Sequence determinants of human gene regulatory elements

Base-resolution models of transcription-factor binding reveal soft motif syntax

(2021) Žiga Avsec et al.   NATURE GENETICS

BANP opens chromatin and activates CpG-island-regulated genes

(2021) Ralph S. Grand et al.   NATURE

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

(2020) Vikram Agarwal et al.   Cell Reports

Occupancy maps of 208 chromatin-associated proteins in one human cell type

(2020) E. Christopher Partridge et al.   NATURE

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

Systematic interrogation of human promoters

(2019) Shira Weingarten-Gabbay et al.   GENOME RESEARCH

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

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

(2019) Martin Kircher et al.   Nature Communications

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

(2019) Carl G. de Boer et al.   NATURE BIOTECHNOLOGY

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility

(2018) Bei Wei et al.   NATURE BIOTECHNOLOGY

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

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

(2018) Brett B Maricque et al.   NATURE BIOTECHNOLOGY

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

(2017) Ahmet Zehir et al.   NATURE MEDICINE

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

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth

(2017) Kashyap Dave et al.   eLife

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

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Genome-wide mapping of autonomous promoter activity in human cells

(2016) Joris van Arensbergen et al.   NATURE BIOTECHNOLOGY

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

(2016) René Dreos et al.   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

The physical size of transcription factors is key to transcriptional regulation in chromatin domains

(2015) Kazuhiro Maeshima et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The bioenergetic costs of a gene

(2015) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Evolution of transcriptional enhancers and animal diversity

(2013) M. Rubinstein et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2013) C. D. Arnold et al.   SCIENCE

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

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

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer

(2011) Biswajyoti Sahu et al.   EMBO JOURNAL

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL