Temporal-spatial analysis of the essentiality of hub proteins in protein-protein interaction networks

X Meng, W Li, J Xiang, HD Bedru… - … on Network Science …, 2022 - ieeexplore.ieee.org
… of PPI networks: the static PPI network, the temporal dynamic … identified from different dynamic
PPI networks compared to … We have found that high noises in the PPI network distract us …

A novel essential protein identification method based on PPI networks and gene expression data

J Zhong, C Tang, W Peng, M Xie, Y Sun, Q Tang… - BMC …, 2021 - Springer
compared JDC with various essential protein prediction methods that are proposed base on
the static PPI network… In this study, we propose a new essential protein recognition algorithm …

Identification of protein complexes and functional modules in E. coli PPI networks

P Kong, G Huang, W Liu - BMC microbiology, 2020 - Springer
… Experiments and data analysis (algorithmic model) are two effective … In this study, E. coli
protein complexes and … results of ELPA were compared with that of MCL, and we found that their …

Statistical analysis of functional genes in human PPI networks

J Lü, P Wang, J Lü, P Wang - … and Analysis of Bio-molecular Networks, 2020 - Springer
compared the HPIN with that for the other species and found … of some functional genes,
which facilitate the identification of … protein interactions are unweighted and static [4,5,6,7,8,9,10,…

Proteinprotein interaction networks as miners of biological discovery

S Wang, R Wu, J Lu, Y Jiang, T Huang, YD Cai - Proteomics, 2022 - Wiley Online Library
… Across different types of PPI networks, the major difference is … in identifying hub genes
and modules within PPI networks. … to detect functional units from static PPI network, time-evolving …

AMEND: active module identification using experimental data and network diffusion

SS Boyd, C Slawson, JA Thompson - BMC bioinformatics, 2023 - Springer
… , network analysis involving only PPI networks is limited when the goal is to study a particular
biological process, since they are static … was compared to other module identification

Inferring cell cycle phases from a partially temporal network of protein interactions

M Lucas, A Morris, A Townsend-Teague, L Tichit… - Cell Reports …, 2023 - cell.com
… , this method will allow the study of temporal regulation in … combined a static PPI network
built from KEGG pathway data … the static PPI network, we then defined its weight w AB (t) at time

Protein function module of deep learning and PPI network prediction

S Huo - Journal of Physics: Conference Series, 2020 - iopscience.iop.org
functional modules were compared among the other three … the identified function module a
and the known function module … , most researchers are taking static PPI network for research, …

Providing SSPCO algorithm to construct static protein-protein interaction (PPI) networks

E Azarm, T Motamedi Nia, R Omidvar - Journal of Soft Computing in …, 2022 - jsoftcivil.com
… In this study, we substitute the random parameters in PSO with … by using gene expression
data is the identification of suitable … algorithms and it was compared with two basic methods of …

Protein interaction networks: Functional and statistical approaches

M Escandón, L Lamelas, V Roces… - … : Methods and Protocols, 2020 - Springer
… each group to identify differentially connected modules, which … used for the proteinprotein
interaction analysis by STRING … that biological systems are static, nonhomogeneous dynamic …