iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization

Y Yu, W He, J **, G **ao, L Cui, R Zeng, L Wei - Bioinformatics, 2021‏ - academic.oup.com
Motivation DNA methylation plays an important role in epigenetic modification, the
occurrence, and the development of diseases. Therefore, identification of DNA methylation …

PUResNet: prediction of protein-ligand binding sites using deep residual neural network

J Kandel, H Tayara, KT Chong - Journal of cheminformatics, 2021‏ - Springer
Background Predicting protein-ligand binding sites is a fundamental step in understanding
the functional characteristics of proteins, which plays a vital role in elucidating different …

ncRDeep: Non-coding RNA classification with convolutional neural network

T Chantsalnyam, DY Lim, H Tayara… - Computational Biology and …, 2020‏ - Elsevier
A non-coding RNA (ncRNA) is a kind of RNA that is not converted into protein, however, it is
involved in many biological processes, diseases, and cancers. Numerous ncRNAs have …

DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites

Q Liu, J Chen, Y Wang, S Li, C Jia… - Briefings in …, 2021‏ - academic.oup.com
Abstract DNA N4-methylcytosine (4mC) is an important epigenetic modification that plays a
vital role in regulating DNA replication and expression. However, it is challenging to detect …

iDNA-OpenPrompt: OpenPrompt learning model for identifying DNA methylation

X Yu, J Ren, H Long, R Zeng, G Zhang, A Bilal… - Frontiers in …, 2024‏ - frontiersin.org
Introduction: DNA methylation is a critical epigenetic modification involving the addition of a
methyl group to the DNA molecule, playing a key role in regulating gene expression without …

C-loss based higher order fuzzy inference systems for identifying DNA N4-methylcytosine sites

Y Ding, P Tiwari, Q Zou, F Guo… - IEEE Transactions on …, 2022‏ - ieeexplore.ieee.org
DNA methylation is an epigenetic marker that plays an important role in the biological
processes of regulating gene expression, maintaining chromatin structure, imprinting genes …

[HTML][HTML] CSatDTA: prediction of drug–target binding affinity using convolution model with self-attention

A Ghimire, H Tayara, Z Xuan, KT Chong - International journal of …, 2022‏ - mdpi.com
Drug discovery, which aids to identify potential novel treatments, entails a broad range of
fields of science, including chemistry, pharmacology, and biology. In the early stages of drug …

[HTML][HTML] A robust drug–target interaction prediction framework with capsule network and transfer learning

Y Huang, HY Huang, Y Chen, YCD Lin, L Yao… - International Journal of …, 2023‏ - mdpi.com
Drug–target interactions (DTIs) are considered a crucial component of drug design and drug
discovery. To date, many computational methods were developed for drug–target …

A deep multiple kernel learning-based higher-order fuzzy inference system for identifying DNA N4-methylcytosine sites

L Wang, Y Ding, P Tiwari, J Xu, W Lu, K Muhammad… - Information …, 2023‏ - Elsevier
Abstract N4-methylcytosine (4mC), as a DNA modification, plays a crucial role in epigenetic
regulation. However, the existing experimentation methods for accurately identifying 4mC …

Deep-4mCW2V: A sequence-based predictor to identify N4-methylcytosine sites in Escherichia coli

H Zulfiqar, ZJ Sun, QL Huang, SS Yuan, H Lv, FY Dao… - Methods, 2022‏ - Elsevier
Abstract N4-methylcytosine (4mC) is a type of DNA modification which could regulate
several biological progressions such as transcription regulation, replication and gene …