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Yu-Yen Ou

Explore the profile of Yu-Yen Ou including associated specialties, affiliations and a list of published articles. Areas
Snapshot
Articles 54
Citations 560
Followers 0
Related Specialties
Biology
Biochemistry
General Medicine
Top 10 Co-Authors
Quang-Thai Ho
Trinh-Trung-Duong Nguyen
Nguyen-Quoc-Khanh Le
Nguyen Quoc Khanh Le
Syed Muazzam Ali Shah
Shu-An Chen
Yu-Chen Liu
M Michael Gromiha
Semmy Wellem Taju
Muhammad Shahid Malik
Published In
Comput Biol Med
Anal Biochem
Comput Biol Chem
BMC Bioinformatics
Brief Bioinform
Affiliations
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Recent Articles
11.
DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models
Le V, Malik M, Tseng Y, Lee Y, Huang C, Ou Y
Comput Biol Chem . 2024 Mar; 110:108055. PMID: 38555810
Accurate classification of membrane proteins like ion channels and transporters is critical for elucidating cellular processes and drug development. We present DeepPLM_mCNN, a novel framework combining Pretrained Language Models (PLMs)...
12.
Integrating Pre-Trained protein language model and multiple window scanning deep learning networks for accurate identification of secondary active transporters in membrane proteins
Malik M, Ou Y
Methods . 2023 Oct; 220:11-20. PMID: 37871661
Secondary active transporters play pivotal roles in regulating ion and molecule transport across cell membranes, with implications in diseases like cancer. However, studying transporters via biochemical experiments poses challenges. We...
13.
Recent advances in features generation for membrane protein sequences: From multiple sequence alignment to pre-trained language models
Ou Y, Ho Q, Chang H
Proteomics . 2023 Oct; 23(23-24):e2200494. PMID: 37863817
Membrane proteins play a crucial role in various cellular processes and are essential components of cell membranes. Computational methods have emerged as a powerful tool for studying membrane proteins due...
14.
Disto-TRP: An approach for identifying transient receptor potential (TRP) channels using structural information generated by AlphaFold
Shah S, Ou Y
Gene . 2023 Apr; 871:147435. PMID: 37075925
The ability to predict 3D protein structures computationally has significantly advanced biological research. The AlphaFold protein structure database, developed by DeepMind, has provided a wealth of predicted protein structures and...
15.
MFPS_CNN: Multi-filter Pattern Scanning from Position-specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters
Nguyen T, Ho Q, Tarn Y, Ou Y
Mol Inform . 2022 Mar; 41(9):e2100271. PMID: 35322557
In cellular transportation mechanisms, the movement of ions across the cell membrane and its proper control are important for cells, especially for life processes. Ion transporters/pumps and ion channel proteins...
16.
Using multiple convolutional window scanning of convolutional neural network for an efficient prediction of ATP-binding sites in transport proteins
Nguyen T, Chen S, Ho Q, Ou Y
Proteins . 2022 Mar; 90(7):1486-1492. PMID: 35246878
Protein multiple sequence alignment information has long been important features to know about functions of proteins inferred from related sequences with known functions. It is therefore one of the underlying...
17.
Using k-mer embeddings learned from a Skip-gram based neural network for building a cross-species DNA N6-methyladenine site prediction model
Duong Nguyen T, Trinh V, Le N, Ou Y
Plant Mol Biol . 2021 Nov; 107(6):533-542. PMID: 34843033
This study used k-mer embeddings as effective feature to identify DNA N6-Methyladenine sites in plant genomes and obtained improved performance without substantial effort in feature extraction, combination and selection. Identification...
18.
Identification of efflux proteins based on contextual representations with deep bidirectional transformer encoders
Taju S, Shah S, Ou Y
Anal Biochem . 2021 Oct; 633:114416. PMID: 34656612
Efflux proteins are the transport proteins expressed in the plasma membrane, which are involved in the movement of unwanted toxic substances through specific efflux pumps. Several studies based on computational...
19.
TRP-BERT: Discrimination of transient receptor potential (TRP) channels using contextual representations from deep bidirectional transformer based on BERT
Shah S, Ou Y
Comput Biol Med . 2021 Sep; 137:104821. PMID: 34508974
Transient receptor potential (TRP) channels are non-selective cation channels that act as ion channels and are primarily found on the plasma membrane of numerous animal cells. These channels are involved...
20.
mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences
Ho Q, Le N, Ou Y
Brief Bioinform . 2021 Sep; 23(1). PMID: 34472594
In the past decade, convolutional neural networks (CNNs) have been used as powerful tools by scientists to solve visual data tasks. However, many efforts of convolutional neural networks in solving...