Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

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

(2016) Jacob C. Ulirsch et al.   CELL

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

(2016) Ryan Tewhey et al.   CELL

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

Massively parallel cis -regulatory analysis in the mammalian central nervous system

(2015) Susan Q. Shen et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Functional footprinting of regulatory DNA

(2015) Jeff Vierstra et al.   NATURE METHODS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity

(2014) Morgan A. Sammons et al.   GENOME RESEARCH

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Function-based identification of mammalian enhancers using site-specific integration

(2014) Diane E Dickel et al.   NATURE METHODS

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

(2014) Matthew Murtha et al.   NATURE METHODS

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

(2013) J. Ernst et al.   GENOME RESEARCH

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

(2013) Stephen S Gisselbrecht et al.   NATURE METHODS

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

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

(2013) C. D. Arnold et al.   SCIENCE

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes

(2013) Adam Blattler et al.   Epigenetics & Chromatin

Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO

(2012) Sunil K. Raghav et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

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

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

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

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

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

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song 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

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

(2011) Jason A. Watts et al.   PLoS Genetics

Comprehensive Analysis of the Palindromic Motif TCTCGCGAGA: A Regulatory Element of the HNRNPK Promoter

(2010) M. Mikula et al.   DNA RESEARCH

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle 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

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS 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

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

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

(2009) Nathaniel D. Heintzman et al.   NATURE

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

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY