Publications

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.
Manzano-Morales S, Liu Y, González-Bodí S, Huerta-Cepas J, Iranzo J.
Genome Biol. 2023 Oct 30;24(1):250. doi: 10.1186/s13059-023-03089-3. 10.1186/s13059-023-03089-3
Article has an altmetric score of 38
Computational exploration of the global microbiome for antibiotic discovery.
Santos-Júnior CD, Der Torossian Torres M, Duan Y, Del Río ÁR, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP.
bioRxiv. 2023 Sep 11:2023.08.31.555663. doi: 10.1101/2023.08.31.555663. Preprint. 10.1101/2023.08.31.555663
Article has an altmetric score of 37
Atlas of mRNA translation and decay for bacteria.
Huch S, Nersisyan L, Ropat M, Barrett D, Wu M, Wang J, Valeriano VD, Vardazaryan N, Huerta-Cepas J, Wei W, Du J, Steinmetz LM, Engstrand L, Pelechano V.
Nat Microbiol. 2023 Jun;8(6):1123-1136. doi: 10.1038/s41564-023-01393-z. Epub 2023 May 22. 10.1038/s41564-023-01393-z
Article has an altmetric score of 158
New globally distributed bacterial phyla within the FCB superphylum.
Gong X, Del Río ÁR, Xu L, Chen Z, Langwig MV, Su L, Sun M, Huerta-Cepas J, De Anda V, Baker BJ.
Nat Commun. 2022 Dec 6;13(1):7516. doi: 10.1038/s41467-022-34388-1. 10.1038/s41467-022-34388-1
Article has an altmetric score of 77
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity.
Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project 500 (EMP500) Consortium.
Nat Microbiol. 2022 Dec;7(12):2128-2150. doi: 10.1038/s41564-022-01266-x. Epub 2022 Nov 28. 10.1038/s41564-022-01266-x
Article has an altmetric score of 185
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J.
Nucleic Acids Res. 2022 Nov 18:gkac1022. doi: 10.1093/nar/gkac1022. Online ahead of print. 10.1093/nar/gkac1022
Article has an altmetric score of 26
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective.
Botas J, Rodríguez Del Río Á, Giner-Lamia J, Huerta-Cepas J.
Nucleic Acids Res. 2022 May 26;50(W1):W352-7. doi: 10.1093/nar/gkac367. Online ahead of print. 10.1093/nar/gkac367
Article has an altmetric score of 108
PhyloCloud: an online platform for making sense of phylogenomic data.
Deng Z, Botas J, Cantalapiedra CP, Hernández-Plaza A, Burguet-Castell J, Huerta-Cepas J.
Nucleic Acids Res. 2022 May 11;50(W1):W577-82. doi: 10.1093/nar/gkac324. Online ahead of print. 10.1093/nar/gkac324
Article has an altmetric score of 30
Towards the biogeography of prokaryotic genes.
Coelho LP, Alves R, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P.
Nature. 2022 Jan;601(7892):252-256. doi: 10.1038/s41586-021-04233-4. Epub 2021 Dec 15. 10.1038/s41586-021-04233-4
Article has an altmetric score of 342
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution.
Musser JM, Schippers KJ, Nickel M, Mizzon G, Kohn AB, Pape C, Ronchi P, Papadopoulos N, Tarashansky AJ, Hammel JU, Wolf F, Liang C, Hernández-Plaza A, Cantalapiedra CP, Achim K, Schieber NL, Pan L, Ruperti F, Francis WR, Vargas S, Kling S, Renkert M, Polikarpov M, Bourenkov G, Feuda R, Gaspar I, Burkhardt P, Wang B, Bork P, Beck M, Schneider TR, Kreshuk A, Wörheide G, Huerta-Cepas J, Schwab Y, Moroz LL, Arendt D.
Science. 2021 Nov 5;374(6568):717-723. doi: 10.1126/science.abj2949. Epub 2021 Nov 4. 10.1126/science.abj2949
Article has an altmetric score of 729
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J.
Mol Biol Evol. 2021 Dec 9;38(12):5825-5829. doi: 10.1093/molbev/msab293. 10.1093/molbev/msab293
Article has an altmetric score of 57
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria.
