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Items: 1 to 20 of 118

1.

Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.

Kim I, Lee H, Han SK, Kim S.

PLoS Comput Biol. 2014 Oct 9;10(10):e1003881. doi: 10.1371/journal.pcbi.1003881. eCollection 2014 Oct.

2.

Applying modularity analysis of PPI networks to sequenced organisms.

Wang X, Ren X, Li B, Yue J, Liang L.

Virulence. 2012 Aug 15;3(5):459-63. doi: 10.4161/viru.21104. Epub 2012 Aug 15.

3.

Determining modular organization of protein interaction networks by maximizing modularity density.

Zhang S, Ning XM, Ding C, Zhang XS.

BMC Syst Biol. 2010 Sep 13;4 Suppl 2:S10. doi: 10.1186/1752-0509-4-S2-S10.

4.

Inferring domain-domain interactions from protein-protein interactions in the complex network conformation.

Chen C, Zhao JF, Huang Q, Wang RS, Zhang XS.

BMC Syst Biol. 2012;6 Suppl 1:S7. doi: 10.1186/1752-0509-6-S1-S7. Epub 2012 Jul 16.

5.

Detecting Functional Modules Based on a Multiple-Grain Model in Large-Scale Protein-Protein Interaction Networks.

Ji J, Lv J, Yang C, Zhang A.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Jul-Aug;13(4):610-22. doi: 10.1109/TCBB.2015.2480066. Epub 2015 Sep 18.

PMID:
26394434
6.

Network simulation reveals significant contribution of network motifs to the age-dependency of yeast protein-protein interaction networks.

Liang C, Luo J, Song D.

Mol Biosyst. 2014 Jul 29;10(9):2277-88. doi: 10.1039/c4mb00230j.

PMID:
24964354
7.

Phylogenetic analysis of modularity in protein interaction networks.

Erten S, Li X, Bebek G, Li J, Koyutürk M.

BMC Bioinformatics. 2009 Oct 14;10:333. doi: 10.1186/1471-2105-10-333.

8.

NEMo: An Evolutionary Model With Modularity for PPI Networks.

Ye M, Zhang X, Racz GC, Jiang Q, Moret BME.

IEEE Trans Nanobioscience. 2017 Mar;16(2):131-139. doi: 10.1109/TNB.2017.2656058. Epub 2017 Jan 19.

PMID:
28113347
9.

Essential protein discovery based on a combination of modularity and conservatism.

Zhao B, Wang J, Li X, Wu FX.

Methods. 2016 Nov 1;110:54-63. doi: 10.1016/j.ymeth.2016.07.005. Epub 2016 Jul 9.

PMID:
27402354
10.

Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks.

Chen B, Fan W, Liu J, Wu FX.

Brief Bioinform. 2014 Mar;15(2):177-94. doi: 10.1093/bib/bbt039. Epub 2013 Jun 18. Review.

PMID:
23780996
11.

Geometric evolutionary dynamics of protein interaction networks.

Przulj N, Kuchaiev O, Stevanović A, Hayes W.

Pac Symp Biocomput. 2010:178-89.

12.

On the role of sparseness in the evolution of modularity in gene regulatory networks.

Espinosa-Soto C.

PLoS Comput Biol. 2018 May 18;14(5):e1006172. doi: 10.1371/journal.pcbi.1006172. eCollection 2018 May.

13.

Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping.

Lo YS, Huang SH, Luo YC, Lin CY, Yang JM.

PLoS One. 2015 Jan 20;10(1):e0116347. doi: 10.1371/journal.pone.0116347. eCollection 2015.

14.

A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification.

Yu L, Gao L, Li K, Zhao Y, Chiu DK.

Comput Biol Chem. 2011 Oct 12;35(5):298-307. doi: 10.1016/j.compbiolchem.2011.07.005. Epub 2011 Jul 20.

PMID:
22000801
15.

In search of the biological significance of modular structures in protein networks.

Wang Z, Zhang J.

PLoS Comput Biol. 2007 Jun;3(6):e107. Epub 2007 Apr 30. Erratum in: PLoS Comput Biol. 2007 Jul;3(7):e146.

16.
17.

Robustness and adaptation reveal plausible cell cycle controlling subnetwork in Saccharomyces cerevisiae.

Huang JY, Huang CW, Kao KC, Lai PY.

Gene. 2013 Apr 10;518(1):35-41. doi: 10.1016/j.gene.2012.11.088. Epub 2012 Dec 27.

PMID:
23274654
18.

Identification and evolution of structurally dominant nodes in protein-protein interaction networks.

Wang P, Yu X, Lü J.

IEEE Trans Biomed Circuits Syst. 2014 Feb;8(1):87-97. doi: 10.1109/TBCAS.2014.2303160.

PMID:
24681922
19.

Path lengths in protein-protein interaction networks and biological complexity.

Xu K, Bezakova I, Bunimovich L, Yi SV.

Proteomics. 2011 May;11(10):1857-67. doi: 10.1002/pmic.201000684. Epub 2011 Apr 8.

PMID:
21480527
20.

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.

BMC Syst Biol. 2012 May 1;6:29. doi: 10.1186/1752-0509-6-29.

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