A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues

(2020) Giulia I M Pasquesi et al.   Genome Biology and Evolution

Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation

(2020) Juan I. Bravo et al.   DEVELOPMENT

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

A Field Guide to Eukaryotic Transposable Elements

(2020) Jonathan N. Wells et al.   Annual Review of Genetics

A single-cell transcriptome atlas of marsupial embryogenesis and X inactivation

(2020) Shantha K. Mahadevaiah et al.   NATURE

Transposable elements drive widespread expression of oncogenes in human cancers

(2019) Hyo Sik Jang et al.   NATURE GENETICS

Mouse germ line mutations due to retrotransposon insertions

(2019) Liane Gagnier et al.   Mobile DNA

WashU Epigenome Browser update 2019

(2019) Daofeng Li et al.   NUCLEIC ACIDS RESEARCH

CRISPR-READI: Efficient Generation of Knockin Mice by CRISPR RNP Electroporation and AAV Donor Infection

(2019) Sean Chen et al.   Cell Reports

Host–transposon interactions: conflict, cooperation, and cooption

(2019) Rachel L Cosby et al.   GENES & DEVELOPMENT

Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements

(2019) Nicky Chung et al.   Mobile DNA

Transposable Elements, Inflammation, and Neurological Disease

(2019) Aurian Saleh et al.   Frontiers in Neurology

CDK2 kinase activity is a regulator of male germ cell fate

(2019) Priti Singh et al.   DEVELOPMENT

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

(2019) Yu Kong et al.   Nature Communications

The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer

(2018) Elissa D. Pastuzyn et al.   CELL

Efficient mouse genome engineering by CRISPR-EZ technology

(2018) Andrew J Modzelewski et al.   Nature Protocols

Knockdown of CDK2AP1 in human embryonic stem cells reduces the threshold of differentiation

(2018) Khaled N. Alsayegh et al.   PLoS One

Multisite dependency of an E3 ligase controls monoubiquitylation-dependent cell fate decisions

(2018) Achim Werner et al.   eLife

Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses

(2018) Nicole Grandi et al.   Frontiers in Immunology

Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

(2018) Thorsten Boroviak et al.   DEVELOPMENT

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos

(2017) Xinyi Wang et al.   GENOME RESEARCH

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Deficiency of microRNAmiR-34aexpands cell fate potential in pluripotent stem cells

(2017) Yong Jin Choi et al.   SCIENCE

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

(2017) Vasavi Sundaram et al.   Nature Communications

Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice

(2017) Kota Inoue et al.   PLoS Genetics

Activation of Lineage Regulators and Transposable Elements across a Pluripotent Spectrum

(2017) Jamie A. Hackett et al.   Stem Cell Reports

The impact of transposable elements on mammalian development

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

CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome

(2016) Jonathan Göke et al.   EMBO REPORTS

Highly Efficient Mouse Genome Editing by CRISPR Ribonucleoprotein Electroporation of Zygotes

(2016) Sean Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Natural courtship song variation caused by an intronic retroelement in an ion channel gene

(2016) Yun Ding et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

The Relationship between Cell Number, Division Behavior and Developmental Potential of Cleavage Stage Human Embryos: A Time-Lapse Study

(2016) Xiangyi Kong et al.   PLoS One

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

(2016) E. B. Chuong et al.   SCIENCE

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

Roles for retrotransposon insertions in human disease

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

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues

(2016) Marco De Cecco et al.   Aging-US

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang et al.   CELL

The mechanism of ageing: primary role of transposable elements in genome disintegration

(2015) Ádám Sturm et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Genome activation in bovine embryos: Review of the literature and new insights from RNA sequencing experiments

(2014) Alexander Graf et al.   ANIMAL REPRODUCTION SCIENCE

Two waves of de novo methylation during mouse germ cell development

(2014) A. Molaro et al.   GENES & DEVELOPMENT

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Matyas Flemr et al.   CELL

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

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

(2013) Edward B Chuong et al.   NATURE GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

LINE-1 Elements in Structural Variation and Disease

(2011) Christine R. Beck et al.   Annual Review of Genomics and Human Genetics

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Coordination of cell proliferation and anterior-posterior axis establishment in the mouse embryo

(2011) D. W. Stuckey et al.   DEVELOPMENT

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Double Edge

(2011) D.T.W. Wong et al.   JOURNAL OF DENTAL RESEARCH

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Retrotransposition is associated with genome instability during chronological aging

(2011) P. H. Maxwell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CDK2AP1/DOC-1 is a bona fide subunit of the Mi-2/NuRD complex

(2010) Cornelia G. Spruijt et al.   Molecular BioSystems

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

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

Targeted Inactivation of p12Cdk2ap1, CDK2 Associating Protein 1, Leads to Early Embryonic Lethality

(2009) Yong Kim et al.   PLoS One

Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene

(2009) A. Dupressoir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta

(2008) Yoichi Sekita et al.   NATURE GENETICS