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Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.
Kunath BJ, Hickl O, Queirós P, Martin-Gallausiaux C, Lebrun LA, Halder R, Laczny CC, Schmidt TSB, Hayward MR, Becher D, Heintz-Buschart A, de Beaufort C, Bork P, May P, Wilmes P. Kunath BJ, et al. Among authors: bork p. Microbiome. 2022 Dec 28;10(1):243. doi: 10.1186/s40168-022-01435-4. Microbiome. 2022. PMID: 36578059 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: bork p. bioRxiv [Preprint]. 2023 Sep 11:2023.08.31.555663. doi: 10.1101/2023.08.31.555663. bioRxiv. 2023. PMID: 37693522 Free PMC article. Preprint.
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: bork p. 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.
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C. Szklarczyk D, et al. Among authors: bork p. Nucleic Acids Res. 2023 Jan 6;51(D1):D638-D646. doi: 10.1093/nar/gkac1000. Nucleic Acids Res. 2023. PMID: 36370105 Free PMC article.
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium; Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium. Nielsen HB, et al. Among authors: bork p. Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6. Nat Biotechnol. 2014. PMID: 24997787
Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases.
Thiele M, Villesen IF, Niu L, Johansen S, Sulek K, Nishijima S, Espen LV, Keller M, Israelsen M, Suvitaival T, Zawadzki A, Juel HB, Brol MJ, Stinson SE, Huang Y, Silva MCA, Kuhn M, Anastasiadou E, Leeming DJ, Karsdal M, Matthijnssens J, Arumugam M, Dalgaard LT, Legido-Quigley C, Mann M, Trebicka J, Bork P, Jensen LJ, Hansen T, Krag A; MicrobLiver consortium; GALAXY consortium. Thiele M, et al. Among authors: bork p. J Hepatol. 2024 Mar 28:S0168-8278(24)00219-8. doi: 10.1016/j.jhep.2024.03.035. Online ahead of print. J Hepatol. 2024. PMID: 38552880 Free article. Review.
Paternal microbiome perturbations impact offspring fitness.
Argaw-Denboba A, Schmidt TSB, Di Giacomo M, Ranjan B, Devendran S, Mastrorilli E, Lloyd CT, Pugliese D, Paribeni V, Dabin J, Pisaniello A, Espinola S, Crevenna A, Ghosh S, Humphreys N, Boruc O, Sarkies P, Zimmermann M, Bork P, Hackett JA. Argaw-Denboba A, et al. Among authors: bork p. Nature. 2024 May;629(8012):652-659. doi: 10.1038/s41586-024-07336-w. Epub 2024 May 1. Nature. 2024. PMID: 38693261 Free PMC article.
688 results