A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information

iMRM:a platform for simultaneously identifying multiple kinds of RNA modifications

(2020) Kewei Liu et al.   BIOINFORMATICS

Using deep neural networks and biological subwords to detect protein S-sulfenylation sites

(2020) Duyen Thi Do et al.   BRIEFINGS IN BIOINFORMATICS

A Convolutional Neural Network Using Dinucleotide One-hot Encoder for identifying DNA N6-Methyladenine Sites in the Rice Genome

(2020) Zhibin Lv et al.   NEUROCOMPUTING

DeepAVP: A Dual-Channel Deep Neural Network for Identifying Variable-Length Antiviral Peptides

(2020) Jiawei Li et al.   IEEE Journal of Biomedical and Health Informatics

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

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

DeepETC: A deep convolutional neural network architecture for investigating and classifying electron transport chain's complexes

(2019) Nguyen Quoc Khanh Le et al.   NEUROCOMPUTING

An improved deep learning method for predicting DNA-binding proteins based on contextual features in amino acid sequences

(2019) Siquan Hu et al.   PLoS One

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

(2019) Nguyen Quoc Khanh Le et al.   Frontiers in Bioengineering and Biotechnology

Modeling aspects of the language of life through transfer-learning protein sequences

(2019) Michael Heinzinger et al.   BMC BIOINFORMATICS

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

(2018) Bin Liu et al.   BIOINFORMATICS

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

Enhancers: bridging the gap between gene control and human disease

(2018) Jaret M Karnuta et al.   HUMAN MOLECULAR GENETICS

Enhancer Logic and Mechanics in Development and Disease

(2018) Ryan Rickels et al.   TRENDS IN CELL BIOLOGY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

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

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS