EpiRegio: analysis and retrieval of regulatory elements linked to genes

The histone demethylase JMJD2B regulates endothelial-to-mesenchymal transition

(2020) Simone F. Glaser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative prediction of gene expression with chromatin accessibility and conformation data

(2020) Florian Schmidt et al.   Epigenetics & Chromatin

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

New Frontiers: ARID3a in SLE

(2019) Joshua Garton et al.   Cells

EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions

(2019) Tianshun Gao et al.   PLoS Computational Biology

Cellular cross-talks in the diseased and aging heart

(2019) Julian U.G. Wagner et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

Endothelial to Mesenchymal Transition Represents a Key Link in the Interaction between Inflammation and Endothelial Dysfunction

(2018) Jin Gu Cho et al.   Frontiers in Immunology

HACER: an atlas of human active enhancers to interpret regulatory variants

(2018) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

TGF-β-Induced Endothelial-Mesenchymal Transition in Fibrotic Diseases

(2017) Evangelia Pardali et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Is a super-enhancer greater than the sum of its parts?

(2017) Noah Dukler et al.   NATURE GENETICS

DiseaseEnhancer: a resource of human disease-associated enhancer catalog

(2017) Guanxiong Zhang et al.   NUCLEIC ACIDS RESEARCH

HEDD: Human Enhancer Disease Database

(2017) Zhen Wang 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

Transcriptional landscape of the human cell cycle

(2017) Yin Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

An Exploratory Association Study of Alcohol Use Disorder and DNA Methylation

(2016) Sarah L. Hagerty et al.   ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The selection and function of cell type-specific enhancers

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

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

Role of LDB1 in the transition from chromatin looping to transcription activation

(2014) I. Krivega et al.   GENES & DEVELOPMENT

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

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

(2013) C. D. Arnold et al.   SCIENCE

Limitations and possibilities of low cell number ChIP-seq

(2012) Gregor D Gilfillan et al.   BMC GENOMICS

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

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

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS