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Results: 1 to 20 of 22

1.

Neuroprotection elicited by P2Y13 receptors against genotoxic stress by inducing DUSP2 expression and MAPK signaling recovery.

Morente V, Pérez-Sen R, Ortega F, Huerta-Cepas J, Delicado EG, Miras-Portugal MT.

Biochim Biophys Acta. 2014 Sep;1843(9):1886-98. doi: 10.1016/j.bbamcr.2014.05.004. Epub 2014 May 20.

PMID:
24851838
[PubMed - in process]
2.

eggNOG v4.0: nested orthology inference across 3686 organisms.

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253. Epub 2013 Dec 1.

PMID:
24297252
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.

Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D897-902. doi: 10.1093/nar/gkt1177. Epub 2013 Nov 25.

PMID:
24275491
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Comparative transcriptomics of early dipteran development.

Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J.

BMC Genomics. 2013 Feb 24;14:123. doi: 10.1186/1471-2164-14-123.

PMID:
23432914
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W470-4. doi: 10.1093/nar/gkr408. Epub 2011 Jun 6.

PMID:
21646336
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.

Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T.

Brief Bioinform. 2011 Sep;12(5):442-8. doi: 10.1093/bib/bbr022. Epub 2011 Apr 22.

PMID:
21515902
[PubMed - indexed for MEDLINE]
Free Article
7.

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S.

Database (Oxford). 2011 Apr 7;2011:bar008. doi: 10.1093/database/bar008. Print 2011.

PMID:
21474551
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

Pryszcz LP, Huerta-Cepas J, Gabaldón T.

Nucleic Acids Res. 2011 Mar;39(5):e32. doi: 10.1093/nar/gkq953. Epub 2010 Dec 11.

PMID:
21149260
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.

Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldón T.

Nucleic Acids Res. 2011 Jan;39(Database issue):D556-60. doi: 10.1093/nar/gkq1109. Epub 2010 Nov 12.

PMID:
21075798
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Assigning duplication events to relative temporal scales in genome-wide studies.

Huerta-Cepas J, Gabaldón T.

Bioinformatics. 2011 Jan 1;27(1):38-45. doi: 10.1093/bioinformatics/btq609. Epub 2010 Nov 11.

PMID:
21075746
[PubMed - indexed for MEDLINE]
Free Article
11.

The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes.

Huerta-Cepas J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldón T.

Insect Mol Biol. 2010 Mar;19 Suppl 2:13-21. doi: 10.1111/j.1365-2583.2009.00947.x.

PMID:
20482636
[PubMed - indexed for MEDLINE]
12.

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.

Peña A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverría J, Lucio M, Schmitt-Kopplin P, Meseguer I, Schenowitz C, Dossat C, Barbe V, Dopazo J, Rosselló-Mora R, Schüler M, Glöckner FO, Amann R, Gabaldón T, Antón J.

ISME J. 2010 Jul;4(7):882-95. doi: 10.1038/ismej.2010.6. Epub 2010 Feb 18.

PMID:
20164864
[PubMed - indexed for MEDLINE]
13.

ETE: a python Environment for Tree Exploration.

Huerta-Cepas J, Dopazo J, Gabaldón T.

BMC Bioinformatics. 2010 Jan 13;11:24. doi: 10.1186/1471-2105-11-24.

PMID:
20070885
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

GEPAS, a web-based tool for microarray data analysis and interpretation.

Tárraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcárate S, Goetz S, Escobar P, Garcia-Garcia F, Conesa A, Montaner D, Dopazo J.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W308-14. doi: 10.1093/nar/gkn303. Epub 2008 May 28.

PMID:
18508806
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano M, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

Brief Bioinform. 2008 May;9(3):220-31. doi: 10.1093/bib/bbn003. Epub 2008 Jan 31. Review.

PMID:
18238804
[PubMed - indexed for MEDLINE]
Free Article
16.

PhylomeDB: a database for genome-wide collections of gene phylogenies.

Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6. Epub 2007 Oct 25.

PMID:
17962297
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Evidence for systems-level molecular mechanisms of tumorigenesis.

Hernández P, Huerta-Cepas J, Montaner D, Al-Shahrour F, Valls J, Gómez L, Capellá G, Dopazo J, Pujana MA.

BMC Genomics. 2007 Jun 20;8:185.

PMID:
17584915
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The human phylome.

Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T.

Genome Biol. 2007;8(6):R109.

PMID:
17567924
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.

Tárraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W38-42. Epub 2007 Apr 22.

PMID:
17452346
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

From genes to functional classes in the study of biological systems.

Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Mínguez P, Montaner D, Dopazo J.

BMC Bioinformatics. 2007 Apr 3;8:114.

PMID:
17407596
[PubMed - indexed for MEDLINE]
Free PMC Article

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