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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. Among authors: gentry ec. 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.
Mass spectrometry searches using MASST.
Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC. Wang M, et al. Among authors: gentry ec. Nat Biotechnol. 2020 Jan;38(1):23-26. doi: 10.1038/s41587-019-0375-9. Nat Biotechnol. 2020. PMID: 31894142 Free PMC article. No abstract available.
Global chemical effects of the microbiome include new bile-acid conjugations.
Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. Quinn RA, et al. Nature. 2020 Mar;579(7797):123-129. doi: 10.1038/s41586-020-2047-9. Epub 2020 Feb 26. Nature. 2020. PMID: 32103176 Free PMC article.
Reproducible molecular networking of untargeted mass spectrometry data using GNPS.
Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. Aron AT, et al. Among authors: gentry ec. Nat Protoc. 2020 Jun;15(6):1954-1991. doi: 10.1038/s41596-020-0317-5. Epub 2020 May 13. Nat Protoc. 2020. PMID: 32405051
Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice.
Dethloff F, Vargas F, Elijah E, Quinn R, Park DI, Herzog DP, Müller MB, Gentry EC, Knight R, Gonzalez A, Dorrestein PC, Turck CW. Dethloff F, et al. Among authors: gentry ec. Front Psychiatry. 2020 Jun 4;11:518. doi: 10.3389/fpsyt.2020.00518. eCollection 2020. Front Psychiatry. 2020. PMID: 32581888 Free PMC article.
ReDU: a framework to find and reanalyze public mass spectrometry data.
Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL 2nd, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. Jarmusch AK, et al. Among authors: gentry ec. Nat Methods. 2020 Sep;17(9):901-904. doi: 10.1038/s41592-020-0916-7. Epub 2020 Aug 17. Nat Methods. 2020. PMID: 32807955 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. Among authors: gentry ec. mSystems. 2020 Sep 29;5(5):e00465-20. doi: 10.1128/mSystems.00465-20. mSystems. 2020. PMID: 32994287 Free PMC article.
A community resource for paired genomic and metabolomic data mining.
Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrión VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, Männle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Süssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorreste… See abstract for full author list ➔ Schorn MA, et al. Among authors: gentry ec. Nat Chem Biol. 2021 Apr;17(4):363-368. doi: 10.1038/s41589-020-00724-z. Nat Chem Biol. 2021. PMID: 33589842 Free PMC article.
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment.
Schmid R, Petras D, Nothias LF, Wang M, Aron AT, Jagels A, Tsugawa H, Rainer J, Garcia-Aloy M, Dührkop K, Korf A, Pluskal T, Kameník Z, Jarmusch AK, Caraballo-Rodríguez AM, Weldon KC, Nothias-Esposito M, Aksenov AA, Bauermeister A, Albarracin Orio A, Grundmann CO, Vargas F, Koester I, Gauglitz JM, Gentry EC, Hövelmann Y, Kalinina SA, Pendergraft MA, Panitchpakdi M, Tehan R, Le Gouellec A, Aleti G, Mannochio Russo H, Arndt B, Hübner F, Hayen H, Zhi H, Raffatellu M, Prather KA, Aluwihare LI, Böcker S, McPhail KL, Humpf HU, Karst U, Dorrestein PC. Schmid R, et al. Among authors: gentry ec. Nat Commun. 2021 Jun 22;12(1):3832. doi: 10.1038/s41467-021-23953-9. Nat Commun. 2021. PMID: 34158495 Free PMC article.
27 results