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Co-evolution and co-adaptation in protein networks.
Juan D, Pazos F, Valencia A. Juan D, et al. FEBS Lett. 2008 Apr 9;582(8):1225-30. doi: 10.1016/j.febslet.2008.02.017. Epub 2008 Feb 20. FEBS Lett. 2008. PMID: 18282476 Review.
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. Pazos F, et al. Among authors: juan d. J Mol Biol. 2005 Sep 30;352(4):1002-15. doi: 10.1016/j.jmb.2005.07.005. J Mol Biol. 2005. PMID: 16139301
TSEMA: interactive prediction of protein pairings between interacting families.
Izarzugaza JM, Juan D, Pons C, Ranea JA, Valencia A, Pazos F. Izarzugaza JM, et al. Among authors: juan d. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W315-9. doi: 10.1093/nar/gkl112. Nucleic Acids Res. 2006. PMID: 16845017 Free PMC article.
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks.
Juan D, Pazos F, Valencia A. Juan D, et al. Proc Natl Acad Sci U S A. 2008 Jan 22;105(3):934-9. doi: 10.1073/pnas.0709671105. Epub 2008 Jan 16. Proc Natl Acad Sci U S A. 2008. PMID: 18199838 Free PMC article.
Enhancing the prediction of protein pairings between interacting families using orthology information.
Izarzugaza JM, Juan D, Pons C, Pazos F, Valencia A. Izarzugaza JM, et al. Among authors: juan d. BMC Bioinformatics. 2008 Jan 23;9:35. doi: 10.1186/1471-2105-9-35. BMC Bioinformatics. 2008. PMID: 18215279 Free PMC article.
Prediction of protein interaction based on similarity of phylogenetic trees.
Pazos F, Juan D, Izarzugaza JM, Leon E, Valencia A. Pazos F, et al. Among authors: juan d. Methods Mol Biol. 2008;484:523-35. doi: 10.1007/978-1-59745-398-1_31. Methods Mol Biol. 2008. PMID: 18592199
EcID. A database for the inference of functional interactions in E. coli.
Andres Leon E, Ezkurdia I, García B, Valencia A, Juan D. Andres Leon E, et al. Among authors: juan d. Nucleic Acids Res. 2009 Jan;37(Database issue):D629-35. doi: 10.1093/nar/gkn853. Epub 2008 Nov 12. Nucleic Acids Res. 2009. PMID: 19004873 Free PMC article.
Protein interactions and ligand binding: from protein subfamilies to functional specificity.
Rausell A, Juan D, Pazos F, Valencia A. Rausell A, et al. Among authors: juan d. Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1995-2000. doi: 10.1073/pnas.0908044107. Epub 2010 Jan 19. Proc Natl Acad Sci U S A. 2010. PMID: 20133844 Free PMC article.
Inference of functional relations in predicted protein networks with a machine learning approach.
García-Jiménez B, Juan D, Ezkurdia I, Andrés-León E, Valencia A. García-Jiménez B, et al. Among authors: juan d. PLoS One. 2010 Apr 1;5(4):e9969. doi: 10.1371/journal.pone.0009969. PLoS One. 2010. PMID: 20376314 Free PMC article.
Selection of organisms for the co-evolution-based study of protein interactions.
Herman D, Ochoa D, Juan D, Lopez D, Valencia A, Pazos F. Herman D, et al. Among authors: juan d. BMC Bioinformatics. 2011 Sep 12;12:363. doi: 10.1186/1471-2105-12-363. BMC Bioinformatics. 2011. PMID: 21910884 Free PMC article.
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