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The metaRbolomics Toolbox in Bioconductor and beyond.
Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. Stanstrup J, et al. Among authors: willighagen e. Metabolites. 2019 Sep 23;9(10):200. doi: 10.3390/metabo9100200. Metabolites. 2019. PMID: 31548506 Free PMC article. Review.
The FAIR Cookbook - the essential resource for and by FAIR doers.
Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S, Chandramouliswaran I, Splendiani A, Burdett T, Giessmann RT, Henderson D, Batista D, Emam I, Gadiya Y, Giovanni L, Willighagen E, Evelo C, Gray AJG, Gribbon P, Juty N, Welter D, Quast K, Peeters P, Plasterer T, Wood C, van der Horst E, Reilly D, van Vlijmen H, Scollen S, Lister A, Thurston M, Granell R; FAIR Cookbook Contributors; Sansone SA. Rocca-Serra P, et al. Among authors: willighagen e. Sci Data. 2023 May 19;10(1):292. doi: 10.1038/s41597-023-02166-3. Sci Data. 2023. PMID: 37208467 Free PMC article.
SPLASH, a hashed identifier for mass spectra.
Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O. Wohlgemuth G, et al. Nat Biotechnol. 2016 Nov 8;34(11):1099-1101. doi: 10.1038/nbt.3689. Nat Biotechnol. 2016. PMID: 27824832 Free PMC article. No abstract available.
The future of metabolomics in ELIXIR.
van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. van Rijswijk M, et al. F1000Res. 2017 Sep 6;6:ELIXIR-1649. doi: 10.12688/f1000research.12342.2. eCollection 2017. F1000Res. 2017. PMID: 29043062 Free PMC article.
The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry.
Mohammed Taha H, Aalizadeh R, Alygizakis N, Antignac JP, Arp HPH, Bade R, Baker N, Belova L, Bijlsma L, Bolton EE, Brack W, Celma A, Chen WL, Cheng T, Chirsir P, Čirka Ľ, D'Agostino LA, Djoumbou Feunang Y, Dulio V, Fischer S, Gago-Ferrero P, Galani A, Geueke B, Głowacka N, Glüge J, Groh K, Grosse S, Haglund P, Hakkinen PJ, Hale SE, Hernandez F, Janssen EM, Jonkers T, Kiefer K, Kirchner M, Koschorreck J, Krauss M, Krier J, Lamoree MH, Letzel M, Letzel T, Li Q, Little J, Liu Y, Lunderberg DM, Martin JW, McEachran AD, McLean JA, Meier C, Meijer J, Menger F, Merino C, Muncke J, Muschket M, Neumann M, Neveu V, Ng K, Oberacher H, O'Brien J, Oswald P, Oswaldova M, Picache JA, Postigo C, Ramirez N, Reemtsma T, Renaud J, Rostkowski P, Rüdel H, Salek RM, Samanipour S, Scheringer M, Schliebner I, Schulz W, Schulze T, Sengl M, Shoemaker BA, Sims K, Singer H, Singh RR, Sumarah M, Thiessen PA, Thomas KV, Torres S, Trier X, van Wezel AP, Vermeulen RCH, Vlaanderen JJ, von der Ohe PC, Wang Z, Williams AJ, Willighagen EL, Wishart DS, Zhang J, Thomaidis NS, Hollender J, Slobodnik J, Schymanski EL. Mohammed Taha H, et al. Among authors: willighagen el. Environ Sci Eur. 2022;34(1):104. doi: 10.1186/s12302-022-00680-6. Epub 2022 Oct 21. Environ Sci Eur. 2022. PMID: 36284750 Free PMC article.
ELIXIR and Toxicology: a community in development.
Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas DΕ, Dave K, Dilger M, Exner T, Geerke DP, Grafström R, Gray A, Hancock JM, Hollert H, Jeliazkova N, Jennen D, Jourdan F, Kahlem P, Klanova J, Kleinjans J, Kondic T, Kone B, Lynch I, Maran U, Martinez Cuesta S, Ménager H, Neumann S, Nymark P, Oberacher H, Ramirez N, Remy S, Rocca-Serra P, Salek RM, Sallach B, Sansone SA, Sanz F, Sarimveis H, Sarntivijai S, Schulze T, Slobodnik J, Spjuth O, Tedds J, Thomaidis N, Weber RJM, van Westen GJP, Wheelock CE, Williams AJ, Witters H, Zdrazil B, Županič A, Willighagen EL. Martens M, et al. Among authors: willighagen el. F1000Res. 2023 Oct 3;10:ELIXIR-1129. doi: 10.12688/f1000research.74502.2. eCollection 2021. F1000Res. 2023. PMID: 37842337 Free PMC article.
Guiding the choice of informatics software and tools for lipidomics research applications.
Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O'Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O'Donnell VB, Fedorova M. Ni Z, et al. Among authors: willighagen el. Nat Methods. 2023 Feb;20(2):193-204. doi: 10.1038/s41592-022-01710-0. Epub 2022 Dec 21. Nat Methods. 2023. PMID: 36543939 Free PMC article. Review.
106 results