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Items: 1 to 20 of 73

1.

Using coevolution to predict protein-protein interactions.

Clark GW, Dar VU, Bezginov A, Yang JM, Charlebois RL, Tillier ER.

Methods Mol Biol. 2011;781:237-56. doi: 10.1007/978-1-61779-276-2_11.

PMID:
21877284
2.

The effects of network neighbours on protein evolution.

Wang GZ, Lercher MJ.

PLoS One. 2011 Apr 12;6(4):e18288. doi: 10.1371/journal.pone.0018288.

3.

A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives.

Thompson JD, Linard B, Lecompte O, Poch O.

PLoS One. 2011 Mar 31;6(3):e18093. doi: 10.1371/journal.pone.0018093.

4.

Interactome networks and human disease.

Vidal M, Cusick ME, Barabási AL.

Cell. 2011 Mar 18;144(6):986-98. doi: 10.1016/j.cell.2011.02.016. Review.

5.

Among-site rate variation and its impact on phylogenetic analyses.

Yang Z.

Trends Ecol Evol. 1996 Sep;11(9):367-72.

PMID:
21237881
6.

Protein binding specificity versus promiscuity.

Schreiber G, Keating AE.

Curr Opin Struct Biol. 2011 Feb;21(1):50-61. doi: 10.1016/j.sbi.2010.10.002. Epub 2010 Nov 9. Review.

7.

The European Nucleotide Archive.

Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G.

Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31. doi: 10.1093/nar/gkq967. Epub 2010 Oct 23.

8.

Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins.

Kelly WP, Stumpf MP.

BMC Bioinformatics. 2010 Sep 20;11:470. doi: 10.1186/1471-2105-11-470.

9.

An integrated view of molecular coevolution in protein-protein interactions.

Lovell SC, Robertson DL.

Mol Biol Evol. 2010 Nov;27(11):2567-75. doi: 10.1093/molbev/msq144. Epub 2010 Jun 14. Review.

10.

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
11.

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.

12.

The effect of sequence evolution on protein structural divergence.

Williams SG, Lovell SC.

Mol Biol Evol. 2009 May;26(5):1055-65. doi: 10.1093/molbev/msp020. Epub 2009 Feb 4.

13.

Correlated evolution of interacting proteins: looking behind the mirrortree.

Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM.

J Mol Biol. 2009 Jan 9;385(1):91-8. doi: 10.1016/j.jmb.2008.09.078. Epub 2008 Oct 9.

14.

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.

15.

Phylogenetic inference using whole genomes.

Rannala B, Yang Z.

Annu Rev Genomics Hum Genet. 2008;9:217-31. doi: 10.1146/annurev.genom.9.081307.164407. Review.

PMID:
18767964
16.

Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking.

Madaoui H, Guerois R.

Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7708-13. doi: 10.1073/pnas.0707032105. Epub 2008 May 29.

17.

Evolution and dynamics of protein interactions and networks.

Levy ED, Pereira-Leal JB.

Curr Opin Struct Biol. 2008 Jun;18(3):349-57. doi: 10.1016/j.sbi.2008.03.003. Epub 2008 Apr 28. Review.

PMID:
18448325
18.

An improved general amino acid replacement matrix.

Le SQ, Gascuel O.

Mol Biol Evol. 2008 Jul;25(7):1307-20. doi: 10.1093/molbev/msn067. Epub 2008 Mar 26.

19.

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks.

Juan D, Pazos F, Valencia A.

Proc Natl Acad Sci U S A. 2008 Jan 22;105(3):934-9. doi: 10.1073/pnas.0709671105. Epub 2008 Jan 16.

20.

The Pfam protein families database.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8. Epub 2007 Nov 26.

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