Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells

(2020) Dana M King et al.   eLife

Index and biological spectrum of human DNase I hypersensitive sites

(2020) Wouter Meuleman et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

(2020) Peng He et al.   NATURE

Systematic interrogation of human promoters

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

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

(2019) Kaia Mattioli et al.   GENOME RESEARCH

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

Novel TBC1D24 Mutations in a Case of Nonconvulsive Status Epilepticus

(2018) Jingjing Li et al.   Frontiers in Neurology

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

(2018) Brett B Maricque et al.   NATURE BIOTECHNOLOGY

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Recessive TBC1D24 Mutations Are Frequent in Moroccan Non-Syndromic Hearing Loss Pedigrees

(2015) Amina Bakhchane et al.   PLoS One

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

The grammar of transcriptional regulation

(2014) Shira Weingarten-Gabbay et al.   HUMAN GENETICS

TBC1D24Mutation Causes Autosomal-Dominant Nonsyndromic Hearing Loss

(2014) Hela Azaiez et al.   HUMAN MUTATION

Epigenetics, chromatin and genome organization: recent advances from the ENCODE project

(2014) L. Siggens et al.   JOURNAL OF INTERNAL MEDICINE

Identifying and mapping cell-type-specific chromatin programming of gene expression

(2014) Troels T. Marstrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

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

(2013) Robin P Smith et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

DNA methylation dynamics in health and disease

(2013) Yehudit Bergman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Sequence features that drive human promoter function and tissue specificity

(2010) J. M. Landolin et al.   GENOME RESEARCH

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

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

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Alan P. Boyle et al.   CELL