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

LS-GKM: a new gkm-SVM for large-scale datasets

(2016) Dongwon Lee   BIOINFORMATICS

Opposite transcriptional regulation of integrated vs unintegrated HIV genomes by the NF-κB pathway

(2016) Sylvain Thierry et al.   Scientific Reports

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

(2015) Daniel Savic et al.   GENOME RESEARCH

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

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

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

(2015) Christopher M. Vockley 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

Multiplex pairwise assembly of array-derived DNA oligonucleotides

(2015) Jason C. Klein et al.   NUCLEIC ACIDS RESEARCH

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

(2014) Eilon Sharon et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

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

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

Sin3: Insight into its transcription regulatory functions

(2013) Rama Kadamb et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

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

(2013) P. Kheradpour et al.   GENOME RESEARCH

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

(2013) Robin P Smith et al.   NATURE GENETICS

Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle

(2013) Soundasse Munir et al.   Retrovirology

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

(2013) C. D. Arnold et al.   SCIENCE

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

Enhanced transgene expression from chromatinized plasmid DNA in mouse liver

(2012) Hiroyuki Kamiya et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   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

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

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation

(2011) Junichi Tsukada et al.   CYTOKINE

Recognition and Suppression of Transfected Plasmids by Protein ZNF511-PRAP1, a Potential Molecular Barrier to Transgene Expression

(2011) Guo-Hua Qiu et al.   MOLECULAR THERAPY

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

(2011) Ghia M. Euskirchen et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection

(2009) B. Kantor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lentivirus Production

(2009) Xiaoyin Wang et al.   Jove-Journal of Visualized Experiments

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

(2008) Minghui Jiang et al.   BMC BIOINFORMATICS

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Viral complementation allows HIV-1 replication without integration

(2008) Huub C Gelderblom et al.   Retrovirology