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Results: 1 to 20 of 26

1.

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.

2.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P.

Nucleic Acids Res. 2014 Dec 16;42(22):13525-33. doi: 10.1093/nar/gku1147. Epub 2014 Nov 14.

3.

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D494-502. doi: 10.1093/nar/gku1081. Epub 2014 Oct 31.

4.

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003. Epub 2014 Oct 28.

5.

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
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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
16.

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
17.

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.

18.

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.

19.

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.

20.

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.

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