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Correction for Brennan et al., "Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution".
Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, Gonzalez A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R. Brennan C, et al. Among authors: belda ferre p. mSystems. 2024 Dec 13:e0128824. doi: 10.1128/msystems.01288-24. Online ahead of print. mSystems. 2024. PMID: 39670765 Free article. No abstract available.
Correction for Zhu et al., "Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy".
Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim H-C, Jain M, Inouye M, Gilbert JA, Knight R. Zhu Q, et al. Among authors: belda ferre p. mSystems. 2024 Nov 19;9(11):e0128924. doi: 10.1128/msystems.01289-24. Epub 2024 Oct 18. mSystems. 2024. PMID: 39422474 Free PMC article. No abstract available.
Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.
Brennan C, Belda-Ferre P, Zuffa S, Charron-Lamoureux V, Mohanty I, Ackermann G, Allaband C, Ambre M, Boyer T, Bryant M, Cantrell K, Gonzalez A, McDonald D, Salido RA, Song SJ, Wright G, Dorrestein PC, Knight R. Brennan C, et al. Among authors: belda ferre p. mSystems. 2024 Oct 22;9(10):e0098524. doi: 10.1128/msystems.00985-24. Epub 2024 Sep 16. mSystems. 2024. PMID: 39283083 Free PMC article.
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals.
Oles RE, Terrazas MC, Loomis LR, Neal MJ, Paulchakrabarti M, Zuffa S, Hsu CY, Vasquez Ayala A, Lee MH, Tribelhorn C, Belda-Ferre P, Bryant M, Zemlin J, Young J, Dulai P, Sandborn WJ, Sivagnanam M, Raffatellu M, Pride D, Dorrestein PC, Zengler K, Choudhury B, Knight R, Chu H. Oles RE, et al. Among authors: belda ferre p. bioRxiv [Preprint]. 2024 Jun 19:2024.06.19.599758. doi: 10.1101/2024.06.19.599758. bioRxiv. 2024. PMID: 38948766 Free PMC article. Preprint.
Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights.
Oles RE, Carrillo Terrazas M, Loomis LR, Hsu C-Y, Tribelhorn C, Belda-Ferre P, Ea AC, Bryant M, Young JA, Carrow HC, Sandborn WJ, Dulai PS, Sivagnanam M, Pride D, Knight R, Chu H. Oles RE, et al. Among authors: belda ferre p. mSystems. 2024 Jul 23;9(7):e0051624. doi: 10.1128/msystems.00516-24. Epub 2024 Jun 27. mSystems. 2024. PMID: 38934546 Free PMC article.
Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting.
Keehner J, Abeles SR, Longhurst CA, Horton LE, Myers FE, Riggs-Rodriguez L, Ahmad M, Baxter S, Boussina A, Cantrell K, Cardenas P, De Hoff P, El-Kareh R, Holland J, Ikeda D, Kurashige K, Laurent LC; SEARCH Alliance; Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ. Keehner J, et al. Clin Infect Dis. 2024 May 15;78(5):1204-1213. doi: 10.1093/cid/ciad738. Clin Infect Dis. 2024. PMID: 38227643
Reverse metabolomics for the discovery of chemical structures from humans.
Gentry EC, Collins SL, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu HH, Zuffa S, Yan T, Avila-Pacheco J, Plichta DR, Aron AT, Wang M, Jarmusch AK, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland BS, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish CB, Xavier RJ, Chu H, Baker ES, Patterson AD, Knight R, Siegel D, Dorrestein PC. Gentry EC, et al. Among authors: belda ferre p. Nature. 2024 Feb;626(7998):419-426. doi: 10.1038/s41586-023-06906-8. Epub 2023 Dec 5. Nature. 2024. PMID: 38052229 Free PMC article.
Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation.
Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP Jr, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Gauglitz JM, et al. Among authors: belda ferre p. Nat Biotechnol. 2023 Nov;41(11):1656. doi: 10.1038/s41587-023-02025-x. Nat Biotechnol. 2023. PMID: 37853256 No abstract available.
Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol.
Pendergraft MA, Belda-Ferre P, Petras D, Morris CK, Mitts BA, Aron AT, Bryant M, Schwartz T, Ackermann G, Humphrey G, Kaandorp E, Dorrestein PC, Knight R, Prather KA. Pendergraft MA, et al. Among authors: belda ferre p. Environ Sci Technol. 2023 Mar 14;57(10):4071-4081. doi: 10.1021/acs.est.2c02312. Epub 2023 Mar 2. Environ Sci Technol. 2023. PMID: 36862087 Free PMC article.
63 results