Publications of J. Huerta-Cepas

Publications of J. Huerta-Cepas

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2023 3 publication(s).
32.
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR
2023 Jan 6; 51: D760-D766. PubMed: 36408900.
Abstract + PDF
31.
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
2023 Jan 6; 51: D389-D394. PubMed: 36399505.
Abstract + PDF
30.
Computational exploration of the global microbiome for antibiotic discovery.
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Michael K, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP
.
2023 Sep 11; [Epub ahead of print] PubMed: 37693522.
Abstract
2022 1 publication(s).
29.
Towards the biogeography of prokaryotic genes.
Coelho LP, Alves RJ, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TSB, 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
2022 Jan 15; 601(7892): 252-256. PubMed: 34912116.
Abstract + PDF
2021 2 publication(s).
28.
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
2021 Dec 9; 38(12): 5825-5829. PubMed: 34597405.
Abstract + PDF
27.
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
2021 Nov 5; 374(6568): 717-723. PubMed: 34735222.
Abstract + PDF
2020 2 publication(s).
26.
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
2020 May 11; 14(5): 1247-1259. PubMed: 32047279.
Abstract + PDF
25.
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
2020 Jan 8; 48: D621-D625. PubMed: 31647096.
Abstract + PDF
2019 6 publication(s).
24.
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho LP, Alves RJ, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P
2019 Jun 3; 7(1): 84. PubMed: 31159881.
Abstract + PDF
23.
Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, 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 18; 68(10): 1781-1790. PubMed: 30658995.
Abstract + PDF
22.
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
2019 Jan 8; 47: D309-D314. PubMed: 30418610.
Abstract + PDF
21.
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves RJ, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S
2019 Mar 4; 10(1): 1014. PubMed: 30833550.
Abstract + PDF
20.
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 Consortium 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
2019 Nov 14; 179(5): 1068-1083.e21. PubMed: 31730850.
Abstract + PDF
19.
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, von Mering C
2019 Jan 8; 47: D607-D613. PubMed: 30476243.
Abstract + PDF
2018 1 publication(s).
18.
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
2018 Aug 1; 560(7717): 233-237. PubMed: 30069051.
Abstract + PDF
2017 5 publication(s).
17.
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
2017 Dec 14; 13(12): 960. PubMed: 29242367.
Abstract + PDF
16.
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.
Czech L, Huerta-Cepas J, Stamatakis A
2017 Jun 1; 34(6): 1535-1542. PubMed: 28369572.
Abstract + PDF
15.
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
2017 Aug 1; 34(8): 2115-2122. PubMed: 28460117.
Abstract + PDF
14.
Metabolic anchor reactions for robust biorefining.
Jouhten P, Huerta-Cepas J, Bork P, Patil KR
2017 Mar 21; 40: 1-4. PubMed: 28232136.
Abstract + PDF
13.
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
2017 Jan 4; 45(D1): D529-D534. PubMed: 28053165.
Abstract + PDF
2016 6 publication(s).
12.
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
2016 May 4; 13(5): 425-30. Epub 2016 Apr 4; PubMed: 27043882.
Abstract + PDF
11.
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
2016; 2016: . PubMed: 27242037.
Abstract + PDF
10.
ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas J, Serra F, Bork P
2016 Jun 26; 33(6): 1635-8. Epub 2016 Feb 26; PubMed: 26921390.
Abstract + PDF
9.
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
2016 Jan 4; 44: D286-93. Epub 2015 Nov 17; PubMed: 26582926.
Abstract + PDF
8.
MOCAT2: a metagenomic assembly, annotation and profiling framework.
2016 Aug 15; 32(16): 2520-3. Epub 2016 Apr 8; PubMed: 27153620.
Abstract + PDF
7.
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
2016 Apr 29; 352(6285): 586-9. PubMed: 27126044.
Abstract + PDF
2015 4 publication(s).
6.
Quest for Orthologs (QfO) entails Quest for Tree of Life (QfToL): 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
2015 Jul 1; 7(7): 1988-99. PubMed: 26133389.
Abstract + PDF
5.
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
2015 Jan 5; 2(1): 5-13. PubMed: 28357258.
Abstract + PDF
4.
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
2015 Jan 28; 43: D494-502. Epub 2014 Oct 31; PubMed: 25361965.
Abstract + PDF
3.
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
2015 Jan 28; 43: D447-52. Epub 2014 Oct 28; PubMed: 25352553.
Abstract + PDF
2014 2 publication(s).
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 S, 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 Dec 16; 42(22): 13525-33. Epub 2014 Nov 14; PubMed: 25398899.
Abstract + PDF
1.
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 CJ, Kuhn M, Jensen LJ, von Mering C, Bork P
2014 Jan 1; 42(Database issue): D231-9. Epub 2013 Dec 1; PubMed: 24297252.
Abstract + PDF