Sanchis-López C, Cerna-Vargas JP, Santamaría-Hernando S, Ramos C, Krell T, Rodríguez-Palenzuela P, López-Solanilla E, Huerta-Cepas J, Rodríguez-Herva JJ.
mSystems. 2021 Oct 26;6(5):e0095121. doi: 10.1128/mSystems.00951-21. Epub 2021 Sep 21. 10.1128/mSystems.00951-21
Article has an altmetric score of 1
Ten Years of Collaborative Progress in the Quest for Orthologs.
Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I; QFO Consortium.
Mol Biol Evol. 2021 Jul 29;38(8):3033-3045. doi: 10.1093/molbev/msab098. 10.1093/molbev/msab098
Article has an altmetric score of 6
The Quest for Orthologs benchmark service and consensus calls in 2020.
Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, For Orthologs Consortium TQ, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C.
Nucleic Acids Res. 2020 Jul 2;48(W1):W538-W545. doi: 10.1093/nar/gkaa308. 10.1093/nar/gkaa308
Article has an altmetric score of 8
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P.
ISME J. 2020 May;14(5):1247-1259. doi: 10.1038/s41396-020-0600-z. Epub 2020 Feb 11. 10.1038/s41396-020-0600-z
Article has an altmetric score of 48
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J; Tara Oceans Coordinators, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S.
Cell. 2019 Nov 14;179(5):1068-1083.e21. doi: 10.1016/j.cell.2019.10.014. 10.1016/j.cell.2019.10.014
Article has an altmetric score of 206
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P.
Nucleic Acids Res. 2020 Jan 8;48(D1):D621-D625. doi: 10.1093/nar/gkz1002. 10.1093/nar/gkz1002
Article has an altmetric score of 28
Advances and Applications in the Quest for Orthologs.
Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD.
Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150. 10.1093/molbev/msz150
Article has an altmetric score of 32
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P.
Microbiome. 2019 Jun 3;7(1):84. doi: 10.1186/s40168-019-0684-8. 10.1186/s40168-019-0684-8
Article has an altmetric score of 39
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S.
Nat Commun. 2019 Mar 4;10(1):1014. doi: 10.1038/s41467-019-08844-4. 10.1038/s41467-019-08844-4
Article has an altmetric score of 86
Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MT, Gossmann TI, Huerta-Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Aalvink S, Belzer C, Forslund SK, Sunagawa S, Hentschel U, Merten C, Patil KR, Benes V, Bork P.
Gut. 2019 Oct;68(10):1781-1790. doi: 10.1136/gutjnl-2018-317715. Epub 2019 Jan 18. 10.1136/gutjnl-2018-317715
Article has an altmetric score of 104
Function, evolution, and structure of J-domain proteins.
Kampinga HH, Andreasson C, Barducci A, Cheetham ME, Cyr D, Emanuelsson C, Genevaux P, Gestwicki JE, Goloubinoff P, Huerta-Cepas J, Kirstein J, Liberek K, Mayer MP, Nagata K, Nillegoda NB, Pulido P, Ramos C, De Los Rios P, Rospert S, Rosenzweig R, Sahi C, Taipale M, Tomiczek B, Ushioda R, Young JC, Zimmermann R, Zylicz A, Zylicz M, Craig EA, Marszalek J.
Cell Stress Chaperones. 2019 Jan;24(1):7-15. doi: 10.1007/s12192-018-0948-4. Epub 2018 Nov 26. 10.1007/s12192-018-0948-4
Article has an altmetric score of 3
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV.
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131. 10.1093/nar/gky1131
Article has an altmetric score of 72
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P.
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. doi: 10.1093/nar/gky1085. 10.1093/nar/gky1085
Article has an altmetric score of 64
Structure and function of the global topsoil microbiome.
Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P.
Nature. 2018 Aug;560(7717):233-237. doi: 10.1038/s41586-018-0386-6. Epub 2018 Aug 1. 10.1038/s41586-018-0386-6
Article has an altmetric score of 217
Subspecies in the global human gut microbiome.
Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P.
Mol Syst Biol. 2017 Dec 14;13(12):960. doi: 10.15252/msb.20177589. 10.15252/msb.20177589
Article has an altmetric score of 45
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, da Silva AS, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT; Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S; Quest for Orthologs Consortium.
Bioinformatics. 2018 Jan 15;34(2):323-329. doi: 10.1093/bioinformatics/btx542. 10.1093/bioinformatics/btx542
Article has an altmetric score of 9
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P.
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122. doi: 10.1093/molbev/msx148. 10.1093/molbev/msx148
Article has an altmetric score of 33
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.
Czech L, Huerta-Cepas J, Stamatakis A.
