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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. Altenhoff AM, et al. Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4. Nat Methods. 2016. PMID: 27043882 Free PMC article.
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. Shaffer JP, et al. Nat Microbiol. 2022 Dec;7(12):2128-2150. doi: 10.1038/s41564-022-01266-x. Epub 2022 Nov 28. Nat Microbiol. 2022. PMID: 36443458 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: huerta cepas j. 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.
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. Santos-Júnior CD, et al. Among authors: huerta cepas j. bioRxiv [Preprint]. 2023 Sep 11:2023.08.31.555663. doi: 10.1101/2023.08.31.555663. bioRxiv. 2023. PMID: 37693522 Free PMC article. Preprint.
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. Huch S, et al. Among authors: huerta cepas j. Nat Microbiol. 2023 Jun;8(6):1123-1136. doi: 10.1038/s41564-023-01393-z. Epub 2023 May 22. Nat Microbiol. 2023. PMID: 37217719 Free PMC article.
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. Gong X, et al. Among authors: huerta cepas j. Nat Commun. 2022 Dec 6;13(1):7516. doi: 10.1038/s41467-022-34388-1. Nat Commun. 2022. PMID: 36473838 Free PMC article.
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. Fullam A, et al. Among authors: huerta cepas j. Nucleic Acids Res. 2023 Jan 6;51(D1):D760-D766. doi: 10.1093/nar/gkac1078. Nucleic Acids Res. 2023. PMID: 36408900 Free PMC article.
70 results