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Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.
Pakkir Shah AK, Walter A, Ottosson F, Russo F, Navarro-Diaz M, Boldt J, Kalinski JJ, Kontou EE, Elofson J, Polyzois A, González-Marín C, Farrell S, Aggerbeck MR, Pruksatrakul T, Chan N, Wang Y, Pöchhacker M, Brungs C, Cámara B, Caraballo-Rodríguez AM, Cumsille A, de Oliveira F, Dührkop K, El Abiead Y, Geibel C, Graves LG, Hansen M, Heuckeroth S, Knoblauch S, Kostenko A, Kuijpers MCM, Mildau K, Papadopoulos Lambidis S, Portal Gomes PW, Schramm T, Steuer-Lodd K, Stincone P, Tayyab S, Vitale GA, Wagner BC, Xing S, Yazzie MT, Zuffa S, de Kruijff M, Beemelmanns C, Link H, Mayer C, van der Hooft JJJ, Damiani T, Pluskal T, Dorrestein P, Stanstrup J, Schmid R, Wang M, Aron A, Ernst M, Petras D. Pakkir Shah AK, et al. Among authors: ernst m. Nat Protoc. 2024 Sep 20. doi: 10.1038/s41596-024-01046-3. Online ahead of print. Nat Protoc. 2024. PMID: 39304763 Review.
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: ernst m. 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.
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: ernst m. 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: ernst m. 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.
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.
Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC. Tripathi A, et al. Among authors: ernst m. Nat Chem Biol. 2021 Feb;17(2):146-151. doi: 10.1038/s41589-020-00677-3. Epub 2020 Nov 16. Nat Chem Biol. 2021. PMID: 33199911 Free PMC article.
Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.
Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL 2nd, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. Aksenov AA, et al. Among authors: ernst m. Nat Biotechnol. 2021 Feb;39(2):169-173. doi: 10.1038/s41587-020-0700-3. Epub 2020 Nov 9. Nat Biotechnol. 2021. PMID: 33169034 Free PMC article.
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden.
Caraballo-Rodríguez AM, Puckett SP, Kyle KE, Petras D, da Silva R, Nothias LF, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC. Caraballo-Rodríguez AM, et al. Among authors: ernst m. mSystems. 2021 Aug 31;6(4):e0060121. doi: 10.1128/mSystems.00601-21. Epub 2021 Aug 3. mSystems. 2021. PMID: 34342533 Free PMC article.
2,226 results