Enhancer target prediction: state-of-the-art approaches and future prospects

The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data

(2023) Dennis Hecker et al.   BIOINFORMATICS

GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks

(2023) Aryan Kamal et al.   Molecular Systems Biology

A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome

(2023) Le Thi Phan et al.   PROTEOMICS

Predicting enhancer-promoter interaction based on epigenomic signals

(2023) Leqiong Zheng et al.   Frontiers in Genetics

PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships

(2023) Caitlin Mills et al.   npj Systems Biology and Applications

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

(2023) Carmen Bravo González-Blas et al.   NATURE METHODS

CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps

(2022) Tom Aharon Hait et al.   NUCLEIC ACIDS RESEARCH

Regulating specificity in enhancer–promoter communication

(2022) Charalampos Chrysovalantis Galouzis et al.   CURRENT OPINION IN CELL BIOLOGY

EPI-Mind: Identifying Enhancer–Promoter Interactions Based on Transformer Mechanism

(2022) Yu Ni et al.   Interdisciplinary Sciences-Computational Life Sciences

Enhancer-Promoter Communication: It’s Not Just About Contact

(2022) Annabelle Wurmser et al.   Frontiers in Molecular Biosciences

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer–target gene regulatory interactions

(2021) Elisa Salviato et al.   NUCLEIC ACIDS RESEARCH

Enhancers in disease: molecular basis and emerging treatment strategies

(2021) Annique Claringbould et al.   TRENDS IN MOLECULAR MEDICINE

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

(2021) Ramzan Umarov et al.   PLoS Computational Biology

Effective gene expression prediction from sequence by integrating long-range interactions

(2021) Žiga Avsec et al.   NATURE METHODS

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

(2020) Hang Xu et al.   Computational and Structural Biotechnology Journal

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Predicting enhancer-promoter interactions by deep learning and matching heuristic

(2020) Xiaoping Min et al.   BRIEFINGS IN BIOINFORMATICS

A Simple Convolutional Neural Network for Prediction of Enhancer-Promoter Interactions with DNA Sequence Data

(2019) Zhong Zhuang et al.   BIOINFORMATICS

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

(2019) Molly Gasperini et al.   CELL

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

(2019) Wenran Li et al.   NUCLEIC ACIDS RESEARCH

InTAD: chromosome conformation guided analysis of enhancer target genes

(2019) Konstantin Okonechnikov et al.   BMC BIOINFORMATICS

Inflated performance measures in enhancer–promoter interaction-prediction methods

(2019) Fan Cao et al.   NATURE GENETICS

Predicting three-dimensional genome organization with chromatin states

(2019) Yifeng Qi et al.   PLoS Computational Biology

Identifying enhancer–promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism

(2019) Zengyan Hong et al.   BIOINFORMATICS

EPIP: a novel approach for condition-specific enhancer–promoter interaction prediction

(2019) Amlan Talukder et al.   BIOINFORMATICS

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

(2019) Josh Tycko et al.   Nature Communications

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

Quantitative prediction of enhancer–promoter interactions

(2019) Polina S. Belokopytova et al.   GENOME RESEARCH

Enhancer–gene maps in the human and zebrafish genomes using evolutionary linkage conservation

(2019) Yves Clément et al.   NUCLEIC ACIDS RESEARCH

In silico prediction of high-resolution Hi-C interaction matrices

(2019) Shilu Zhang et al.   Nature Communications

Identifying Novel Enhancer Elements with CRISPR-Based Screens

(2018) Jason C. Klein et al.   ACS Chemical Biology

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods

(2018) Yifeng Li et al.   BMC BIOINFORMATICS

Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

(2018) Sarah Rennie et al.   Nature Communications

3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering

(2018) Jinlei Han et al.   Molecular Cytogenetics

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods

(2018) Fei Sun et al.   MOLECULAR CELL

Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy

(2018) Wang Xi et al.   PLoS Computational Biology

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

(2017) Qin Cao et al.   NATURE GENETICS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro 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

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits

(2016) Suhn Kyong Rhie et al.   Epigenetics & Chromatin

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

PETModule: a motif module based approach for enhancer target gene prediction

(2016) Changyong Zhao et al.   Scientific Reports

A predictive modeling approach for cell line-specific long-range regulatory interactions

(2015) Sushmita Roy et al.   NUCLEIC ACIDS RESEARCH

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

(2015) Lijing Yao et al.   GENOME BIOLOGY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

(2013) Waseem Akhtar et al.   CELL

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

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

(2013) C. D. Arnold et al.   SCIENCE

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

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

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY