Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

Estrogen‐dependent control and cell‐to‐cell variability of transcriptional bursting

(2018) Christoph Fritzsch et al.   Molecular Systems Biology

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

(2017) Liyang Zhang et al.   GENOME RESEARCH

Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

(2017) Lin Yang et al.   Molecular Systems Biology

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

(2017) Xuebing Wu et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

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

HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions

(2017) Jie Zheng et al.   Nature Communications

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

(2016) Stefanie Schöne et al.   Nature Communications

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

(2016) Anthony Mathelier et al.   Cell Systems

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Deconvolving the Recognition of DNA Shape from Sequence

(2015) Namiko Abe et al.   CELL

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

(2015) Stephan R. Starick et al.   GENOME RESEARCH

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

(2015) S. S. Dey et al.   Molecular Systems Biology

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

(2015) Laurent Vanhille et al.   Nature Communications

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

(2014) Eilon Sharon et al.   GENOME RESEARCH

Hormone-Responsive Enhancer-Activity Maps Reveal Predictive Motifs, Indirect Repression, and Targeting of Closed Chromatin

(2014) Daria Shlyueva et al.   MOLECULAR CELL

Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise

(2013) M. Dadiani et al.   GENOME RESEARCH

The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals

(2013) Lisa C Watson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) C. D. Arnold et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Noise-mean relationship in mutated promoters

(2012) G. Hornung et al.   GENOME RESEARCH

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

DNA binding alters coactivator interaction surfaces of the intact VDR–RXR complex

(2011) Jun Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Transcriptional Bursting from the HIV-1 Promoter Is a Significant Source of Stochastic Noise in HIV-1 Gene Expression

(2010) Abhyudai Singh et al.   BIOPHYSICAL JOURNAL

Single-Molecule Approaches to Stochastic Gene Expression

(2009) Arjun Raj et al.   Annual Review of Biophysics

3D-DART: a DNA structure modelling server

(2009) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome

(2009) S. C. J. Parker et al.   SCIENCE

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols