DeePromoter: Robust Promoter Predictor Using Deep Learning

Prediction of human protein subcellular localization using deep learning

(2018) Leyi Wei et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Promoter analysis and prediction in the human genome using sequence-based deep learning models

(2018) Ramzan Umarov et al.   BIOINFORMATICS

iPSW(2L)-PseKNC: A two-layer predictor for identifying promoters and their strength by hybrid features via pseudo K-tuple nucleotide composition

(2018) Xuan Xiao et al.   GENOMICS

PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence

(2018) Ramit Bharanikumar et al.   PeerJ

iRNA-PseKNC(2methyl): Identify RNA 2'-O-methylation sites by convolution neural network and Chou's pseudo components

(2018) Muhammad Tahir et al.   JOURNAL OF THEORETICAL BIOLOGY

Identifying sigma70 promoters with novel pseudo nucleotide composition

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

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks

(2017) Ramzan Kh. Umarov et al.   PLoS One

Core promoter-specific gene regulation: TATA box selectivity and Initiator-dependent bi-directionality of serum response factor-activated transcription

(2016) Muyu Xu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

What is next generation sequencing?

(2013) Sam Behjati et al.   Archives of Disease in Childhood-Education and Practice Edition

Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set

(2013) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

(2012) René Dreos et al.   NUCLEIC ACIDS RESEARCH

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

The RNA polymerase II core promoter — the gateway to transcription

(2008) Tamar Juven-Gershon et al.   CURRENT OPINION IN CELL BIOLOGY

A rapid micro chromatin immunoprecipitation assay (ChIP)

(2008) John Arne Dahl et al.   Nature Protocols