Total: 43 publication


Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas, J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. (2017)
Subspecies in the global human gut microbiome.
Mol. Syst. Biol. 13(12) doi: 10.15252/msb.20177589
Europe PMC | doi

Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas, J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Fernández Breis JT, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S. (2017)
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Bioinformatics doi: 10.1093/bioinformatics/btx542
Europe PMC | doi

Huerta-Cepas, J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P. (2017)
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Mol Biol Evol 34(8):2115-2122. doi: 10.1093/molbev/msx148
Europe PMC | doi

Czech L, Huerta-Cepas, J, Stamatakis A. (2017)
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.
Mol. Biol. Evol. doi: 10.1093/molbev/msx055
Europe PMC | doi

Jouhten P, Huerta-Cepas, J, Bork P, Patil KR. (2017)
Metabolic anchor reactions for robust biorefining.
Metab. Eng. 40:1-4. doi: 10.1016/j.ymben.2017.02.010
Europe PMC | doi


Mende DR, Letunic I, Huerta-Cepas, J, Li SS, Forslund K, Sunagawa S, Bork P. (2016)
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Nucleic Acids Res. 45(D1):D529-D534. doi: 10.1093/nar/gkw989
Europe PMC | doi

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas, J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. (2016)
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Bioinformatics 32(16):2520-2523. doi: 10.1093/bioinformatics/btw183
Europe PMC | doi

Huerta-Cepas, J, Serra F, Bork P. (2016)
ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Mol. Biol. Evol. 33(6):1635-1638. doi: 10.1093/molbev/msw046
Europe PMC | doi

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas, J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. (2016)
Standardized benchmarking in the quest for orthologs.
Nat. Methods 13(5):425-430. doi: 10.1038/nmeth.3830
Europe PMC | doi

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas, J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. (2016)
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Science 352(6285):586-589. doi: 10.1126/science.aad8852
Europe PMC | doi

Huerta-Cepas, J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. (2016)
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Nucleic Acids Res 44(D1):D286-D293. doi: 10.1093/nar/gkv1248
Europe PMC | doi


Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas, J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldon T. (2015)
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream
Genome Biol. Evol. 7(7):1988-1999. doi: 10.1093/gbe/evv121
Europe PMC | doi


Djuika CF, Huerta-Cepas J, Przyborski JM, Deil S, Sanchez CP, Doerks T, Bork P, Lanzer M, Deponte M.
Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites.
Microb Cell. 2015 Jan 5;2(1):5-13. doi: 10.15698/mic2015.01.182.
Europe PMC | doi


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. (2014)
Whole-genome analyses resolve early branches in the tree of life of modern birds.
Science 346(6215):1320-1331. doi: 10.1126/science.1253451
Europe PMC | doi

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. 42(22):13525-13533. 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. doi: 10.1093/nar/gku1081
Europe PMC | doi

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. doi: 10.1093/nar/gku1003
Europe PMC | doi

Huerta-Cepas, J, Marcet-Houben M, Gabaldón T. (2014)
A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life
PeerJ 1(223) doi: 10.7287/peerj.preprints.223v1

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.
BBA 1843(9):1886-1898. doi: 10.1016/j.bbamcr.2014.05.004
Europe PMC | 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-D239. doi: 10.1093/nar/gkt1253
Europe PMC | doi


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 14:123. doi: 10.1186/1471-2164-14-123
Europe PMC | 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
Europe PMC | 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 12(5):442-448. doi: 10.1093/bib/bbr022
Europe PMC | doi

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(5):e32. doi: 10.1093/nar/gkq953
Europe PMC | 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
Europe PMC | 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
Europe PMC | 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
Europe PMC | doi


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
Europe PMC | 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
Europe PMC | 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(2):e1000313. doi: 10.1371/journal.pbio.1000313
Europe PMC | doi

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


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.


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
Europe PMC | 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
Europe PMC | doi


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 8:185. doi: 10.1186/1471-2164-8-185
Europe PMC | 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
Europe PMC | doi


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