The landscape of viral expression and host gene fusion and adaptation in human cancer

(2013) Ka-Wei Tang et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Constitutive AP-1 Activity and EBV Infection Induce PD-L1 in Hodgkin Lymphomas and Posttransplant Lymphoproliferative Disorders: Implications for Targeted Therapy

(2012) M. R. Green et al.   CLINICAL CANCER RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Genetic Aspects of Gastric Cancer Instability

(2012) Petra Hudler   TheScientificWorldJOURNAL

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

T-cell exhaustion: characteristics, causes and conversion

(2010) John S. Yi et al.   IMMUNOLOGY

Identification in Daily Practice of Patients With Lynch Syndrome (Hereditary Nonpolyposis Colorectal Cancer): Revised Bethesda Guidelines-Based ApproachVersusMolecular Screening

(2008) Catherine Julié et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY