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Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

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Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

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On the design of CRISPR-based single-cell molecular screens

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Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

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High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

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

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The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

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Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

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A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

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Genome-wide mapping of autonomous promoter activity in human cells

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Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

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Integrative analysis of 111 reference human epigenomes

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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

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Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Multiplex pairwise assembly of array-derived DNA oligonucleotides

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

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High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

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High-throughput functional testing of ENCODE segmentation predictions

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An atlas of active enhancers across human cell types and tissues

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Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

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Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

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The UCSC Genome Browser database: 2014 update

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

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HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

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An integrated encyclopedia of DNA elements in the human genome

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

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Massively parallel functional dissection of mammalian enhancers in vivo

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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

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BEDTools: a flexible suite of utilities for comparing genomic features

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The NIH Roadmap Epigenomics Mapping Consortium

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High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

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