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Staff at EMBL

Jaime Huerta Cepas

Postdoctoral Fellow
Bork Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Tel: +49 6221 387-8305
E-mail: jaime.huerta@embl.de

Publications

Total: 29 publication(s)

2014

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. (2014)
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.
Nucleic Acids Res. doi:10.1093/nar/gku1147
Europe PMC | doi

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. (2014)
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res.
Europe PMC

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. (2014)
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Nucleic Acids Res.
Europe PMC

Morente V, Perez-Sen R, Ortega F, Huerta-Cepas J, Delicado EG, Miras-Portugal MT. (2014)
Neuroprotection elicited by P2Y(13) receptors against genotoxic stress by inducing DUSP2 expression and MAPK signaling recovery
BBA-MOL CELL RES 1843:1886-1898. doi:10.1016/j.bbamcr.2014.05.004
doi

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. (2014)
eggNOG v4.0: nested orthology inference across 3686 organisms
Nucleic Acids Res. 42(Database issue):D231-9. doi:10.1093/nar/gkt1253
Europe PMC | doi

Morente V, Pérez-Sen R, Ortega F, Huerta-Cepas J, Delicado EG, Miras-Portugal MT. (2014)
Neuroprotection elicited by P2Y13 receptors against genotoxic stress by inducing DUSP2 expression and MAPK signaling recovery.
Biochim. Biophys. Acta doi:10.1016/j.bbamcr.2014.05.004
doi


2013

Jimenez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldon T, Jaeger J. (2013)
Comparative transcriptomics of early dipteran development
BMC GENOMICS 14 doi:10.1186/1471-2164-14-123
doi

Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Marcet-Houben M, Gabaldon T. (2013)
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
Nucleic Acids Research 42(D1) doi:10.1093/nar/gkt1177
doi


2011

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. (2011)
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
Nucleic Acids Res. 39(Web Server issue):W470-4. doi:10.1093/nar/gkr408
Europe PMC | doi

Pryszcz LP, Huerta-Cepas J, Gabaldon T. (2011)
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
NUCLEIC ACIDS RES 39 doi:10.1093/nar/gkq953
doi

Huerta-Cepas J, Gabaldon T. (2011)
Assigning duplication events to relative temporal scales in genome-wide studies
BIOINFORMATICS 27:38-45. doi:10.1093/bioinformatics/btq609
doi

Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot M, Charles H, Colella S. (2011)
CycADS: an annotation database system to ease the development and update of BioCyc databases.
Database (Oxford) 2011 doi:10.1093/database/bar008
doi

Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T. (2011)
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings in bioinformatics doi:10.1093/bib/bbr022
doi

Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldon T. (2011)
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
NUCLEIC ACIDS RES 39:D556-D560. doi:10.1093/nar/gkq1109
doi


2010

Pena A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverria J, Lucio M, Schmitt-Kopplin P, Meseguer I, Schenowitz C, Dossat C, Barbe V, Dopazo J, Rossello-Mora R, Schuler M, Glockner FO, Amann R, Gabaldon T, Anton J. (2010)
Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains
ISME J 4:882-895. doi:10.1038/ismej.2010.6
doi

Huerta-Cepas J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldon T. (2010)
The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes
INSECT MOL BIOL 19:13-21. doi:10.1111/j.1365-2583.2009.00947.x
doi

