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Co-evolution and co-adaptation in protein networks.
Juan D, Pazos F, Valencia A. Juan D, et al. Among authors: valencia a. 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.
Determination and validation of principal gene products.
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Tress ML, et al. Among authors: valencia a. Bioinformatics. 2008 Jan 1;24(1):11-7. doi: 10.1093/bioinformatics/btm547. Epub 2007 Nov 15. Bioinformatics. 2008. PMID: 18006548 Free PMC article.
RESULTS: We have combined five methods into a pipeline that allows us to detect the principal variant for a gene. Most of the methods were based on conservation between species, at the level of both gene and protein. ...The pipeline was able to determine a pr …
RESULTS: We have combined five methods into a pipeline that allows us to detect the principal variant for a gene. Most of the …
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.
Abascal F, Tress ML, Valencia A. Abascal F, et al. Among authors: valencia a. Bioinformatics. 2015 Jul 15;31(14):2257-61. doi: 10.1093/bioinformatics/btv132. Epub 2015 Mar 2. Bioinformatics. 2015. PMID: 25735770 Free PMC article.
Transposable elements constitute a large fraction of vertebrate genomes and, during evolution, may be co-opted for new functions. ...We found that these LAP2alpha domains have sequence similarity to repetitive sequences in non-mammalian genomes, which are in turn related t …
Transposable elements constitute a large fraction of vertebrate genomes and, during evolution, may be co-opted for new functions. ... …
Mirroring co-evolving trees in the light of their topologies.
Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC. Hajirasouliha I, et al. Among authors: valencia a. Bioinformatics. 2012 May 1;28(9):1202-8. doi: 10.1093/bioinformatics/bts109. Epub 2012 Mar 6. Bioinformatics. 2012. PMID: 22399677
RESULTS: Our algorithm is significantly faster than those methods based on distance matrix comparison: 1 min on a single processor versus 730 h on a supercomputer. ...AVAILABILITY: A C implementation of the method demonstrated in this article is available at …
RESULTS: Our algorithm is significantly faster than those methods based on distance matrix comparison: 1 min on a single processor ve …
Transcriptional dissection of pancreatic tumors engrafted in mice.
Martinez-Garcia R, Juan D, Rausell A, Muñoz M, Baños N, Menéndez C, Lopez-Casas PP, Rico D, Valencia A, Hidalgo M. Martinez-Garcia R, et al. Among authors: valencia a. Genome Med. 2014 Apr 16;6(4):27. doi: 10.1186/gm544. eCollection 2014. Genome Med. 2014. PMID: 24739241 Free PMC article.
We developed a robust analysis protocol to explore the gene expression space. In addition, we completed the analysis with a functional characterization of PDX models, including if changes were caused by murine environment or by serial passing. ...Expression changes …
We developed a robust analysis protocol to explore the gene expression space. In addition, we completed the analysis with a fu …
Colorectal cancer classification based on gene expression is not associated with FOLFIRI response.
Martinez-Garcia R, Lopez-Casas PP, Rico D, Valencia A, Hidalgo M. Martinez-Garcia R, et al. Among authors: valencia a. Nat Med. 2014 Nov;20(11):1230-1. doi: 10.1038/nm.3701. Nat Med. 2014. PMID: 25375918 No abstract available.
ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.
Frenkel-Morgenstern M, Gorohovski A, Tagore S, Sekar V, Vazquez M, Valencia A. Frenkel-Morgenstern M, et al. Among authors: valencia a. Nucleic Acids Res. 2017 Jul 7;45(12):7094-7105. doi: 10.1093/nar/gkx423. Nucleic Acids Res. 2017. PMID: 28549153 Free PMC article.
Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). ...Thus, the ChiPPI method represents a comprehensive …
Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have catal …
Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.
Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A. Juan D, et al. Among authors: valencia a. Cell Rep. 2016 Feb 9;14(5):1246-1257. doi: 10.1016/j.celrep.2016.01.008. Epub 2016 Jan 28. Cell Rep. 2016. PMID: 26832418
Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. ...Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related pr …
Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic mod …
The Functional Genomics Network in the evolution of biological text mining over the past decade.
Blaschke C, Valencia A. Blaschke C, et al. Among authors: valencia a. N Biotechnol. 2013 Mar 25;30(3):278-85. doi: 10.1016/j.nbt.2012.11.020. Epub 2012 Nov 30. N Biotechnol. 2013. PMID: 23202358 Review.
From residue coevolution to protein conformational ensembles and functional dynamics.
Sutto L, Marsili S, Valencia A, Gervasio FL. Sutto L, et al. Among authors: valencia a. Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13567-72. doi: 10.1073/pnas.1508584112. Epub 2015 Oct 20. Proc Natl Acad Sci U S A. 2015. PMID: 26487681 Free PMC article.
The analysis of evolutionary amino acid correlations has recently attracted a surge of renewed interest, also due to their successful use in de novo protein native structure prediction. ...To that end, we adapt the Boltzmann-learning algorithm to the analysis of homologous …
The analysis of evolutionary amino acid correlations has recently attracted a surge of renewed interest, also due to their successful …
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