Integrating Diverse Datasets Improves Developmental Enhancer Prediction

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

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

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

Function and Regulation of AUTS2, a Gene Implicated in Autism and Human Evolution

(2013) Nir Oksenberg et al.   PLoS Genetics

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalis

(2012) Arielle Woznica et al.   DEVELOPMENTAL BIOLOGY

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

(2012) G. M. Burzynski et al.   GENOME RESEARCH

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

(2012) D. U. Gorkin et al.   GENOME RESEARCH

A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat-Wilson syndrome phenotypes

(2012) M. M. El-Kasti et al.   HUMAN MOLECULAR GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

Dual-Mode Modulation of Smad Signaling by Smad-Interacting Protein Sip1 Is Required for Myelination in the Central Nervous System

(2012) Qinjie Weng et al.   NEURON

Computational localization of transcription factor binding sites using extreme learning machines

(2012) Dianhui Wang et al.   SOFT COMPUTING

A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis

(2012) Brian W. Busser et al.   PLoS Genetics

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Transcriptional enhancers in development and disease

(2012) Noboru Sakabe et al.   GENOME BIOLOGY

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida et al.   BIOINFORMATICS

CLARE: Cracking the LAnguage of Regulatory Elements

(2011) Leila Taher et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics of Long-Range Regulatory Elements

(2010) James P. Noonan et al.   Annual Review of Genomics and Human Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Developmental Stages in Human Embryos: Revised and New Measurements

(2010) Ronan O’Rahilly et al.   CELLS TISSUES ORGANS

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Hourglass theory gets molecular approval

(2010) Tanita Casci   NATURE REVIEWS GENETICS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

miR-200 family and targets, ZEB1 and ZEB2, modulate uterine quiescence and contractility during pregnancy and labor

(2010) N. E. Renthal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Gene regulation and the origins of human biological uniqueness

(2010) Samuel J. Sholtis et al.   TRENDS IN GENETICS

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

A systematic approach to identify functional motifs within vertebrate developmental enhancers

(2009) Qiang Li et al.   DEVELOPMENTAL BIOLOGY

Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse

(2009) Miriam R. Kantorovitz et al.   DEVELOPMENTAL CELL

Functional autonomy of distant-acting human enhancers

(2009) Axel Visel et al.   GENOMICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Reptilian heart development and the molecular basis of cardiac chamber evolution

(2009) Kazuko Koshiba-Takeuchi et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

FOXC1 is required for normal cerebellar development and is a major contributor to chromosome 6p25.3 Dandy-Walker malformation

(2009) Kimberly A Aldinger et al.   NATURE GENETICS

Sip1 regulates sequential fate decisions by feedback signaling from postmitotic neurons to progenitors

(2009) Eve Seuntjens et al.   NATURE NEUROSCIENCE

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources

(2008) Harri Lähdesmäki et al.   PLoS One

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

(2007) D. M. McGaughey et al.   GENOME RESEARCH