Network-based methods for predicting essential genes or proteins: a survey

X Li, W Li, M Zeng, R Zheng, M Li - Briefings in bioinformatics, 2020 - academic.oup.com
Genes that are thought to be critical for the survival of organisms or cells are called essential
genes. The prediction of essential genes and their products (essential proteins) is of great …

Protein interaction networks: centrality, modularity, dynamics, and applications

X Meng, W Li, X Peng, Y Li, M Li - Frontiers of Computer Science, 2021 - Springer
In the post-genomic era, proteomics has achieved significant theoretical and practical
advances with the development of high-throughput technologies. Especially the rapid …

DPPIN: A biological repository of dynamic protein-protein interaction network data

D Fu, J He - 2022 IEEE International Conference on Big Data …, 2022 - ieeexplore.ieee.org
In the big data era, the relationship between entries becomes more and more complex.
Many graph (or network) algorithms have already paid attention to dynamic networks, which …

Identification of protein complexes by using a spatial and temporal active protein interaction network

M Li, X Meng, R Zheng, FX Wu, Y Li… - … /ACM transactions on …, 2017 - ieeexplore.ieee.org
The rapid development of proteomics and high-throughput technologies has produced a
large amount of Protein-Protein Interaction (PPI) data, which makes it possible for …

A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks

L Ou-Yang, H Yan, XF Zhang - BMC bioinformatics, 2017 - Springer
Background The accurate identification of protein complexes is important for the
understanding of cellular organization. Up to now, computational methods for protein …

Neighbor affinity based algorithm for discovering temporal protein complex from dynamic PPI network

X Shen, L Yi, X Jiang, Y Zhao, X Hu, T He, J Yang - Methods, 2016 - Elsevier
Detection of temporal protein complexes would be a great aid in furthering our knowledge of
the dynamic features and molecular mechanism in cell life activities. Most existing clustering …

[HTML][HTML] Unveiling network-based functional features through integration of gene expression into protein networks

M Jalili, T Gebhardt, O Wolkenhauer… - … et Biophysica Acta (BBA …, 2018 - Elsevier
Decoding health and disease phenotypes is one of the fundamental objectives in
biomedicine. Whereas high-throughput omics approaches are available, it is evident that …

A node ranking method based on multiple layers for dynamic protein interaction networks

B Li, L Pan, J Sun, H Wang, J Jiang, B Yang… - IEEE Access, 2022 - ieeexplore.ieee.org
Constructing dynamic protein interaction networks (DPIN) is a common way to improve
identification accuracy of essential proteins. The existing methods usually aggregate DPIN …

Dynamic protein–protein interaction networks construction using firefly algorithm

M Mohammadi Jenghara… - Pattern Analysis and …, 2018 - Springer
Protein–protein interaction (PPI) networks are dynamic in the real world. That is, at different
times and under different conditions, the interaction among proteins may or may not be …

A protein network refinement method based on module discovery and biological information

L Pan, H Wang, B Yang, W Li - BMC bioinformatics, 2024 - Springer
Background The identification of essential proteins can help in understanding the minimum
requirements for cell survival and development to discover drug targets and prevent …