A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity

Systematic dissection of genomic features determining transcription factor binding and enhancer function

(2017) Sharon R. Grossman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

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

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Understanding how cis -regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences

(2015) Michael A. White   GENOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

High-throughput functional testing of ENCODE segmentation predictions

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

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

(2013) Waseem Akhtar et al.   CELL

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

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

(2013) P. Kheradpour et al.   GENOME RESEARCH

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

(2013) C. D. Arnold et al.   SCIENCE

Using the Cre/lox system for targeted integration into the human genome: loxFAS-loxP pairing and delayed introduction of Cre DNA improve gene swapping efficiency

(2012) Amanda M. Lanza et al.   Biotechnology Journal

"Calling Cards" for DNA-Binding Proteins in Mammalian Cells

(2012) H. Wang et al.   GENETICS

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   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

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

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

High Cleavage Efficiency of a 2A Peptide Derived from Porcine Teschovirus-1 in Human Cell Lines, Zebrafish and Mice

(2011) Jin Hee Kim et al.   PLoS One

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency

(2010) Ron Skupsky et al.   PLoS Computational Biology

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE