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Items: 1 to 20 of 103

1.
2.

Modification of gene duplicability during the evolution of protein interaction network.

D'Antonio M, Ciccarelli FD.

PLoS Comput Biol. 2011 Apr;7(4):e1002029. doi: 10.1371/journal.pcbi.1002029. Epub 2011 Apr 7.

3.

Preferential duplication in the sparse part of yeast protein interaction network.

Li L, Huang Y, Xia X, Sun Z.

Mol Biol Evol. 2006 Dec;23(12):2467-73. Epub 2006 Sep 15.

PMID:
16980576
4.

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.

Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A.

Nat Genet. 2006 Mar;38(3):285-93.

PMID:
16501559
5.

The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks.

Hsing M, Byler KG, Cherkasov A.

BMC Syst Biol. 2008 Sep 16;2:80. doi: 10.1186/1752-0509-2-80.

6.

Global alignment of protein-protein interaction networks.

Mongiovì M, Sharan R.

Methods Mol Biol. 2013;939:21-34. doi: 10.1007/978-1-62703-107-3_3.

PMID:
23192538
7.

Birth and death of protein domains: a simple model of evolution explains power law behavior.

Karev GP, Wolf YI, Rzhetsky AY, Berezovskaya FS, Koonin EV.

BMC Evol Biol. 2002 Oct 14;2:18.

8.

Gene duplicability-connectivity-complexity across organisms and a neutral evolutionary explanation.

Zhu Y, Du P, Nakhleh L.

PLoS One. 2012;7(9):e44491. doi: 10.1371/journal.pone.0044491. Epub 2012 Sep 11.

9.

Upstream plasticity and downstream robustness in evolution of molecular networks.

Maslov S, Sneppen K, Eriksen KA, Yan KK.

BMC Evol Biol. 2004 Mar 8;4:9.

10.

OrthoMCL: identification of ortholog groups for eukaryotic genomes.

Li L, Stoeckert CJ Jr, Roos DS.

Genome Res. 2003 Sep;13(9):2178-89.

11.

A methodology for detecting the orthology signal in a PPI network at a functional complex level.

Jancura P, Mavridou E, Carrillo-de Santa Pau E, Marchiori E.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S18. doi: 10.1186/1471-2105-13-S10-S18.

12.

Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites.

Liu X, Huang Y, Liang J, Zhang S, Li Y, Wang J, Shen Y, Xu Z, Zhao Y.

BMC Bioinformatics. 2014 Nov 30;15:393. doi: 10.1186/s12859-014-0393-z.

13.

The relative vertex clustering value--a new criterion for the fast discovery of functional modules in protein interaction networks.

Ibrahim ZM, Ngom A.

BMC Bioinformatics. 2015;16 Suppl 4:S3. doi: 10.1186/1471-2105-16-S4-S3. Epub 2015 Feb 23.

14.
15.

Comparison of protein interaction networks reveals species conservation and divergence.

Liang Z, Xu M, Teng M, Niu L.

BMC Bioinformatics. 2006 Oct 17;7:457.

16.

Information flow analysis of interactome networks.

Missiuro PV, Liu K, Zou L, Ross BC, Zhao G, Liu JS, Ge H.

PLoS Comput Biol. 2009 Apr;5(4):e1000350. doi: 10.1371/journal.pcbi.1000350. Epub 2009 Apr 10.

17.

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.

18.

Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans.

Katju V, Farslow JC, Bergthorsson U.

Genome Biol. 2009;10(7):R75. doi: 10.1186/gb-2009-10-7-r75. Epub 2009 Jul 13.

19.

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses.

On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, Zhang Z, Greenblatt J, Wodak SJ, Parkinson J.

Proteins. 2010 Jul;78(9):2075-89. doi: 10.1002/prot.22723.

PMID:
20455264
20.

Maximum likelihood inference of the evolutionary history of a PPI network from the duplication history of its proteins.

Li S, Choi KP, Wu T, Zhang L.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1412-21. doi: 10.1109/TCBB.2013.14.

PMID:
24407300

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