Epigenome signature as an immunophenotype indicator prompts durable clinical immunotherapy benefits in lung adenocarcinoma

A genomic mutation signature predicts the clinical outcomes of immunotherapy and characterizes immunophenotypes in gastrointestinal cancer

(2021) Xi Jiao et al.   npj Precision Oncology

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

(2021) Alexander Bagaev et al.   CANCER CELL

Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability

(2020) Noam Auslander et al.   Nature Communications

Tumor microenvironment complexity and therapeutic implications at a glance

(2020) Roghayyeh Baghban et al.   Cell Communication and Signaling

Immune checkpoint signaling and cancer immunotherapy

(2020) Xing He et al.   CELL RESEARCH

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

(2020) Michael A. Gillette et al.   CELL

Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer

(2020) Jae-Won Cho et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment

(2020) David A. Wheeler et al.   CANCER CELL

Nivolumab plus Ipilimumab in Advanced Non–Small-Cell Lung Cancer

(2019) Matthew D. Hellmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Efficacy of Pembrolizumab in Patients With Noncolorectal High Microsatellite Instability/Mismatch Repair–Deficient Cancer: Results From the Phase II KEYNOTE-158 Study

(2019) Aurelien Marabelle et al.   JOURNAL OF CLINICAL ONCOLOGY

DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load

(2019) Hyunchul Jung et al.   Nature Communications

Basal subtype bladder tumours demonstrate a “hot” immunophenotype

(2018) Anjelica Hodgson et al.   HISTOPATHOLOGY

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Pembrolizumab plus Chemotherapy in Metastatic Non–Small-Cell Lung Cancer

(2018) Leena Gandhi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

(2018) Joel Saltz et al.   Cell Reports

Pan-cancer deconvolution of tumour composition using DNA methylation

(2018) Ankur Chakravarthy et al.   Nature Communications

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

EWAS Atlas: a curated knowledgebase of epigenome-wide association studies

(2018) Mengwei Li et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

DNA methylation–based immune response signature improves patient diagnosis in multiple cancers

(2017) Jana Jeschke et al.   JOURNAL OF CLINICAL INVESTIGATION

Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

(2017) Martin Lauss et al.   Nature Communications

Non–Small Cell Lung Cancer

(2017) David S. Ettinger et al.   Journal of the National Comprehensive Cancer Network

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Genome-wide DNA methylation analyses in lung adenocarcinomas: Association with EGFR, KRAS and TP53 mutation status, gene expression and prognosis

(2015) Maria Moksnes Bjaanaes et al.   Molecular Oncology

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

The future of immune checkpoint therapy

(2015) P. Sharma et al.   SCIENCE

Cancer statistics, 2014

(2014) Rebecca Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Genome-wide DNA Methylation Analysis of Lung Carcinoma Reveals One Neuroendocrine and Four Adenocarcinoma Epitypes Associated with Patient Outcome

(2014) A. Karlsson et al.   CLINICAL CANCER RESEARCH

Gene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity

(2014) Denise M. Wolf et al.   PLoS One

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

A Prognostic DNA Methylation Signature for Stage I Non–Small-Cell Lung Cancer

(2013) Juan Sandoval et al.   JOURNAL OF CLINICAL ONCOLOGY

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

(2013) Jessica Nordlund et al.   GENOME BIOLOGY

Potentially estrogenic polychlorinated biphenyls congeners serum levels and its relation with lung cancer

(2012) Rogelio Recio-Vega et al.   JOURNAL OF APPLIED TOXICOLOGY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

DNA methylation profiling reveals a predominant immune component in breast cancers

(2011) Sarah Dedeurwaerder et al.   EMBO Molecular Medicine

Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules

(2010) Andrew E Teschendorff et al.   BMC CANCER

Macrophage Diversity Enhances Tumor Progression and Metastasis

(2010) Bin-Zhi Qian et al.   CELL

The Macrophage Colony-Stimulating Factor 1 Response Signature in Breast Carcinoma

(2009) A. H. Beck et al.   CLINICAL CANCER RESEARCH

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Effects of infiltrating lymphocytes and estrogen receptor on gene expression and prognosis in breast cancer

(2008) Alberto Calabrò et al.   BREAST CANCER RESEARCH AND TREATMENT

Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer

(2008) Alexandros Daskalos et al.   INTERNATIONAL JOURNAL OF CANCER