TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

(2019) Gabriel E. Rech et al.   PLoS Genetics

L1 drives IFN in senescent cells and promotes age-associated inflammation

(2019) Marco De Cecco et al.   NATURE

Dysregulated expression of repetitive DNA in ER+/HER2- breast cancer

(2019) Cihangir Yandım et al.   Cancer Genetics

PARP9 is overexpressed in human breast cancer and promotes cancer cell migration

(2018) Xinghong Tang et al.   Oncology Letters

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

(2018) Alexander Solovyov et al.   Cell Reports

Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins

(2018) Daniil Nikitin et al.   Frontiers in Immunology

Computational tools to unmask transposable elements

(2018) Patricia Goerner-Potvin et al.   NATURE REVIEWS GENETICS

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

(2018) Jiangping He et al.   Nature Communications

Transposable elements are the primary source of novelty in primate gene regulation

(2017) Marco Trizzino et al.   GENOME RESEARCH

PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants

(2017) Gökhan Karakülah et al.   GENOMICS

RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes

(2017) Gökhan Karakülah   GENOMICS

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

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

Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer

(2017) Stephane Wenric et al.   Scientific Reports

The impact of transposable elements on mammalian development

(2016) Jose L. Garcia-Perez et al.   DEVELOPMENT

DNA methylation variation of human-specific Alu repeats

(2016) Arundhati Bakshi et al.   Epigenetics

Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170

(2016) Alison M Dunning et al.   NATURE GENETICS

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

(2016) Emmanuelle Lerat et al.   NUCLEIC ACIDS RESEARCH

Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers

(2016) Inna Tishchenko et al.   PLoS One

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2

(2016) Solenne Bire et al.   PLoS Genetics

Roles for retrotransposon insertions in human disease

(2016) Dustin C. Hancks et al.   Mobile DNA

Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes

(2016) A. Forero et al.   Cancer Immunology Research

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species

(2015) Darshan Shimoga Chandrashekar et al.   PLoS One

Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes

(2015) Moritz Gerstung et al.   Nature Communications

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Multi-gene fluorescence in situ hybridization to detect cell cycle gene copy number aberrations in young breast cancer patients

(2014) Chunyan Li et al.   CELL CYCLE

Genomic and protein expression analysis reveals flap endonuclease 1 (FEN1) as a key biomarker in breast and ovarian cancer

(2014) Tarek M.A. Abdel-Fatah et al.   Molecular Oncology

The FEN1 E359K germline mutation disrupts the FEN1–WRN interaction and FEN1 GEN activity, causing aneuploidy-associated cancers

(2014) L Chung et al.   ONCOGENE

Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia

(2014) Yue Li et al.   PLoS Computational Biology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Causes of Genome Instability

(2013) Andrés Aguilera et al.   Annual Review of Genetics

A Retrotransposon-Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes

(2013) Matyas Flemr et al.   CELL

Endogenous retroviruses function as species-specific enhancer elements in the placenta

(2013) Edward B Chuong et al.   NATURE GENETICS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Identification of a mimotope for circulating anti-cytokeratin 8/18 antibody and its usage for the diagnosis of breast cancer

(2012) CHANG-KYU HEO et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Gene expression profiling assigns CHEK2 1100delC breast cancers to the luminal intrinsic subtypes

(2011) Jord H. A. Nagel et al.   BREAST CANCER RESEARCH AND TREATMENT

Exploring giant plant genomes with next-generation sequencing technology

(2011) Laura J. Kelly et al.   CHROMOSOME RESEARCH

Convergent Evolution of Endometrial Prolactin Expression in Primates, Mice, and Elephants Through the Independent Recruitment of Transposable Elements

(2011) Deena Emera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Genomic instability in breast cancer: Pathogenesis and clinical implications

(2010) Kevin A. Kwei et al.   Molecular Oncology

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Repetitive DNA elements, nucleosome binding and human gene expression

(2009) Ahsan Huda et al.   GENE

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

(2009) Carla J. Cohen et al.   GENE

SAFB1 Mediates Repression of Immune Regulators and Apoptotic Genes in Breast Cancer Cells

(2009) Stephanie Hammerich-Hille et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Copine-III interacts with ErbB2 and promotes tumor cell migration

(2009) C Heinrich et al.   ONCOGENE

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH