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30 results

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Page 1
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables.
Burcham ZM, Belk AD, McGivern BB, Bouslimani A, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel HL, Xu ZZ, Nieciecki V, Zhu Q, Shaffer M, Panitchpakdi M, Weldon KC, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Chan SHJ, Connor M, Boyd D, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Dorrestein PC, Wrighton KC, Carter DO, Knight R, Metcalf JL. Burcham ZM, et al. Among authors: weldon kc. Nat Microbiol. 2024 Mar;9(3):595-613. doi: 10.1038/s41564-023-01580-y. Epub 2024 Feb 12. Nat Microbiol. 2024. PMID: 38347104 Free PMC article.
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.
Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC. Gauglitz JM, et al. Food Chem. 2020 Jan 1;302:125290. doi: 10.1016/j.foodchem.2019.125290. Epub 2019 Jul 30. Food Chem. 2020. PMID: 31404873
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. 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. Among authors: weldon kc. 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: weldon kc. Nat Protoc. 2020 Jun;15(6):1954-1991. doi: 10.1038/s41596-020-0317-5. Epub 2020 May 13. Nat Protoc. 2020. PMID: 32405051
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: weldon kc. 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.
Feature-based molecular networking in the GNPS analysis environment.
Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin H C, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, Dorrestein PC. Nothias LF, et al. Among authors: weldon kc. Nat Methods. 2020 Sep;17(9):905-908. doi: 10.1038/s41592-020-0933-6. Epub 2020 Aug 24. Nat Methods. 2020. PMID: 32839597 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: weldon kc. mSystems. 2020 Sep 29;5(5):e00465-20. doi: 10.1128/mSystems.00465-20. mSystems. 2020. PMID: 32994287 Free PMC article.
30 results