Mol Biol Evol. 2017 Jun 1;34(6):1535-1542. doi: 10.1093/molbev/msx055. 10.1093/molbev/msx055
Article has an altmetric score of 37
Metabolic anchor reactions for robust biorefining.
Jouhten P, Huerta-Cepas J, Bork P, Patil KR.
Metab Eng. 2017 Mar;40:1-4. doi: 10.1016/j.ymben.2017.02.010. Epub 2017 Feb 21. 10.1016/j.ymben.2017.02.010
Article has an altmetric score of 7
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P.
Nucleic Acids Res. 2017 Jan 4;45(D1):D529-D534. doi: 10.1093/nar/gkw989. Epub 2016 Oct 24. 10.1093/nar/gkw989
Article has an altmetric score of 20
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.
Baa-Puyoulet P, Parisot N, Febvay G, Huerta-Cepas J, Vellozo AF, Gabaldón T, Calevro F, Charles H, Colella S.
Database (Oxford). 2016 May 30;2016:baw081. doi: 10.1093/database/baw081. Print 2016. 10.1093/database/baw081
Article has an altmetric score of 2
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.
Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183. Epub 2016 Apr 8. 10.1093/bioinformatics/btw183
Article has an altmetric score of 44
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
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.
Science. 2016 Apr 29;352(6285):586-9. doi: 10.1126/science.aad8852. 10.1126/science.aad8852
Article has an altmetric score of 200
Standardized benchmarking in the quest for orthologs.
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.
Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4. 10.1038/nmeth.3830
Article has an altmetric score of 55
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.
Huerta-Cepas J, Serra F, Bork P.
Mol Biol Evol. 2016 Jun;33(6):1635-8. doi: 10.1093/molbev/msw046. Epub 2016 Feb 26. 10.1093/molbev/msw046
Article has an altmetric score of 51
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
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.
Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93. doi: 10.1093/nar/gkv1248. Epub 2015 Nov 17. 10.1093/nar/gkv1248
Article has an altmetric score of 10
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group.
Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121. 10.1093/gbe/evv121
Article has an altmetric score of 8
Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites.
Djuika CF, Huerta-Cepas J, Przyborski JM, Deil S, Sanchez CP, Doerks T, Bork P, Lanzer M, Deponte M.
Microb Cell. 2015 Jan 5;2(1):5-13. doi: 10.15698/mic2015.01.182. 10.15698/mic2015.01.182
Article has an altmetric score of 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, et al.
Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451. 10.1126/science.1253451
Article has an altmetric score of 677
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. 10.1093/nar/gku1147
Article has an altmetric score of 6
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. 10.1093/nar/gku1081
Article has an altmetric score of 2
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. 10.1093/nar/gku1003
Article has an altmetric score of 10
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. 10.1016/j.bbamcr.2014.05.004
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. 10.1093/nar/gkt1253
Article has an altmetric score of 8
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. 10.1093/nar/gkt1177
Article has an altmetric score of 7
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. 10.1186/1471-2164-14-123
Article has an altmetric score of 11
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. 10.1093/nar/gkr408
Article has an altmetric score of 2
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. 10.1093/bib/bbr022
Article has an altmetric score of 2
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. 10.1093/database/bar008
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. 10.1093/nar/gkq953
Article has an altmetric score of 7
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. 10.1093/nar/gkq1109
Article has an altmetric score of 3
Assigning duplication events to relative temporal scales in genome-wide studies.
Huerta-Cepas J, Gabaldón T.
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Article has an altmetric score of 1
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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. 10.1111/j.1365-2583.2009.00947.x
Genome sequence of the pea aphid Acyrthosiphon pisum.
International Aphid Genomics Consortium.
PLoS Biol. 2010 Feb 23;8(2):e1000313. doi: 10.1371/journal.pbio.1000313. 10.1371/journal.pbio.1000313
Article has an altmetric score of 47
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. 10.1038/ismej.2010.6
Article has an altmetric score of 6
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BMC Bioinformatics. 2010 Jan 13;11:24. doi: 10.1186/1471-2105-11-24. 10.1186/1471-2105-11-24
Article has an altmetric score of 4
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. 10.1093/nar/gkn303
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. 10.1093/bib/bbn003
Article has an altmetric score of 2
PhylomeDB: a database for genome-wide collections of gene phylogenies.
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Article has an altmetric score of 5
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.
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The human phylome.
Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T.
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Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
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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.
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Article has an altmetric score of 3
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
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Next station in microarray data analysis: GEPAS.
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.
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