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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. Musser JM, et al. Among authors: hernandez plaza a. Science. 2021 Nov 5;374(6568):717-723. doi: 10.1126/science.abj2949. Epub 2021 Nov 4. Science. 2021. PMID: 34735222 Free PMC article.
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. Deng Z, et al. Among authors: hernandez plaza a. Nucleic Acids Res. 2022 Jul 5;50(W1):W577-W582. doi: 10.1093/nar/gkac324. Nucleic Acids Res. 2022. PMID: 35544233 Free PMC article.
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. Huerta-Cepas J, et al. Among authors: hernandez plaza a. Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. doi: 10.1093/nar/gky1085. Nucleic Acids Res. 2019. PMID: 30418610 Free PMC article.
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. Mende DR, et al. Among authors: hernandez plaza a. Nucleic Acids Res. 2020 Jan 8;48(D1):D621-D625. doi: 10.1093/nar/gkz1002. Nucleic Acids Res. 2020. PMID: 31647096 Free PMC article.
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. Altenhoff AM, et al. Among authors: hernandez plaza a. Nucleic Acids Res. 2020 Jul 2;48(W1):W538-W545. doi: 10.1093/nar/gkaa308. Nucleic Acids Res. 2020. PMID: 32374845 Free PMC article.
Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez Del Río Á, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernández-Plaza A, Munar-Palmer M, Santamaría-Hernando S, Rodríguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, López-Solanilla E, Coelho LP, Huerta-Cepas J. Rodríguez Del Río Á, et al. Among authors: hernandez plaza a. Nature. 2024 Feb;626(7998):377-384. doi: 10.1038/s41586-023-06955-z. Epub 2023 Dec 18. Nature. 2024. PMID: 38109938 Free PMC article.
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. Hernández-Plaza A, et al. Nucleic Acids Res. 2023 Jan 6;51(D1):D389-D394. doi: 10.1093/nar/gkac1022. Nucleic Acids Res. 2023. PMID: 36399505 Free PMC article.