Widespread contribution of transposable elements to the innovation of gene regulatory networks
Published 2014 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Widespread contribution of transposable elements to the innovation of gene regulatory networks
Authors
Keywords
-
Journal
GENOME RESEARCH
Volume 24, Issue 12, Pages 1963-1976
Publisher
Cold Spring Harbor Laboratory
Online
2014-10-16
DOI
10.1101/gr.168872.113
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Principles of regulatory information conservation between mouse and human
- (2014) Yong Cheng et al. NATURE
- A comparative encyclopedia of DNA elements in the mouse genome
- (2014) Feng Yue et al. NATURE
- CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets
- (2013) Matthias Merkenschlager et al. CELL
- Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- (2013) B. Zhang et al. GENOME RESEARCH
- Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
- (2013) M. Stevens et al. GENOME RESEARCH
- Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
- (2013) F. S. J. de Souza et al. MOLECULAR BIOLOGY AND EVOLUTION
- 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
- The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
- (2013) Pierre-Étienne Jacques et al. PLoS Genetics
- Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
- (2013) Aurélie Kapusta et al. PLoS Genetics
- Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes
- (2012) Rita Rebollo et al. Annual Review of Genetics
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Retrotransposons as a major source of epigenetic variations in the mammalian genome
- (2012) Muhammad B. Ekram et al. Epigenetics
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- (2012) S. G. Landt et al. GENOME RESEARCH
- Endogenous viruses: insights into viral evolution and impact on host biology
- (2012) Cédric Feschotte et al. NATURE REVIEWS GENETICS
- Epigenetic interplay between mouse endogenous retroviruses and host genes
- (2012) Rita Rebollo et al. GENOME BIOLOGY
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- (2011) F. Sievers et al. Molecular Systems Biology
- Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
- (2011) Vincent J Lynch et al. NATURE GENETICS
- RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity
- (2011) Anja Nitzsche et al. PLoS One
- Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
- (2011) A. P. Jason de Koning et al. PLoS Genetics
- Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates
- (2011) Keith R Oliver et al. Mobile DNA
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species
- (2010) D. Xie et al. GENOME RESEARCH
- 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
- Conserved role of intragenic DNA methylation in regulating alternative promoters
- (2010) Alika K. Maunakea et al. NATURE
- GREAT improves functional interpretation of cis-regulatory regions
- (2010) Cory Y McLean et al. NATURE BIOTECHNOLOGY
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
- (2010) Galih Kunarso et al. NATURE GENETICS
- Long-range function of an intergenic retrotransposon
- (2010) W. Pi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Variation in Transcription Factor Binding Among Humans
- (2010) M. Kasowski et al. SCIENCE
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- CTCF: Master Weaver of the Genome
- (2009) Jennifer E. Phillips et al. CELL
- Transposable elements in gene regulation and in the evolution of vertebrate genomes
- (2009) Guillaume Bourque CURRENT OPINION IN GENETICS & DEVELOPMENT
- Endogenous retroviral LTRs as promoters for human genes: A critical assessment
- (2009) Carla J. Cohen et al. GENE
- ChIP-seq accurately predicts tissue-specific activity of enhancers
- (2009) Axel Visel et al. NATURE
- Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
- (2008) Nalini Polavarapu et al. BMC GENOMICS
- Evolution of the mammalian transcription factor binding repertoire via transposable elements
- (2008) G. Bourque et al. GENOME RESEARCH
- Cohesin mediates transcriptional insulation by CCCTC-binding factor
- (2008) Kerstin S. Wendt et al. NATURE
- Design and analysis of ChIP-seq experiments for DNA-binding proteins
- (2008) Peter V Kharchenko et al. NATURE BIOTECHNOLOGY
- Transposable elements and the evolution of regulatory networks
- (2008) Cédric Feschotte NATURE REVIEWS GENETICS
- Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo
- (2008) A. C. Roman et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Possible involvement of SINEs in mammalian-specific brain formation
- (2008) T. Sasaki et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Become a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get StartedAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started