Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

Resolving systematic errors in widely used enhancer activity assays in human cells

(2017) Felix Muerdter et al.   NATURE METHODS

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

(2017) Yupeng He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications

(2015) Yiming Lu et al.   PLoS One

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features

(2014) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

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

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

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

(2013) Alex S. Nord et al.   CELL

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

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

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

Characterization of Enhancer Function from Genome-Wide Analyses

(2012) Glenn A. Maston et al.   Annual Review of Genomics and Human Genetics

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

(2012) Justin Cotney et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

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

(2011) Jason Ernst et al.   NATURE

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

(2011) Chao Cheng et al.   NUCLEIC ACIDS RESEARCH

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Statistical performance of support vector machines

(2008) Gilles Blanchard et al.   ANNALS OF STATISTICS

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS