Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

CDK4/6 inhibition triggers anti-tumour immunity

(2017) Shom Goel et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes

(2017) Pumipat Tongyoo et al.   PLoS One

Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer

(2016) Elena Cherkasova et al.   CANCER RESEARCH

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

Immune targets and neoantigens for cancer immunotherapy and precision medicine

(2016) Rong-Fu Wang et al.   CELL RESEARCH

Genomic Analysis of Immune Cell Infiltrates Across 11 Tumor Types

(2016) Michael D. Iglesia et al.   JNCI-Journal of the National Cancer Institute

Tumour-specific proline vulnerability uncovered by differential ribosome codon reading

(2016) Fabricio Loayza-Puch et al.   NATURE

Classification and characterization of human endogenous retroviruses; mosaic forms are common

(2016) Laura Vargiu et al.   Retrovirology

Genomic Analysis of Immune Cell Infiltrates Across 11 Tumor Types

(2016) Michael D. Iglesia et al.   JNCI-Journal of the National Cancer Institute

Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data

(2015) Kerstin Haase et al.   BMC Medical Genomics

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

(2015) Michael S. Rooney et al.   CELL

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

(2015) Katherine B. Chiappinelli et al.   CELL

EAU Guidelines on Renal Cell Carcinoma: 2014 Update

(2015) Borje Ljungberg et al.   EUROPEAN UROLOGY

More tricks with tetramers: a practical guide to staining T cells with peptide-MHC multimers

(2015) Garry Dolton et al.   IMMUNOLOGY

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer

(2014) M. D. Iglesia et al.   CLINICAL CANCER RESEARCH

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Inactivation of the von Hippel–Lindau tumor suppressor leads to selective expression of a human endogenous retrovirus in kidney cancer

(2011) E Cherkasova et al.   ONCOGENE

Regulation of human endogenous retrovirus-K expression in melanomas by CpG methylation

(2010) Sven Stengel et al.   GENES CHROMOSOMES & CANCER

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells

(2009) K. S. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regression of human kidney cancer following allogeneic stem cell transplantation is associated with recognition of an HERV-E antigen by T cells

(2008) Yoshiyuki Takahashi et al.   JOURNAL OF CLINICAL INVESTIGATION

Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles

(2008) K. Boller et al.   JOURNAL OF GENERAL VIROLOGY

Human Endogenous Retrovirus K (HML-2) Elements in the Plasma of People with Lymphoma and Breast Cancer

(2008) R. Contreras-Galindo et al.   JOURNAL OF VIROLOGY

Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7

(2008) A. H. Bakker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA