Detecting overlapping protein complexes in protein-protein interaction networks

Tamás Nepusz; Haiyuan Yu; Alberto Paccanaro

doi:10.1038/nmeth.1938

Detecting overlapping protein complexes in protein-protein interaction networks

Nature Methods ◽

10.1038/nmeth.1938 ◽

2012 ◽

Vol 9 (5) ◽

pp. 471-472 ◽

Cited By ~ 701

Author(s):

Tamás Nepusz ◽

Haiyuan Yu ◽

Alberto Paccanaro

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

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Identifying Protein Complexes from Protein-protein Interaction Networks Based on Fuzzy Clustering and GO Semantic Information

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2021.3095947 ◽

2021 ◽

pp. 1-1

Author(s):

Xiangyu Pan ◽

Lun Hu ◽

Pengwei Hu ◽

Zhu-Hong You

Keyword(s):

Fuzzy Clustering ◽

Protein Interaction ◽

Semantic Information ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

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Identification of overlapping protein complexes by fuzzy K-medoids clustering algorithm in yeast protein-protein interaction networks

Journal of Intelligent & Fuzzy Systems ◽

10.3233/jifs-17026 ◽

2018 ◽

Vol 34 (1) ◽

pp. 93-103 ◽

Cited By ~ 2

Author(s):

Buwen Cao ◽

Shuguang Deng ◽

Jiawei Luo ◽

Pingjian Ding ◽

Shulin Wang

Keyword(s):

Protein Interaction ◽

Clustering Algorithm ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Yeast Protein ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

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Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks

BMC Bioinformatics ◽

10.1186/s12859-018-2364-2 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Xiaoxia Liu ◽

Zhihao Yang ◽

Shengtian Sang ◽

Ziwei Zhou ◽

Lei Wang ◽

...

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks ◽

Node Embeddings

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A Core-Attachment Algorithm Based on Expected-Density and GO Terms to Detect Protein Complexes in Uncertain Protein-Protein Interaction Networks

International Journal of Digital Content Technology and its Applications ◽

10.4156/jdcta.vol7.issue8.6 ◽

2013 ◽

Vol 7 (8) ◽

pp. 49-57

Author(s):

Jiawei Luo ◽

Weifeng Hu

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks ◽

Go Terms ◽

Expected Density

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PCE-FR: A Novel Method for Identifying Overlapping Protein Complexes in Weighted Protein-Protein Interaction Networks Using Pseudo-Clique Extension Based on Fuzzy Relation

IEEE Transactions on NanoBioscience ◽

10.1109/tnb.2016.2611683 ◽

2016 ◽

Vol 15 (7) ◽

pp. 728-738 ◽

Cited By ~ 4

Author(s):

Buwen Cao ◽

Jiawei Luo ◽

Cheng Liang ◽

Shulin Wang ◽

Pingjian Ding

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Fuzzy Relation ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Novel Method ◽

Protein Protein Interaction Networks

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Identifying protein complexes in protein-protein interaction networks by using clique seeds and graph entropy

PROTEOMICS ◽

10.1002/pmic.201200336 ◽

2012 ◽

Vol 13 (2) ◽

pp. 269-277 ◽

Cited By ~ 28

Author(s):

Bolin Chen ◽

Jinhong Shi ◽

Shenggui Zhang ◽

Fang-Xiang Wu

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

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An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks

BMC Genomics ◽

10.1186/s12864-017-4131-6 ◽

2017 ◽

Vol 18 (S7) ◽

Cited By ~ 5

Author(s):

Yijia Zhang ◽

Hongfei Lin ◽

Zhihao Yang ◽

Jian Wang ◽

Yiwei Liu

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Model Based ◽

Uncertain Model ◽

Protein Protein Interaction Networks

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RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks

BMC Bioinformatics ◽

10.1186/s12859-017-1920-5 ◽

2017 ◽

Vol 18 (S15) ◽

Author(s):

Osamu Maruyama ◽

Yuki Kuwahara

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

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Detecting temporal protein complexes from dynamic protein-protein interaction networks

BMC Bioinformatics ◽

10.1186/1471-2105-15-335 ◽

2014 ◽

Vol 15 (1) ◽

pp. 335 ◽

Cited By ~ 37

Author(s):

Le Ou-Yang ◽

Dao-Qing Dai ◽

Xiao-Li Li ◽

Min Wu ◽

Xiao-Fei Zhang ◽

...

Keyword(s):

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

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Weighted edge based clustering to identify protein complexes in protein–protein interaction networks incorporating gene expression profile

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2016.10.001 ◽

2016 ◽

Vol 65 ◽

pp. 69-79 ◽

Cited By ~ 17

Author(s):

Seketoulie Keretsu ◽

Rosy Sarmah

Keyword(s):

Gene Expression ◽

Gene Expression Profile ◽

Expression Profile ◽

Protein Interaction ◽

Protein Complexes ◽

Protein Interaction Networks ◽

Interaction Networks ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks ◽

Edge Based

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