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2019 1
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Long-read amplicon denoising.
Kumar V, Vollbrecht T, Chernyshev M, Mohan S, Hanst B, Bavafa N, Lorenzo A, Kumar N, Ketteringham R, Eren K, Golden M, Oliveira MF, Murrell B. Kumar V, et al. Nucleic Acids Res. 2019 Oct 10;47(18):e104. doi: 10.1093/nar/gkz657. Nucleic Acids Res. 2019. PMID: 31418021 Free PMC article.
Evaluation of Archival HIV DNA in Brain and Lymphoid Tissues.
Oliveira MF, Pankow A, Vollbrecht T, Kumar NM, Cabalero G, Ignacio C, Zhao M, Vitomirov A, Gouaux B, Nakawawa M, Murrell B, Ellis RJ, Gianella S. Oliveira MF, et al. J Virol. 2023 Jun 29;97(6):e0054323. doi: 10.1128/jvi.00543-23. Epub 2023 May 15. J Virol. 2023. PMID: 37184401 Free PMC article.
Large Mitochondrial DNA Deletions in HIV Sensory Neuropathy.
Roda RH, Bargiela D, Chen W, Perry K, Ellis RJ, Clifford DB, Bharti A, Kallianpur AR, Oliveira MF, Diaz MM, Rubin LH, Gavegnano C, McArthur JC, Hoke A, Polydefkis M. Roda RH, et al. Neurology. 2021 Jul 13;97(2):e156-e165. doi: 10.1212/WNL.0000000000012142. Epub 2021 May 4. Neurology. 2021. PMID: 33947785 Free PMC article. Clinical Trial.
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. Nat Biotechnol. 2022 Dec;40(12):1774-1779. doi: 10.1038/s41587-022-01368-1. Epub 2022 Jul 7. Nat Biotechnol. 2022. PMID: 35798960 Free PMC article.
Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome.
Taylor BC, Weldon KC, Ellis RJ, Franklin D, Groth T, Gentry EC, Tripathi A, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Oliveira MF, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. Taylor BC, et al. mSystems. 2020 Sep 29;5(5):e00465-20. doi: 10.1128/mSystems.00465-20. mSystems. 2020. PMID: 32994287 Free PMC article.
Quick-start infrastructure for untargeted metabolomics analysis in GNPS.
Leao TF, Clark CM, Bauermeister A, Elijah EO, Gentry EC, Husband M, Oliveira MF, Bandeira N, Wang M, Dorrestein PC. Leao TF, et al. Nat Metab. 2021 Jul;3(7):880-882. doi: 10.1038/s42255-021-00429-0. Nat Metab. 2021. PMID: 34244695 Free PMC article. No abstract available.