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Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

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Evolution of Mutator transposable elements across eukaryotic diversity

(2019) Mathilde Dupeyron et al.   Mobile DNA

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

(2019) Julien Pontis et al.   Cell Stem Cell

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis

(2019) Therese Mitros et al.   DEVELOPMENTAL BIOLOGY

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(2019) Stephen Branden Van Oss et al.   PLoS Genetics

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

(2019) Pierre‐Yves Helleboid et al.   EMBO JOURNAL

CDD/SPARCLE: the conserved domain database in 2020

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OUP accepted manuscript

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Transposable elements generate regulatory novelty in a tissue-specific fashion

(2018) Marco Trizzino et al.   BMC GENOMICS

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control

(2018) Christopher HC Tie et al.   EMBO REPORTS

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

(2018) Daniel R Fuentes et al.   eLife

Identification of regulatory elements from nascent transcription using dREG

(2018) Zhong Wang et al.   GENOME RESEARCH

Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome

(2018) Michael Tellier et al.   NUCLEIC ACIDS RESEARCH

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

(2017) Cibele G. Sotero-Caio et al.   Genome Biology and Evolution

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith 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

Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders

(2016) Holly A.F. Stessman et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Transcriptomic and epigenomic characterization of the developing bat wing

(2016) Walter L Eckalbar et al.   NATURE GENETICS

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Regulatory activities of transposable elements: from conflicts to benefits

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

Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes

(2016) Juan C. Oliveros et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

POGZ truncating alleles cause syndromic intellectual disability

(2016) Janson White et al.   Genome Medicine

The Transcriptional Repressive Activity of KRAB Zinc Finger Proteins Does Not Correlate with Their Ability to Recruit TRIM28

(2016) Kristin E. Murphy et al.   PLoS One

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

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

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

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

New Gene Evolution: Little Did We Know

(2013) Manyuan Long et al.   Annual Review of Genetics

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions

(2013) Alexander Hayward et al.   PLoS One

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

(2013) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

SET for life: biochemical activities and biological functions of SET domain-containing proteins

(2013) Hans-Martin Herz et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii

(2013) Inge Seim et al.   Nature Communications

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

The conserved Cockayne syndrome B-piggyBac fusion protein (CSB-PGBD3) affects DNA repair and induces both interferon-like and innate antiviral responses in CSB-null cells

(2012) Arnold D. Bailey et al.   DNA REPAIR

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

(2012) G. Zhang et al.   SCIENCE

Tethering of the Conserved piggyBac Transposase Fusion Protein CSB-PGBD3 to Chromosomal AP-1 Proteins Regulates Expression of Nearby Genes in Humans

(2012) Lucas T. Gray et al.   PLoS Genetics

Comparative biology of mammalian telomeres: hypotheses on ancestral states and the roles of telomeres in longevity determination

(2011) Nuno M. V. Gomes et al.   AGING CELL

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies

(2011) Y.-W. Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crypton transposons: identification of new diverse families and ancient domestication events

(2011) Kenji K Kojima et al.   Mobile DNA

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Transposases are the most abundant, most ubiquitous genes in nature

(2010) Ramy K. Aziz et al.   NUCLEIC ACIDS RESEARCH

Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict

(2010) C. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

(2010) Weidong Bao et al.   Mobile DNA

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Molecular Architecture of the Mos1 Paired-End Complex: The Structural Basis of DNA Transposition in a Eukaryote

(2009) Julia M. Richardson et al.   CELL

Population genetic models of duplicated genes

(2009) Hideki Innan   GENETICA

Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE

(2009) G. Yang et al.   SCIENCE

Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus

(2008) D. A. Ray et al.   GENOME RESEARCH

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

An Abundant Evolutionarily Conserved CSB-PiggyBac Fusion Protein Expressed in Cockayne Syndrome

(2008) John C. Newman et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY