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

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

(2016) E. B. Chuong et al.   SCIENCE

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

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

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

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

(2014) Yan Li et al.   PLoS One

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

(2014) Ken Daigoro Yokoyama et al.   PLoS Computational Biology

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

(2013) M. Stevens et al.   GENOME RESEARCH

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

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network

(2013) C. E. Ellison et al.   SCIENCE

The angiogenesis suppressor gene AKAP12 is under the epigenetic control of HDAC7 in endothelial cells

(2012) Andrei Turtoi et al.   ANGIOGENESIS

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

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic interplay between mouse endogenous retroviruses and host genes

(2012) Rita Rebollo et al.   GENOME BIOLOGY

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

The Human Epigenome Browser at Washington University

(2011) Xin Zhou et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Galih Kunarso et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The transcriptional foundation of pluripotency

(2009) I. Chambers et al.   DEVELOPMENT

Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb

(2009) Bo Feng et al.   NATURE CELL BIOLOGY

The evolution of hierarchical gene regulatory networks

(2009) Douglas H. Erwin et al.   NATURE REVIEWS GENETICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

G-protein-coupled receptor-associated A-kinase anchoring proteins AKAP5 and AKAP12: Differential trafficking and distribution

(2008) M CHEN et al.   CELLULAR SIGNALLING

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Ultraconserved Elements in the Olig2 Promoter

(2008) Christina T. L. Chen et al.   PLoS One