LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly

Transposable elements drive widespread expression of oncogenes in human cancers

(2019) Hyo Sik Jang et al.   NATURE GENETICS

Accumulation of potential driver genes with genomic alterations predicts survival of high-risk neuroblastoma patients

(2018) Chen Suo et al.   Biology Direct

LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade

(2018) Wanqiang Sheng et al.   CELL

Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses

(2018) Israel Cañadas et al.   NATURE MEDICINE

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

(2018) Yafeng Zhu et al.   Nature Communications

Global Cancer Transcriptome Quantifies Repeat Element Polarization between Immunotherapy Responsive and T Cell Suppressive Classes

(2018) Alexander Solovyov et al.   Cell Reports

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

(2018) André Kahles et al.   CANCER CELL

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

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

(2018) Christof C. Smith et al.   JOURNAL OF CLINICAL INVESTIGATION

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

CDK4/6 inhibition triggers anti-tumour immunity

(2017) Shom Goel et al.   NATURE

Making a virtue of necessity: the pleiotropic role of human endogenous retroviruses in cancer

(2017) George Kassiotis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes

(2017) Jan Attig et al.   Frontiers in Microbiology

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

(2016) Elena Cherkasova et al.   CANCER RESEARCH

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Endogenous retroviral promoter exaptation in human cancer

(2016) Artem Babaian et al.   Mobile DNA

Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer

(2016) Sudhanshu Shukla et al.   NEOPLASIA

Identification of a new subclass of ALK-negative ALCL expressing aberrant levels of ERBB4 transcripts

(2015) I. Scarfo et al.   BLOOD

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

(2015) Michael S. Rooney et al.   CELL

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

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

(2015) Katherine B. Chiappinelli et al.   CELL

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

(2015) Thomas Wiesner et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Human endogenous retrovirus HERV-K(HML-2) activity in prostate cancer is dominated by a few loci

(2015) Wolfgang Goering et al.   PROSTATE

Neoantigens in cancer immunotherapy

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

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

The proinflammatory role of HECTD2 in innate immunity and experimental lung injury

(2015) Tiffany A. Coon et al.   Science Translational Medicine

Expression of young HERV-H loci in the course of colorectal carcinoma and correlation with molecular subtypes

(2015) Philippe Pérot et al.   Oncotarget

A promoter-level mammalian expression atlas

(2014)   NATURE

MiR-221 promotes the development of androgen independence in prostate cancer cells via downregulation of HECTD2 and RAB1A

(2013) T Sun et al.   ONCOGENE

Human Transposon Tectonics

(2012) Kathleen H. Burns et al.   CELL

Endogenous viruses: insights into viral evolution and impact on host biology

(2012) Cédric Feschotte et al.   NATURE REVIEWS GENETICS

Endogenous retrovirus sequences as a novel class of tumor-specific antigens: an example of HERV-H env encoding strong CTL epitopes

(2011) Christina S. Mullins et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma

(2010) Björn Lamprecht et al.   NATURE MEDICINE

Potential mechanisms of endogenous retroviral-mediated genomic instability in human cancer

(2010) M.T. Romanish et al.   SEMINARS IN CANCER BIOLOGY

HECTD2 Is Associated with Susceptibility to Mouse and Human Prion Disease

(2009) Sarah E. Lloyd et al.   PLoS Genetics

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