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microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.
Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Si… See abstract for full author list ➔ Zuffa S, et al. Nat Microbiol. 2024 Feb;9(2):336-345. doi: 10.1038/s41564-023-01575-9. Epub 2024 Feb 5. Nat Microbiol. 2024. PMID: 38316926 Free PMC article.
Design of Synthetic Surrogates for the Macrolactone Linker Motif in Coibamide A.
Suzuki R, Mattos DR, Kitamura T, Tsujioka R, Kobayashi K, Inuki S, Ohno H, Ishmael JE, McPhail KL, Oishi S. Suzuki R, et al. ACS Med Chem Lett. 2023 Sep 19;14(10):1344-1350. doi: 10.1021/acsmedchemlett.3c00232. eCollection 2023 Oct 12. ACS Med Chem Lett. 2023. PMID: 37849553 Free PMC article.
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.
Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Si… See abstract for full author list ➔ Zuffa S, et al. Res Sq [Preprint]. 2023 Aug 3:rs.3.rs-3189768. doi: 10.21203/rs.3.rs-3189768/v1. Res Sq. 2023. PMID: 37577622 Free PMC article. Updated. Preprint.
TSignal: a transformer model for signal peptide prediction.
Dumitrescu A, Jokinen E, Paatero A, Kellosalo J, Paavilainen VO, Lähdesmäki H. Dumitrescu A, et al. Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i347-i356. doi: 10.1093/bioinformatics/btad228. Bioinformatics. 2023. PMID: 37387131 Free PMC article.
Tolypocladamide H and the Proposed Tolypocladamide NRPS in Tolypocladium Species.
Tehan RM, Blount RR, Goold RL, Mattos DR, Spatafora NR, Tabima JF, Gazis R, Wang C, Ishmael JE, Spatafora JW, McPhail KL. Tehan RM, et al. J Nat Prod. 2022 May 27;85(5):1363-1373. doi: 10.1021/acs.jnatprod.2c00153. Epub 2022 May 2. J Nat Prod. 2022. PMID: 35500108 Free PMC article. Review.
Design of Coibamide A Mimetics with Improved Cellular Bioactivity.
Kitamura T, Suzuki R, Inuki S, Ohno H, McPhail KL, Oishi S. Kitamura T, et al. ACS Med Chem Lett. 2021 Dec 29;13(1):105-110. doi: 10.1021/acsmedchemlett.1c00591. eCollection 2022 Jan 13. ACS Med Chem Lett. 2021. PMID: 35059129 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. Nat Commun. 2021 Jun 22;12(1):3832. doi: 10.1038/s41467-021-23953-9. Nat Commun. 2021. PMID: 34158495 Free PMC article.
Coibamide A Targets Sec61 to Prevent Biogenesis of Secretory and Membrane Proteins.
Tranter D, Paatero AO, Kawaguchi S, Kazemi S, Serrill JD, Kellosalo J, Vogel WK, Richter U, Mattos DR, Wan X, Thornburg CC, Oishi S, McPhail KL, Ishmael JE, Paavilainen VO. Tranter D, et al. ACS Chem Biol. 2020 Aug 21;15(8):2125-2136. doi: 10.1021/acschembio.0c00325. Epub 2020 Jul 20. ACS Chem Biol. 2020. PMID: 32608972 Free PMC article.
12 results