Richards S, Gibbs RA, Gerardo NM, Moran N, Nakabachi A, Stern D, Tagu D, Wilson ACC, Muzny D, Kovar C, Cree A, Chacko J, Chandrabose MN, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangian SN, Joshi V, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang JK, Nazareth LV, Chavez D, Davis C, Lee SL, Patel BM, Pu LL, Bell SN, Johnson AJ, Vattathil S, Williams RL, Shigenobu S, Dang PM, Morioka M, Fukatsu T, Kudo T, Miyagishima SY, Jiang HY, Worley KC, Legeai F, Gauthier JP, Collin O, Zhang L, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Murphy T, Pruitt K, Sapojnikov V, Souvorov A, Thibaud-Nissen F, Camara F, Guigo R, Stanke M, Solovyev V, Kosarev P, Gilbert D, Gabaldon T, Huerta-Cepas J, Marcet-Houben M, Pignatelli M, Moya A, Rispe C, Ollivier M, Quesneville H, Permal E, Llorens C, Futami R, Hedges D, Robertson HM, Alioto T, Mariotti M, Nikoh N, McCutcheon JP, Burke G, Kamins A, Latorre A, Kudo T, Moran NA, Ashton P, Calevro F, Charles H, Colella S, Douglas A, Jander G, Jones DH, Febvay G, Kamphuis LG, Kushlan PF, Macdonald S, Ramsey J, Schwartz J, Seah S, Thomas G, Vellozo A, Cass B, Degnan P, Hurwitz B, Leonardo T, Koga R, Altincicek B, Anselme C, Atamian H, Barribeau SM, de Vos M, Duncan EJ, Evans J, Ghanim M, Heddi A, Kaloshian I, Vincent-Monegat C, Parker BJ, Perez-Brocal V, Rahbe Y, Spragg CJ, Tamames J, Tamarit D, Tamborindeguy C, Vilcinskas A, Bickel RD, Brisson JA, Butts T, Chang CC, Christiaens O, Davis GK, Duncan E, Ferrier D, Iga M, Janssen R, Lu HL, McGregor A, Miura T, Smagghe G, Smith J, van der Zee M, Velarde R, Wilson M, Dearden P, Edwards OR, Gordon K, Hilgarth RS, Rider SD, Robertson HM, Srinivasan D, Walsh TK, Ishikawa A, Jaubert-Possamai S, Fenton B, Huang WT, Jones DH, Rizk G, Lavenier D, Nicolas J, Smadja C, Robertson HM, Zhou JJ, Vieira FG, He XL, Liu RH, Rozas J, Field LM, Ashton PD, Campbell P, Carolan JC, Douglas AE, Fitzroy CIJ, Reardon KT, Reeck GR, Singh K, Wilkinson TL, Huybrechts J, Abdel-latief M, Robichon A, Veenstra JA, Hauser F, Cazzamali G, Schneider M, Williamson M, Stafflinger E, Hansen KK, Grimmelikhuijzen CJP, Price DRG, Caillaud M, van Fleet E, Ren QH, Gatehouse JA, Brault V, Monsion B, Diaz J, Hunnicutt L, Ju HJ, Pechuan X, Aguilar J, Cortes T, Ortiz-Rivas B, Martinez-Torres D, Dombrovsky A, Dale RP, Davies TGE, Williamson MS, Jones A, Sattelle D, Williamson S, Wolstenholme A, Vellozo A, Cottret L, Febvay G, Calevro F, Sagot MF, Heckel DG, Hunter W. (2010)
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
PLOS BIOL 8 doi:10.1371/journal.pbio.1000313
doi

Huerta-Cepas J, Dopazo J, Gabaldon T. (2010)
ETE: a python Environment for Tree Exploration
BMC BIOINFORMATICS 11 doi:10.1186/1471-2105-11-24
doi


2009

Patricio M, Huerta-Cepas J, Gabaldon T, Zardoya R, Posada D. (2009)
Automatic Prediction of the Genetic Code
LECT NOTES COMPUT SC 5518:1125-1129.


2008

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. (2008)
GEPAS, a web-based tool for microarray data analysis and interpretation
Nucleic Acids Res. 36(Web Server issue):W308-14. doi:10.1093/nar/gkn303
Europe PMC | doi

Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz ED, Wang D, Gibbons F, Gordon PMK, Sensen CW, Carrasco JMR, Fernandez JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PBT, Leunissen JAM, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Parraga I, Ramirez 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, Perez AJ, Aldana J, Rojano MM, Cruz RFS, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A. (2008)
Interoperability with Moby 1.0 - Its better than sharing your toothbrush
BRIEF BIOINFORM 9:220-231. doi:10.1093/bib/bbn003
doi

Gabaldón T, Marcet-Houben M, Huerta-Cepas J. (2008)
Computational Biology: New Research
Russe AS. Nova Science Publishers. New York..

Huerta-Cepas J, Bueno A, Dopazo JQ, Gabaldon T. (2008)
PhylomeDB: a database for genome-wide collections of gene phylogenies
NUCLEIC ACIDS RES 36:D491-D496. doi:10.1093/nar/gkm899
doi


2007

Tárraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H. (2007)
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics
Nucleic Acids Res. 35(Web Server issue):W38-42. doi:10.1093/nar/gkm224
Europe PMC | doi

Hernandez P, Huerta-Cepas J, Montaner D, Al-Shahrour F, Valls J, Gomez L, Capella G, Dopazo J, Pujana MA. (2007)
Evidence for systems-level molecular mechanisms of tumorigenesis
BMC GENOMICS 8 doi:10.1186/1471-2164-8-185
doi

Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Mínguez P, Montaner D, Dopazo J. (2007)
From genes to functional classes in the study of biological systems
BMC Bioinformatics 8:114. doi:10.1186/1471-2105-8-114
Europe PMC | doi

Schlüter A, Fourcade S, Domènech-Estévez E, Gabaldón T, Huerta-Cepas J, Berthommier G, Ripp R, Wanders RJA, Poch O, Pujol A. (2007)
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
doi:10.1093/nar/gkl935
doi


2006

Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T. (2006)
The human phylome.
Genome Biol. 8(6) doi:10.1186/gb-2007-8-6-r109
Europe PMC | doi

Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J. (2006)
Next station in microarray data analysis: GEPAS
Nucleic Acids Res. 34(Web Server issue):W486-91. doi:10.1093/nar/gkl197
Europe PMC | doi