iEnhancer-GAN: A Deep Learning Framework in Combination with Word Embedding and Sequence Generative Adversarial Net to Identify Enhancers and Their Strength

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

(2020) Kailong Li et al.   Nature Communications

miRNAs as Influencers of Cell–Cell Communication in Tumor Microenvironment

(2020) Ilaria Conti et al.   Cells

GLIS2 promotes colorectal cancer through repressing enhancer activation

(2020) Jie Yao et al.   Oncogenesis

Variational posterior approximation using stochastic gradient ascent with adaptive stepsize

(2020) Kart-Leong Lim et al.   PATTERN RECOGNITION

Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming

(2019) Lei Xiong et al.   Nature Communications

Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions

(2019) Joshua R. Beytebiere et al.   GENES & DEVELOPMENT

iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding

(2019) Nguyen Quoc Khanh Le et al.   ANALYTICAL BIOCHEMISTRY

Perturbing Enhancer Activity in Cancer Therapy

(2019) Feda H. Hamdan et al.   Cancers

PaleAle 5.0: prediction of protein relative solvent accessibility by deep learning

(2019) Manaz Kaleel et al.   AMINO ACIDS

Protein–protein interaction site prediction through combining local and global features with deep neural networks

(2019) Min Zeng et al.   BIOINFORMATICS

Harvest Stage Recognition and Potential Fruit Damage Indicator for Berries Based on Hidden Markov Models and the Viterbi Algorithm

(2019) Marcos Orchard et al.   SENSORS

iEnhancer-ECNN: identifying enhancers and their strength using ensembles of convolutional neural networks

(2019) Quang H. Nguyen et al.   BMC GENOMICS

iEnhancer-EL: Identifying enhancers and their strength with ensemble learning approach

(2018) Bin Liu et al.   BIOINFORMATICS

iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC

(2018) Bin Liu et al.   BIOINFORMATICS

Enhancer transcription: what, where, when, and why?

(2018) Nathaniel D. Tippens et al.   GENES & DEVELOPMENT

Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou's PseKNC

(2018) M. Fazli Sabooh et al.   JOURNAL OF THEORETICAL BIOLOGY

NucPosPred: Predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC

(2018) Cangzhi Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines

(2018) Julia B. Carleton et al.   Jove-Journal of Visualized Experiments

Sequence based prediction of enhancer regions from DNA random walk

(2018) Anand Pratap Singh et al.   Scientific Reports

Identifying sigma70 promoters with novel pseudo nucleotide composition

(2017) Hao Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

(2017) Andrea J. Cohen et al.   Nature Communications

Enhancer deregulation in cancer and other diseases

(2016) Hans-Martin Herz   BIOESSAYS

iEnhancer-PsedeKNC: Identification of enhancers and their subgroups based on Pseudo degenerate kmer nucleotide composition

(2016) Bin Liu   NEUROCOMPUTING

EnhancerPred: a predictor for discovering enhancers based on the combination and selection of multiple features

(2016) Cangzhi Jia et al.   Scientific Reports

iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudok-tuple nucleotide composition

(2015) Bin Liu et al.   BIOINFORMATICS

In the loop: promoter–enhancer interactions and bioinformatics

(2015) Antonio Mora et al.   BRIEFINGS IN BIOINFORMATICS

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

What is the expectation maximization algorithm?

(2008) Chuong B Do et al.   NATURE BIOTECHNOLOGY