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

Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells

(2019) Boris Reznik et al.   DEVELOPMENT

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

LINE-1 Evasion of Epigenetic Repression in Humans

(2019) Francisco J. Sanchez-Luque et al.   MOLECULAR CELL

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pedigree-based estimation of human mobile element retrotransposition rates

(2019) Julie Feusier et al.   GENOME RESEARCH

TRIM28 and the control of transposable elements in the brain

(2018) Daniela A. Grassi et al.   BRAIN RESEARCH

Mammalian transposable elements and their impacts on genome evolution

(2018) Roy N. Platt et al.   CHROMOSOME RESEARCH

Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling

(2018) Alexander T Xue et al.   Genome Biology and Evolution

Pairwise comparisons across species are problematic when analyzing functional genomic data

(2018) Casey W. Dunn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

(2018) Giulia I. M. Pasquesi et al.   Nature Communications

Transposable elements and gene expression during the evolution of amniotes

(2018) Lu Zeng et al.   Mobile DNA

L1 retrotransposition in the soma: a field jumping ahead

(2018) Geoffrey J. Faulkner et al.   Mobile DNA

Database resources of the National Center for Biotechnology Information

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Jiangping He et al.   Nature Communications

PIWI family emerging as a decisive factor of cell fate: An overview

(2017) Murugavel Ponnusamy et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

(2017) Sandra R. Richardson et al.   GENOME RESEARCH

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

L1 Mosaicism in Mammals: Extent, Effects, and Evolution

(2017) Geoffrey J. Faulkner et al.   TRENDS IN GENETICS

The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity

(2017) Christina Ernst et al.   Nature Communications

Identification and Characterization of a Class of MALAT1 -like Genomic Loci

(2017) Bin Zhang et al.   Cell Reports

Domestic chickens activate a piRNA defense against avian leukosis virus

(2017) Yu Huining Sun et al.   eLife

Activation of Lineage Regulators and Transposable Elements across a Pluripotent Spectrum

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

P53 and the defenses against genome instability caused by transposons and repetitive elements

(2016) Arnold J. Levine et al.   BIOESSAYS

A Mechanism for Somatic Brain Mosaicism

(2016) Irving L. Weissman et al.   CELL

The impact of transposable elements on mammalian development

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

Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories

(2016) Michael W. Vandewege et al.   Genome Biology and Evolution

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

A comprehensive approach to expression of L1 loci

(2016) Prescott Deininger et al.   NUCLEIC ACIDS RESEARCH

Establishment and functions of DNA methylation in the germline

(2016) Kathleen R Stewart et al.   Epigenomics

Environment-driven somatic mosaicism in brain disorders

(2016) Tracy A. Bedrosian et al.   Genome Medicine

Restricting retrotransposons: a review

(2016) John L. Goodier   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

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners

(2015) Robyn S.M. Lim et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

(2015) Vincent J. Lynch et al.   Cell Reports

Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes

(2015) Paula Stein et al.   PLoS Genetics

Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs

(2015) Andrew Paul Hutchins et al.   Science Bulletin

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

piRNAs: from biogenesis to function

(2014) E.-M. Weick et al.   DEVELOPMENT

A Role for Retrotransposon LINE-1 in Fetal Oocyte Attrition in Mice

(2014) Safia Malki et al.   DEVELOPMENTAL CELL

Ovarian germline stem cells: an unlimited source of oocytes?

(2014) Carol B. Hanna et al.   FERTILITY AND STERILITY

Two waves of de novo methylation during mouse germ cell development

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

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

(2014) Julia Vogt et al.   GENOME BIOLOGY

Development, differentiation and manipulation of chicken germ cells

(2013) Yoshiaki Nakamura et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

LINE-1 Elements in Structural Variation and Disease

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

Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles

(2011) C. Gilbert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

PIWI-interacting small RNAs: the vanguard of genome defence

(2011) Mikiko C. Siomi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Profiling Sex-Specific piRNAs in Zebrafish

(2010) X. Zhou et al.   GENETICS

Genetics of mammalian meiosis: regulation, dynamics and impact on fertility

(2010) Mary Ann Handel et al.   NATURE REVIEWS GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability

(2009) Yohei Kirino et al.   NATURE CELL BIOLOGY

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Analysis of chicken primordial germ cells

(2008) Makoto Motono et al.   CYTOTECHNOLOGY

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE