Transposable elements are the primary source of novelty in primate gene regulation

The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes

(2016) Václav Janoušek et al.   Genome Biology and Evolution

Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome

(2016) Xinran Dong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel evolution of male germline epigenetic poising and somatic development in animals

(2016) Bluma J Lesch et al.   NATURE GENETICS

Origin and evolution of developmental enhancers in the mammalian neocortex

(2016) Deena Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory evolution ofTbx5and the origin of paired appendages

(2016) Noritaka Adachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) E. B. Chuong et al.   SCIENCE

Massive contribution of transposable elements to mammalian regulatory sequences

(2016) Nirmala Arul Rayan et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Chromatin variation associated with liver metabolism is mediated by transposable elements

(2016) Juan Du et al.   Epigenetics & Chromatin

ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis -Regulatory Evolution in Lepidoptera

(2016) James J. Lewis et al.   Cell Reports

Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline

(2016) Emily L. Landeen et al.   PLOS BIOLOGY

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Comprehensive identification and analysis of human accelerated regulatory DNA

(2015) Rachel M. Gittelman et al.   GENOME RESEARCH

Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor

(2015) Alisha K. Holloway et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Evolutionary insights into host–pathogen interactions from mammalian sequence data

(2015) Manuela Sironi et al.   NATURE REVIEWS GENETICS

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1

(2015) Cong Guo et al.   Nature Communications

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

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

Genome-wide Identification and Characterization of Fixed Human-Specific Regulatory Regions

(2014) Davide Marnetto et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Systems-Level Analysis of Innate Immunity

(2014) Daniel E. Zak et al.   Annual Review of Immunology

The Ensembl REST API: Ensembl Data for Any Language

(2014) Andrew Yates et al.   BIOINFORMATICS

Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems

(2014) Arnaud Martin et al.   DEVELOPMENTAL BIOLOGY

Evolution of a Cellular Immune Response in Drosophila: A Phenotypic and Genomic Comparative Analysis

(2014) Laura Salazar-Jaramillo et al.   Genome Biology and Evolution

Noncoding origins of anthropoid traits and a new null model of transposon functionalization

(2014) Ricardo C.H. del Rosario et al.   GENOME RESEARCH

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

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Tempo and mode of regulatory evolution in Drosophila

(2014) J. D. Coolon et al.   GENOME RESEARCH

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

Episodic Positive Selection in the Evolution of Avian Toll-Like Receptor Innate Immunity Genes

(2014) Catherine E. Grueber et al.   PLoS One

The Genetics of Immunity

(2014) Brian P. Lazzaro et al.   G3-Genes Genomes Genetics

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(2014) Benoit Ballester et al.   eLife

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

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

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

(2013) Christopher D. Brown 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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Population-Specific Uncommon Variant in GRIN3A Associated with Schizophrenia

(2012) Atsushi Takata et al.   BIOLOGICAL PSYCHIATRY

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand

(2012) A. Martin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells

(2011) A. DeLaForest et al.   DEVELOPMENT

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

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

(2011) Vincent J Lynch et al.   NATURE GENETICS

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

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

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

SVA retrotransposons: Evolution and genetic instability

(2010) Dustin C. Hancks et al.   SEMINARS IN CANCER BIOLOGY

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

(2010) Alexander M. Tsankov et al.   PLOS BIOLOGY

Epigenetic histone modifications of human transposable elements: genome defense versus exaptation

(2010) Ahsan Huda et al.   Mobile DNA

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

(2009) Carla J. Cohen et al.   GENE

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

A New Role for Sterol Regulatory Element Binding Protein 1 Transcription Factors in the Regulation of Muscle Mass and Muscle Cell Differentiation

(2009) V. Lecomte et al.   MOLECULAR AND CELLULAR BIOLOGY

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

(2009) Ola Wallerman et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth

(2009) Ellen Markljung et al.   PLOS BIOLOGY

Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila

(2009) Margaret C. W. Ho et al.   PLoS Genetics

Quantifying Adaptive Evolution in the Drosophila Immune System

(2009) Darren J. Obbard et al.   PLoS Genetics

PAX5/TEL Acts as a Transcriptional Repressor Causing Down-modulation of CD19, Enhances Migration to CXCL12, and Confers Survival Advantage in pre-BI Cells

(2008) G. Fazio et al.   CANCER RESEARCH

Qualifying the relationship between sequence conservation and molecular function

(2008) G. M. Cooper et al.   GENOME RESEARCH

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

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

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE