HERVs characterize normal and leukemia stem cells and represent a source of shared epitopes for cancer immunotherapy

Identification of shared tumor epitopes from endogenous retroviruses inducing high-avidity cytotoxic T cells for cancer immunotherapy

(2022) Paola Bonaventura et al.   Science Advances

Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes

(2021) Grégory Ehx et al.   IMMUNITY

Personalized Survival Prediction of Patients With Acute Myeloblastic Leukemia Using Gene Expression Profiling

(2021) Adrián Mosquera Orgueira et al.   Frontiers in Oncology

Improving prediction accuracy in acute myeloid leukaemia: micro-environment, immune and metabolic models

(2021) Fang Hu et al.   LEUKEMIA

A hypoxia risk signature for the tumor immune microenvironment evaluation and prognosis prediction in acute myeloid leukemia

(2021) Feng Jiang et al.   Scientific Reports

Improving the prediction of acute myeloid leukaemia outcomes by complementing mutational profiling with ex vivo chemosensitivity

(2020) Esther Onecha et al.   BRITISH JOURNAL OF HAEMATOLOGY

Human Endogenous Retroviruses (HERVs): Shaping the Innate Immune Response in Cancers

(2020) Vincent Alcazer et al.   Cancers

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues

(2020) Jean-David Larouche et al.   Genome Medicine

IFN-III is selectively produced by cDC1 and predicts good clinical outcome in breast cancer

(2020) Margaux Hubert et al.   Science Immunology

Immune landscapes predict chemotherapy resistance and immunotherapy response in acute myeloid leukemia

(2020) Jayakumar Vadakekolathu et al.   Science Translational Medicine

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia

(2020) Özgen Deniz et al.   Nature Communications

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

(2020) Daniel K. Wells et al.   CELL

Precision medicine treatment in acute myeloid leukemia using prospective genomic profiling: feasibility and preliminary efficacy of the Beat AML Master Trial

(2020) Amy Burd et al.   NATURE MEDICINE

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing

(2020) Timothy J. O’Donnell et al.   Cell Systems

Origins and evolutionary consequences of ancient endogenous retroviruses

(2019) Welkin E. Johnson   NATURE REVIEWS MICROBIOLOGY

A modular transcriptome map of mature B cell lymphomas

(2019) Henry Loeffler-Wirth et al.   Genome Medicine

arcasHLA: high resolution HLA typing from RNAseq

(2019) R Orenbuch et al.   BIOINFORMATICS

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

(2019) Matthew L. Bendall et al.   PLoS Computational Biology

Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus

(2019) Luis P. Iñiguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic therapy of myelodysplastic syndromes connects to cellular differentiation independently of endogenous retroelement derepression

(2019) Anastasiya Kazachenka et al.   Genome Medicine

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Human endogenous retroviruses and their implication for immunotherapeutics of cancer

(2018) A S Attermann et al.   ANNALS OF ONCOLOGY

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

Functional genomic landscape of acute myeloid leukaemia

(2018) Jeffrey W. Tyner et al.   NATURE

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

A 29-gene and cytogenetic score for the prediction of resistance to induction treatment in acute myeloid leukemia

(2017) Tobias Herold et al.   HAEMATOLOGICA

How good are we at predicting the fate of someone with acute myeloid leukaemia?

(2017) E Estey et al.   LEUKEMIA

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease

(2017) Magnus Tobiasson et al.   Oncotarget

A 29-gene and cytogenetic score for the prediction of resistance to induction treatment in acute myeloid leukemia

(2017) Tobias Herold et al.   HAEMATOLOGICA

Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype

(2017) Gary L. Johanning et al.   Scientific Reports

Suppression of Transposable Elements in Leukemic Stem Cells

(2017) Anthony R. Colombo et al.   Scientific Reports

A 17-gene stemness score for rapid determination of risk in acute leukaemia

(2016) Stanley W. K. Ng et al.   NATURE

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

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

(2016) Laura Vargiu et al.   Retrovirology

‘Acute myeloid leukemia: a comprehensive review and 2016 update’

(2016) I De Kouchkovsky et al.   Blood Cancer Journal

Human Endogenous Retroviruses-K (HML-2) Expression Is Correlated with Prognosis and Progress of Hepatocellular Carcinoma

(2016) Weijie Ma et al.   Biomed Research International

Neoantigens in cancer immunotherapy

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

Human endogenous retrovirus-K contributes to motor neuron disease

(2015) Wenxue Li et al.   Science Translational Medicine

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Reactivation of codogenic endogenous retroviral (ERV) envelope genes in human endometrial carcinoma and prestages: Emergence of new molecular targets.

(2015) Pamela L. Strissel et al.   Oncotarget

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A revised nomenclature for transcribed human endogenous retroviral loci

(2011) Jens Mayer et al.   Mobile DNA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

B cells and monocytes from patients with active multiple sclerosis exhibit increased surface expression of both HERV-H Env and HERV-W Env, accompanied by increased seroreactivity

(2009) Tomasz Brudek et al.   Retrovirology

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS