Recent advances in deep learning for protein-protein interaction analysis: A comprehensive review

M Lee - Molecules, 2023 - mdpi.com
Deep learning, a potent branch of artificial intelligence, is steadily leaving its transformative
imprint across multiple disciplines. Within computational biology, it is expediting progress in …

GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation

M Li, B Zhao, R Yin, C Lu, F Guo… - Briefings in …, 2023 - academic.oup.com
The subcellular localization of long non-coding RNAs (lncRNAs) is crucial for understanding
lncRNA functions. Most of existing lncRNA subcellular localization prediction methods use k …

DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning

Y Li, M Zeng, F Zhang, FX Wu, M Li - Bioinformatics, 2023 - academic.oup.com
Motivation Protein essentiality is usually accepted to be a conditional trait and strongly
affected by cellular environments. However, existing computational methods often do not …

'Bingo'—a large language model-and graph neural network-based workflow for the prediction of essential genes from protein data

J Ma, J Song, ND Young, BCH Chang… - Briefings in …, 2024 - academic.oup.com
The identification and characterization of essential genes are central to our understanding of
the core biological functions in eukaryotic organisms, and has important implications for the …

Comprehensive prediction and analysis of human protein essentiality based on a pretrained large language model

B Kang, R Fan, C Cui, Q Cui - Nature Computational Science, 2024 - nature.com
Human essential proteins (HEPs) are indispensable for individual viability and development.
However, experimental methods to identify HEPs are often costly, time consuming and labor …

ECDEP: identifying essential proteins based on evolutionary community discovery and subcellular localization

C Ye, Q Wu, S Chen, X Zhang, W Xu, Y Wu, Y Zhang… - BMC genomics, 2024 - Springer
Background In cellular activities, essential proteins play a vital role and are instrumental in
comprehending fundamental biological necessities and identifying pathogenic genes …

[HTML][HTML] AttentionEP: Predicting essential proteins via fusion of multiscale features by attention mechanisms

C Wu, B Lin, J Zhang, R Gao, R Song, ZP Liu - Computational and …, 2024 - Elsevier
Identifying essential proteins is of utmost importance in the field of biomedical research due
to their essential functions in cellular activities and their involvement in mechanisms related …

MEM‐FET: Essential protein prediction using membership feature and machine learning approach

AK Payra, B Saha, A Ghosh - Proteins: Structure, Function, and …, 2024 - Wiley Online Library
Proteins are played key roles in different functionalities in our daily life. All functional roles of
a protein are a bit enhanced in interaction compared to individuals. Identification of essential …

ACDMBI: A deep learning model based on community division and multi-source biological information fusion predicts essential proteins

P Lu, J Tian - Computational Biology and Chemistry, 2024 - Elsevier
Accurately identifying essential proteins is vital for drug research and disease diagnosis.
Traditional centrality methods and machine learning approaches often face challenges in …

LDAGSO: Predicting IncRNA-Disease Associations from Graph Sequences and Disease Ontology via Deep Learning techniques

NS Awn, Y Li, B Zhao, M Zeng… - 2022 IEEE International …, 2022 - ieeexplore.ieee.org
Recent studies have confirmed the significant effects of long non-coding RNAs (IncRNAs) in
understanding the mechanism of diseases. Because of the relatively small number of …