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

Briefings in bioinformatics, 2021-09, Vol.22 (5)

2021

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Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins

Journal of computational chemistry, 2017-09, Vol.38 (23), p.2000-2006

2017

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Recent advances in features generation for membrane protein sequences: From multiple sequence alignment to pre‐trained language models

Proteomics (Weinheim), 2023-12, Vol.23 (23-24), p.e2200494-n/a

2023

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Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks

Analytical biochemistry, 2018-08, Vol.555, p.33-41

2018

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Deep transformers and convolutional neural network in identifying DNA N6-methyladenine sites in cross-species genomes

Methods (San Diego, Calif.), 2022-08, Vol.204, p.199-206

2022

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Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins

Proteins, structure, function, and bioinformatics, 2022-07, Vol.90 (7), p.1486-1492

2022

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FAD-BERT: Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers

Computers in biology and medicine, 2021-04, Vol.131, p.104258-104258, Article 104258

2021

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

Neurocomputing (Amsterdam), 2020-01, Vol.375, p.71-79

2020

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MFPS_CNN: Multi‐filter Pattern Scanning from Position‐specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters

Molecular informatics, 2022-09, Vol.41 (9), p.e2100271-n/a

2022

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Using word embedding technique to efficiently represent protein sequences for identifying substrate specificities of transporters

Analytical biochemistry, 2019-07, Vol.577, p.73-81

2019

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Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles

Journal of chemical information and modeling, 2022-10, Vol.62 (19), p.4820-4826

2022

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GT-Finder: Classify the family of glucose transporters with pre-trained BERT language models

Computers in biology and medicine, 2021-04, Vol.131, p.104259-104259, Article 104259

2021

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TNFPred: identifying tumor necrosis factors using hybrid features based on word embeddings

BMC medical genomics, 2020-10, Vol.13 (Suppl 10), p.155-155, Article 155

2020

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Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins

Journal of bioinformatics and computational biology, 2019-02, Vol.17 (1), p.1950005

2019

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

Analytical biochemistry, 2019-04, Vol.571, p.53-61

2019

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Automatic Detection of Meniscus Tears Using Backbone Convolutional Neural Networks on Knee MRI

Journal of magnetic resonance imaging, 2023-03, Vol.57 (3), p.740-749

2023

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BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection

Computational biology and chemistry, 2022-08, Vol.99, p.107732-107732, Article 107732

2022

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m CNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences

Briefings in bioinformatics, 2022-01, Vol.23 (1)

2022

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Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model

IEEE/ACM transactions on computational biology and bioinformatics, 2022-03, Vol.19 (2), p.1235-1244

2022

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

Analytical biochemistry, 2019-04, Vol.571, p.53-61

2019

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Numerical simulation of wall shear stress and boundary layer flow from jetting cavitation bubble on unheated and heated surfaces

International journal of heat and mass transfer, 2024-05, Vol.222, p.125189, Article 125189

2024

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Numerical study of dynamics of cavitation bubble collapse near oscillating walls

Physics of fluids (1994), 2023-01, Vol.35 (1)

2023

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Spatiotemporal Patterns of Anthrax, Vietnam, 1990-2015

Emerging infectious diseases, 2022-11, Vol.28 (11), p.2206-2213

2022

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Numerical study of bubble dynamics near a solid wall with a gas-entrapping hole

Ocean engineering, 2023-10, Vol.285, p.115344, Article 115344

2023

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Numerical study of shock waves and supersonic jets triggered by cavitation bubble collapse in different pressurized ambiences

Journal of Mechanical Science and Technology, 2024, 38(8), , pp.4167-4173

2024

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

Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins

Recent advances in features generation for membrane protein sequences: From multiple sequence alignment to pre‐trained language models

Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks

Deep transformers and convolutional neural network in identifying DNA N6-methyladenine sites in cross-species genomes

Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP‐binding sites in transport proteins

FAD-BERT: Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers

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

MFPS_CNN: Multi‐filter Pattern Scanning from Position‐specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters

Using word embedding technique to efficiently represent protein sequences for identifying substrate specificities of transporters

Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles

GT-Finder: Classify the family of glucose transporters with pre-trained BERT language models

TNFPred: identifying tumor necrosis factors using hybrid features based on word embeddings

Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins

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

Automatic Detection of Meniscus Tears Using Backbone Convolutional Neural Networks on Knee MRI

BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection

m CNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences

Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model

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

Numerical simulation of wall shear stress and boundary layer flow from jetting cavitation bubble on unheated and heated surfaces

Numerical study of dynamics of cavitation bubble collapse near oscillating walls

Spatiotemporal Patterns of Anthrax, Vietnam, 1990-2015

Numerical study of bubble dynamics near a solid wall with a gas-entrapping hole

Numerical study of shock waves and supersonic jets triggered by cavitation bubble collapse in different pressurized ambiences

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