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Items: 1 to 20 of 96

2.

Evolutionary cores of domain co-occurrence networks.

Wuchty S, Almaas E.

BMC Evol Biol. 2005 Mar 23;5:24.

3.

Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity.

Kanapin AA, Mulder N, Kuznetsov VA.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S4. doi: 10.1186/1471-2164-11-S1-S4.

4.

Global patterns of protein domain gain and loss in superkingdoms.

Nasir A, Kim KM, Caetano-Anollés G.

PLoS Comput Biol. 2014 Jan 30;10(1):e1003452. doi: 10.1371/journal.pcbi.1003452. eCollection 2014 Jan.

5.

Evolution of the PWWP-domain encoding genes in the plant and animal lineages.

Alvarez-Venegas R, Avramova Z.

BMC Evol Biol. 2012 Jun 26;12:101.

6.

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks.

Xie X, Jin J, Mao Y.

BMC Evol Biol. 2011 Aug 18;11:242. doi: 10.1186/1471-2148-11-242.

7.

Functional fingerprints of folds: evidence for correlated structure-function evolution.

Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI.

J Mol Biol. 2003 Feb 7;326(1):1-9.

PMID:
12547186
8.
9.

Proteome compression via protein domain compositions.

Hayashida M, Ruan P, Akutsu T.

Methods. 2014 Jun 1;67(3):380-5. doi: 10.1016/j.ymeth.2014.01.012. Epub 2014 Jan 29.

PMID:
24486717
10.

Global phylogeny determined by the combination of protein domains in proteomes.

Wang M, Caetano-Anollés G.

Mol Biol Evol. 2006 Dec;23(12):2444-54. Epub 2006 Sep 13.

11.

Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes.

Kawashima S, Kawashima T, Putnam NH, Rokhsar DS, Wada H, Kanehisa M.

Genome Inform. 2007;19:50-60.

PMID:
18546504
12.

Analyses of domains and domain fusions in human proto-oncogenes.

Liu Q, Huang J, Liu H, Wan P, Ye X, Xu Y.

BMC Bioinformatics. 2009 Mar 17;10:88. doi: 10.1186/1471-2105-10-88.

13.

The relationship between domain duplication and recombination.

Vogel C, Teichmann SA, Pereira-Leal J.

J Mol Biol. 2005 Feb 11;346(1):355-65. Epub 2004 Dec 23.

PMID:
15663950
15.

Diversity and evolution of the thyroglobulin type-1 domain superfamily.

Novinec M, Kordis D, Turk V, Lenarcic B.

Mol Biol Evol. 2006 Apr;23(4):744-55. Epub 2005 Dec 20.

16.

Protein domain organisation: adding order.

Kummerfeld SK, Teichmann SA.

BMC Bioinformatics. 2009 Jan 29;10:39. doi: 10.1186/1471-2105-10-39.

17.

Phylomat: an automated protein motif analysis tool for phylogenomics.

Graham WV, Tcheng DK, Shirk AL, Attene-Ramos MS, Welge ME, Gaskins HR.

J Proteome Res. 2004 Nov-Dec;3(6):1289-91.

PMID:
15595740
18.

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

Kemmer D, Podowski RM, Arenillas D, Lim J, Hodges E, Roth P, Sonnhammer EL, Höög C, Wasserman WW.

BMC Genomics. 2006 Mar 13;7:48.

19.

Protein families and their evolution-a structural perspective.

Orengo CA, Thornton JM.

Annu Rev Biochem. 2005;74:867-900. Review.

PMID:
15954844
20.

Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.

Bukhari SA, Caetano-Anollés G.

PLoS Comput Biol. 2013;9(3):e1003009. doi: 10.1371/journal.pcbi.1003009. Epub 2013 Mar 28.

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