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Items: 1 to 20 of 69

1.

Selection of organisms for the co-evolution-based study of protein interactions.

Herman D, Ochoa D, Juan D, Lopez D, Valencia A, Pazos F.

BMC Bioinformatics. 2011 Sep 12;12:363. doi: 10.1186/1471-2105-12-363.

2.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

Ochoa D, García-Gutiérrez P, Juan D, Valencia A, Pazos F.

Mol Biosyst. 2013 Jan 27;9(1):70-6. doi: 10.1039/c2mb25325a. Epub 2012 Oct 26.

PMID:
23104128
3.

Prediction of protein interaction based on similarity of phylogenetic trees.

Pazos F, Juan D, Izarzugaza JM, Leon E, Valencia A.

Methods Mol Biol. 2008;484:523-35. doi: 10.1007/978-1-59745-398-1_31.

PMID:
18592199
4.

Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction.

Muley VY, Ranjan A.

PLoS One. 2012;7(7):e42057. doi: 10.1371/journal.pone.0042057. Epub 2012 Jul 26.

5.

Refined phylogenetic profiles method for predicting protein-protein interactions.

Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y.

Bioinformatics. 2005 Aug 15;21(16):3409-15. Epub 2005 Jun 9.

PMID:
15947018
6.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
7.

Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling.

Simonsen M, Maetschke SR, Ragan MA.

Bioinformatics. 2012 Mar 15;28(6):851-7. doi: 10.1093/bioinformatics/btr720. Epub 2012 Jan 4.

PMID:
22219205
8.
9.

Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?

Sun J, Li Y, Zhao Z.

Biochem Biophys Res Commun. 2007 Feb 23;353(4):985-91. Epub 2006 Dec 27.

PMID:
17207465
10.

Analysis of coevolving gene families using mutually exclusive orthologous modules.

Zhang X, Kupiec M, Gophna U, Tuller T.

Genome Biol Evol. 2011;3:413-23. doi: 10.1093/gbe/evr030. Epub 2011 Apr 17.

PMID:
21498882
11.

Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.

Watanabe RL, Morett E, Vallejo EE.

BMC Bioinformatics. 2008 Jun 17;9:285. doi: 10.1186/1471-2105-9-285.

12.

Construction of phylogenetic profiles based on the genetic distance of hundreds of genomes.

Sun J, Zhao Z.

Biochem Biophys Res Commun. 2007 Apr 13;355(3):849-53. Epub 2007 Feb 20.

PMID:
17320815
13.

Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

Pazos F, Ranea JA, Juan D, Sternberg MJ.

J Mol Biol. 2005 Sep 30;352(4):1002-15.

PMID:
16139301
14.

Phylogenetic comparison of metabolic capacities of organisms at genome level.

Ma HW, Zeng AP.

Mol Phylogenet Evol. 2004 Apr;31(1):204-13.

PMID:
15019620
15.

Prediction of protein subcellular localization.

Yu CS, Chen YC, Lu CH, Hwang JK.

Proteins. 2006 Aug 15;64(3):643-51.

PMID:
16752418
16.

Exploiting the co-evolution of interacting proteins to discover interaction specificity.

Ramani AK, Marcotte EM.

J Mol Biol. 2003 Mar 14;327(1):273-84.

PMID:
12614624
17.

Protein co-evolution, co-adaptation and interactions.

Pazos F, Valencia A.

EMBO J. 2008 Oct 22;27(20):2648-55. doi: 10.1038/emboj.2008.189. Epub 2008 Sep 25. Review.

18.

The human protein coevolution network.

Tillier ER, Charlebois RL.

Genome Res. 2009 Oct;19(10):1861-71. doi: 10.1101/gr.092452.109. Epub 2009 Aug 20.

19.

Predicting protein-protein interactions in the context of protein evolution.

Lewis AC, Saeed R, Deane CM.

Mol Biosyst. 2010 Jan;6(1):55-64. doi: 10.1039/b916371a. Epub 2009 Sep 28. Review.

PMID:
20024067
20.

Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).

Kim WK, Bolser DM, Park JH.

Bioinformatics. 2004 May 1;20(7):1138-50. Epub 2004 Feb 5.

PMID:
14764552

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