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Items: 1 to 20 of 69

1.

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs.

Casey F, Krogan N, Shields DC, Cagney G.

BMC Syst Biol. 2011 Aug 22;5:133. doi: 10.1186/1752-0509-5-133.

2.

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.

Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, Lesage G, Andrews B, Bussey H, Boone C, Roth FP.

J Biol. 2005;4(2):6. Epub 2005 Jun 1.

3.

Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.

Babu M, Gagarinova A, Emili A.

Methods Mol Biol. 2011;781:99-126. doi: 10.1007/978-1-61779-276-2_7.

PMID:
21877280
4.

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
5.

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A.

PLoS Genet. 2014 Feb 20;10(2):e1004120. doi: 10.1371/journal.pgen.1004120. eCollection 2014 Feb.

6.

A quantitative analysis of monochromaticity in genetic interaction networks.

Hsu CH, Wang TY, Chu HT, Kao CY, Chen KC.

BMC Bioinformatics. 2011;12 Suppl 13:S16. doi: 10.1186/1471-2105-12-S13-S16. Epub 2011 Nov 30.

7.

Crosstalk between transcription factors and microRNAs in human protein interaction network.

Lin CC, Chen YJ, Chen CY, Oyang YJ, Juan HF, Huang HC.

BMC Syst Biol. 2012 Mar 13;6:18. doi: 10.1186/1752-0509-6-18.

8.

Categorizing biases in high-confidence high-throughput protein-protein interaction data sets.

Yu X, Ivanic J, Memisević V, Wallqvist A, Reifman J.

Mol Cell Proteomics. 2011 Dec;10(12):M111.012500. doi: 10.1074/mcp.M111.012500. Epub 2011 Aug 29.

9.

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ.

Nature. 2007 Apr 12;446(7137):806-10. Epub 2007 Feb 21.

PMID:
17314980
10.

Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.

Brady A, Maxwell K, Daniels N, Cowen LJ.

PLoS One. 2009;4(4):e5364. doi: 10.1371/journal.pone.0005364. Epub 2009 Apr 28.

11.

Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.

Babu M, Gagarinova A, Greenblatt J, Emili A.

Methods Mol Biol. 2011;765:125-53. doi: 10.1007/978-1-61779-197-0_9.

PMID:
21815091
12.

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
13.

Improved functional overview of protein complexes using inferred epistatic relationships.

Ryan C, Greene D, Guénolé A, van Attikum H, Krogan NJ, Cunningham P, Cagney G.

BMC Syst Biol. 2011 May 23;5:80. doi: 10.1186/1752-0509-5-80.

14.

Network motifs that recur across species, including gene regulatory and protein-protein interaction networks.

Borotkanics R, Lehmann H.

Arch Toxicol. 2015 Apr;89(4):489-99. doi: 10.1007/s00204-014-1274-y. Epub 2014 May 22. Review.

PMID:
24847787
15.

Differential network biology.

Ideker T, Krogan NJ.

Mol Syst Biol. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. Review.

16.

Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination.

Srivastava R, Rai KM, Pandey B, Singh SP, Sawant SV.

PLoS One. 2015 Aug 11;10(8):e0134709. doi: 10.1371/journal.pone.0134709. eCollection 2015.

17.

A correlated motif approach for finding short linear motifs from protein interaction networks.

Tan SH, Hugo W, Sung WK, Ng SK.

BMC Bioinformatics. 2006 Nov 16;7:502.

18.

Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks.

Michoel T, Joshi A, Nachtergaele B, Van de Peer Y.

Mol Biosyst. 2011 Oct;7(10):2769-78. doi: 10.1039/c1mb05241a. Epub 2011 Aug 23.

PMID:
21860879
19.

Constructing module maps for integrated analysis of heterogeneous biological networks.

Amar D, Shamir R.

Nucleic Acids Res. 2014 Apr;42(7):4208-19. doi: 10.1093/nar/gku102. Epub 2014 Feb 4.

20.

Biological interaction networks are conserved at the module level.

Zinman GE, Zhong S, Bar-Joseph Z.

BMC Syst Biol. 2011 Aug 23;5:134. doi: 10.1186/1752-0509-5-134.

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