Classifying Promoters by Interpreting the Hidden Information of DNA Sequences via Deep Learning and Combination of Continuous FastText N-Grams

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

iN6-methylat (5-step): identifying DNA N6-methyladenine sites in rice genome using continuous bag of nucleobases via Chou’s 5-step rule

(2019) Nguyen Quoc Khanh Le   MOLECULAR GENETICS AND GENOMICS

Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles

(2019) Nguyen Quoc Khanh Le et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Prediction of ATP-binding sites in membrane proteins using a two-dimensional convolutional neural network

(2019) Trinh-Trung-Duong Nguyen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

A novel methodology on distributed representations of proteins using their interacting ligands

(2018) Hakime Öztürk 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

Identifying sigma70 promoters with novel pseudo nucleotide composition

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

CPPred-RF: A Sequence-based Predictor for Identifying Cell-Penetrating Peptides and Their Uptake Efficiency

(2017) Leyi Wei et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy

(2016) Quan Zou et al.   BMC Systems Biology

A novel features ranking metric with application to scalable visual and bioinformatics data classification

(2016) Quan Zou et al.   NEUROCOMPUTING

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Structural Properties of Gene Promoters Highlight More than Two Phenotypes of Diabetes

(2015) Constantin Ionescu-Tîrgovişte et al.   PLoS One

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

(2014) Hao Lin et al.   NUCLEIC ACIDS RESEARCH

DNA duplex stability as discriminative characteristic for Escherichia coli σ54- and σ28- dependent promoter sequences

(2013) Scheila de Avila e Silva et al.   BIOLOGICALS

Recognition of prokaryotic promoters based on a novel variable-window Z-curve method

(2011) Kai Song   NUCLEIC ACIDS RESEARCH