A Novel Core‐Attachment–Based Method to Identify Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks
Sign Up to like & getrecommendations! Published in 2019 at "PROTEOMICS"
DOI: 10.1002/pmic.201800129
Abstract: Cellular functions are always performed by protein complexes. At present, many approaches have been proposed to identify protein complexes from protein–protein interaction (PPI) networks. Some approaches focus on detecting local dense subgraphs in PPI networks… read more here.
Keywords: protein; ppi networks; method; expression ... See more keywords
EMDIP: An Entropy Measure to Discover Important Proteins in PPI networks
Sign Up to like & getrecommendations! Published in 2020 at "Computers in biology and medicine"
DOI: 10.1016/j.compbiomed.2020.103740
Abstract: Discovering important proteins in Protein-Protein Interaction (PPI) networks has attracted a lot of attention in recent years. Most of the previous work applies different network centrality measures such as Closeness, Betweenness, PageRank and many others… read more here.
Keywords: important proteins; ppi networks; annotation; proteins ppi ... See more keywords
BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad091
Abstract: Abstract Summary The BioPlex project has created two proteome scale, cell-line-specific protein–protein interaction (PPI) networks: the first in 293T cells, including 120k interactions among 15k proteins; and the second in HCT116 cells, including 70k interactions… read more here.
Keywords: bioplexpy integrated; ppi networks; domain; analysis ... See more keywords
Viewing the Meso-Scale Structures in Protein-Protein Interaction Networks Using 2-Clubs
Sign Up to like & getrecommendations! Published in 2018 at "IEEE Access"
DOI: 10.1109/access.2018.2852275
Abstract: Many current analyses on protein-protein interaction (PPI) networks concentrate on developing the algorithms for identifying the functional modules within the PPI networks. However, understanding the internal structure in the functional modules is needed to define… read more here.
Keywords: protein interaction; meso scale; functional modules; ppi networks ... See more keywords
An Iteration Method for Identifying Yeast Essential Proteins From Weighted PPI Network Based on Topological and Functional Features of Proteins
Sign Up to like & getrecommendations! Published in 2020 at "IEEE Access"
DOI: 10.1109/access.2020.2993860
Abstract: Accumulating studies have indicated that essential proteins play critical roles in numerous biological processes. With the rapid development of high-throughput technologies, a large number of Protein-Protein Interaction (PPI) data have been found in Saccharomyces cerevisiae,… read more here.
Keywords: essential proteins; prediction; ppi networks; ppi ... See more keywords
A Robust Algorithm Based on Link Label Propagation for Identifying Functional Modules from Protein-protein Interaction Networks.
Sign Up to like & getrecommendations! Published in 2020 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2020.3038815
Abstract: Identifying functional modules in protein-protein interaction (PPI) networks elucidates cellular organization and mechanism. Various methods have been proposed to identify the functional modules in PPI networks, but most of these methods do not consider the… read more here.
Keywords: modules protein; functional modules; protein protein; noisy links ... See more keywords
Temporal-Spatial Analysis of the Essentiality of Hub Proteins in Protein-Protein Interaction Networks
Sign Up to like & getrecommendations! Published in 2022 at "IEEE Transactions on Network Science and Engineering"
DOI: 10.1109/tnse.2022.3185717
Abstract: Hubs are generally defined as nodes with a high degree centrality, and they are important for maintaining the stability of complex networks. Previous studies have shown that hub proteins tend to be essential in protein-protein… read more here.
Keywords: hub proteins; ppi networks; essentiality; analysis ... See more keywords
LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules
Sign Up to like & getrecommendations! Published in 2019 at "BMC Genomics"
DOI: 10.1186/s12864-019-6271-3
Abstract: Cross-species analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved interaction patterns. Identifying such conserved substructures between PPI networks of different species increases our understanding of the principles deriving evolution of… read more here.
Keywords: network alignment; conserved modules; network; ppi networks ... See more keywords
Identification of protein complexes and functional modules in E. coli PPI networks
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DOI: 10.1186/s12866-020-01904-6
Abstract: Escherichia coli always plays an important role in microbial research, and it has been a benchmark model for the study of molecular mechanisms of microorganisms. Molecular complexes, operons, and functional modules are valuable molecular functional… read more here.
Keywords: protein; identification protein; functional modules; ppi networks ... See more keywords
From communities to protein complexes: A local community detection algorithm on PPI networks
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0260484
Abstract: Identifying protein complexes in protein-protein interaction (ppi) networks is often handled as a community detection problem, with algorithms generally relying exclusively on the network topology for discovering a solution. The advancement of experimental techniques on… read more here.
Keywords: topology; network; ppi networks; community ... See more keywords