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Items: 16

1.

Interoperable and scalable data analysis with microservices: Applications in Metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran A, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O.

Bioinformatics. 2019 Mar 9. pii: btz160. doi: 10.1093/bioinformatics/btz160. [Epub ahead of print]

PMID:
30851093
2.

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C.

Gigascience. 2019 Feb 1;8(2). pii: giy149. doi: 10.1093/gigascience/giy149.

3.

"MS-Ready" structures for non-targeted high-resolution mass spectrometry screening studies.

McEachran AD, Mansouri K, Grulke C, Schymanski EL, Ruttkies C, Williams AJ.

J Cheminform. 2018 Aug 30;10(1):45. doi: 10.1186/s13321-018-0299-2.

4.

Current Challenges in Plant Eco-Metabolomics.

Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV.

Int J Mol Sci. 2018 May 6;19(5). pii: E1385. doi: 10.3390/ijms19051385. Review.

5.

Performance of combined fragmentation and retention prediction for the identification of organic micropollutants by LC-HRMS.

Hu M, Müller E, Schymanski EL, Ruttkies C, Schulze T, Brack W, Krauss M.

Anal Bioanal Chem. 2018 Mar;410(7):1931-1941. doi: 10.1007/s00216-018-0857-5. Epub 2018 Jan 30.

PMID:
29380019
6.

Critical Assessment of Small Molecule Identification 2016: automated methods.

Schymanski EL, Ruttkies C, Krauss M, Brouard C, Kind T, Dührkop K, Allen F, Vaniya A, Verdegem D, Böcker S, Rousu J, Shen H, Tsugawa H, Sajed T, Fiehn O, Ghesquière B, Neumann S.

J Cheminform. 2017 Mar 27;9(1):22. doi: 10.1186/s13321-017-0207-1.

7.

Qualitative screening for new psychoactive substances in wastewater collected during a city festival using liquid chromatography coupled to high-resolution mass spectrometry.

Causanilles A, Kinyua J, Ruttkies C, van Nuijs ALN, Emke E, Covaci A, de Voogt P.

Chemosphere. 2017 Oct;184:1186-1193. doi: 10.1016/j.chemosphere.2017.06.101. Epub 2017 Jun 26.

PMID:
28672699
8.

Bioinformatics can boost metabolomics research.

Meier R, Ruttkies C, Treutler H, Neumann S.

J Biotechnol. 2017 Nov 10;261:137-141. doi: 10.1016/j.jbiotec.2017.05.018. Epub 2017 May 26. Review.

9.

LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome.

Witting M, Ruttkies C, Neumann S, Schmitt-Kopplin P.

PLoS One. 2017 Mar 9;12(3):e0172311. doi: 10.1371/journal.pone.0172311. eCollection 2017.

10.

MetFrag relaunched: incorporating strategies beyond in silico fragmentation.

Ruttkies C, Schymanski EL, Wolf S, Hollender J, Neumann S.

J Cheminform. 2016 Jan 29;8:3. doi: 10.1186/s13321-016-0115-9. eCollection 2016.

11.

Effect-directed analysis supporting monitoring of aquatic environments--An in-depth overview.

Brack W, Ait-Aissa S, Burgess RM, Busch W, Creusot N, Di Paolo C, Escher BI, Mark Hewitt L, Hilscherova K, Hollender J, Hollert H, Jonker W, Kool J, Lamoree M, Muschket M, Neumann S, Rostkowski P, Ruttkies C, Schollee J, Schymanski EL, Schulze T, Seiler TB, Tindall AJ, De Aragão Umbuzeiro G, Vrana B, Krauss M.

Sci Total Environ. 2016 Feb 15;544:1073-118. doi: 10.1016/j.scitotenv.2015.11.102. Epub 2016 Jan 11. Review.

PMID:
26779957
12.

Meeting Report: Plant Science Student Conference (PSSC) 2015--Young researchers in green biotechnology.

Mönchgesang S, Ruttkies C, Treutler H, Heisters M.

Biotechnol J. 2015 Sep;10(11):1666-7. doi: 10.1002/biot.201500393. Epub 2015 Sep 10. No abstract available.

PMID:
26356578
13.

Annotation of metabolites from gas chromatography/atmospheric pressure chemical ionization tandem mass spectrometry data using an in silico generated compound database and MetFrag.

Ruttkies C, Strehmel N, Scheel D, Neumann S.

Rapid Commun Mass Spectrom. 2015 Aug 30;29(16):1521-9. doi: 10.1002/rcm.7244.

PMID:
26212167
14.

Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS.

Schymanski EL, Gerlich M, Ruttkies C, Neumann S.

Mass Spectrom (Tokyo). 2014;3(Spec Iss 2):S0036. doi: 10.5702/massspectrometry.S0036. Epub 2014 Aug 16.

15.

In vitro cross-linking of elastin peptides and molecular characterization of the resultant biomaterials.

Heinz A, Ruttkies CK, Jahreis G, Schräder CU, Wichapong K, Sippl W, Keeley FW, Neubert RH, Schmelzer CE.

Biochim Biophys Acta. 2013 Apr;1830(4):2994-3004. doi: 10.1016/j.bbagen.2013.01.014. Epub 2013 Jan 30.

PMID:
23375722
16.

Tackling CASMI 2012: Solutions from MetFrag and MetFusion.

Ruttkies C, Gerlich M, Neumann S.

Metabolites. 2013 Aug 5;3(3):623-36. doi: 10.3390/metabo3030623.

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