Predicting active enhancers with DNA methylation and histone modification

Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information

(2023) Yongtian Wang et al.   BRIEFINGS IN BIOINFORMATICS

Enhancer-LSTMAtt: A Bi-LSTM and Attention-Based Deep Learning Method for Enhancer Recognition

(2022) Guohua Huang et al.   Biomolecules

Cap analysis of gene expression (CAGE) and noncoding regulatory elements

(2021) Matteo Maurizio Guerrini et al.   Seminars in Immunopathology

iEnhancer-RD: Identification of enhancers and their strength using RKPK features and deep neural networks

(2021) Huan Yang et al.   ANALYTICAL BIOCHEMISTRY

Integrative Analysis of Epigenome and Transcriptome Data Reveals Aberrantly Methylated Promoters and Enhancers in Hepatocellular Carcinoma

(2021) Peng Huang et al.   Frontiers in Oncology

A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer

(2020) Han Chen et al.   CANCER CELL

Enhancer prediction with histone modification marks using a hybrid neural network model

(2019) A. Lim et al.   METHODS

Enhancer DNA methylation: implications for gene regulation

(2019) Allegra Angeloni et al.   Essays in Biochemistry

DNA Methylation of Enhancer Elements in Myeloid Neoplasms: Think Outside the Promoters?

(2019) Ordoñez et al.   Cancers

Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer

(2019) Zhao Zhang et al.   Nature Communications

From Super-Enhancer Non-coding RNA to Immune Checkpoint: Frameworks to Functions

(2019) Manqing Wu et al.   Frontiers in Oncology

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

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis

(2018) Wanju Jiao et al.   ONCOGENE

Causal Transcription Regulatory Network Inference Using Enhancer Activity as a Causal Anchor

(2018) Deepti Vipin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Enhancer RNA and NFκB-dependent P300 regulation of ADAMDEC1

(2018) Lihua Shi et al.   MOLECULAR IMMUNOLOGY

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Enhancer RNAs: a missing regulatory layer in gene transcription

(2018) Renfang Mao et al.   Science China-Life Sciences

EnhancerDB: a resource of transcriptional regulation in the context of enhancers

(2018) Ran Kang et al.   Database-The Journal of Biological Databases and Curation

Enhancer-derived RNA: A Primer

(2017) Feng Liu   GENOMICS PROTEOMICS & BIOINFORMATICS

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues

(2015) Jen-Hao Cheng et al.   Scientific Reports

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions

(2013) Kirthi Pulakanti et al.   Epigenetics

Predicting enhancer transcription and activity from chromatin modifications

(2013) Yun Zhu et al.   NUCLEIC ACIDS RESEARCH

Comparative annotation of functional regions in the human genome using epigenomic data

(2013) Kyoung-Jae Won et al.   NUCLEIC ACIDS RESEARCH

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

(2013) Christopher Fletez-Brant et al.   NUCLEIC ACIDS RESEARCH

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines

(2012) Michael Fernández et al.   NUCLEIC ACIDS RESEARCH

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Enhancer-driven chromatin interactions during development promote escape from silencing by a long non-coding RNA

(2011) Lisa Korostowski et al.   Epigenetics & Chromatin

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias 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