Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome

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

(2017) Marco Trizzino et al.   GENOME RESEARCH

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Promoter shape varies across populations and affects promoter evolution and expression noise

(2017) Ignacio E Schor et al.   NATURE GENETICS

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

(2017) Margherita Francescatto et al.   Scientific Data

Monitoring transcription initiation activities in rat and dog

(2017) Marina Lizio et al.   Scientific Data

Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk

(2016) Ashley K. Tehranchi et al.   CELL

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen et al.   GENOME RESEARCH

NF-κB and IRF1 Induce Endogenous Retrovirus K Expression via Interferon-Stimulated Response Elements in Its 5′ Long Terminal Repeat

(2016) Mamneet Manghera et al.   JOURNAL OF VIROLOGY

Genome-wide mapping of autonomous promoter activity in human cells

(2016) Joris van Arensbergen et al.   NATURE BIOTECHNOLOGY

Regulatory activities of transposable elements: from conflicts to benefits

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

OUP accepted manuscript

(2016)   NUCLEIC ACIDS RESEARCH

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

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

(2016) E. B. Chuong et al.   SCIENCE

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

The frequent evolutionary birth and death of functional promoters in mouse and human

(2015) Robert S. Young et al.   GENOME RESEARCH

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

(2015) Tugce Bilgin Sonay et al.   GENOME RESEARCH

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

(2015) Jens Durruthy-Durruthy et al.   NATURE GENETICS

Abundant contribution of short tandem repeats to gene expression variation in humans

(2015) Melissa Gymrek et al.   NATURE GENETICS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Core promoter short tandem repeats as evolutionary switch codes for primate speciation

(2014) Mina Ohadi et al.   AMERICAN JOURNAL OF PRIMATOLOGY

The landscape of human STR variation

(2014) Thomas Willems et al.   GENOME RESEARCH

A promoter-level mammalian expression atlas

(2014)   NATURE

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

(2014) Alexandre Fort et al.   NATURE GENETICS

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Evidence for Evolutionary and Nonevolutionary Forces Shaping the Distribution of Human Genetic Variants near Transcription Start Sites

(2014) Giovanni Scala et al.   PLoS One

Recombination initiation maps of individual human genomes

(2014) F. Pratto et al.   SCIENCE

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

Transcription Start Site Evolution in Drosophila

(2013) Bradley J. Main et al.   MOLECULAR BIOLOGY AND EVOLUTION

Endogenous retroviruses function as species-specific enhancer elements in the placenta

(2013) Edward B Chuong et al.   NATURE GENETICS

Meiotic recombination in mammals: localization and regulation

(2013) Frédéric Baudat et al.   NATURE REVIEWS GENETICS

Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements

(2013) Sterling Sawaya et al.   PLoS One

Transposable element recruitments in the mammalian placenta: impacts and mechanisms

(2012) D. Emera et al.   Briefings in Functional Genomics

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection

(2011) Netta Mendelson Cohen et al.   CELL

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution

(2010) Ken Daigoro Yokoyama et al.   Genome Biology and Evolution

Every microsatellite is different: Intrinsic DNA features dictate mutagenesis of common microsatellites present in the human genome

(2009) Kristin A. Eckert et al.   MOLECULAR CARCINOGENESIS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Automated paleontology of repetitive DNA with REANNOTATE

(2008) Vini Pereira   BMC GENOMICS

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE