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Characterisation of the dynamic nature of lipids throughout the lifespan of genetically identical female and male Daphnia magna.

Constantinou JK, Southam AD, Kvist J, Jones MR, Viant MR, Mirbahai L.

Sci Rep. 2020 Mar 27;10(1):5576. doi: 10.1038/s41598-020-62476-z.


Erratum for "Comparison of modified Matyash method to conventional solvent systems for polar metabolite and lipid extractions" [Anal. Chim. Acta 1037 (2018) 301-315].

Sostare E, Di Guida R, Kirwan J, Chalal K, Palmer E, Dunn WB, Viant MR.

Anal Chim Acta. 2019 Dec 24;1091:169. doi: 10.1016/j.aca.2019.09.069. Epub 2019 Oct 16. No abstract available.


Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment.

Rivetti C, Allen TEH, Brown JB, Butler E, Carmichael PL, Colbourne JK, Dent M, Falciani F, Gunnarsson L, Gutsell S, Harrill JA, Hodges G, Jennings P, Judson R, Kienzler A, Margiotta-Casaluci L, Muller I, Owen SF, Rendal C, Russell PJ, Scott S, Sewell F, Shah I, Sorrel I, Viant MR, Westmoreland C, White A, Campos B.

Toxicol In Vitro. 2020 Feb;62:104692. doi: 10.1016/j.tiv.2019.104692. Epub 2019 Oct 25.


Use cases, best practice and reporting standards for metabolomics in regulatory toxicology.

Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT, Kamp H, Leonards PEG, Loizou GD, MacRae JI, van Ravenzwaay B, Rocca-Serra P, Salek RM, Walk T, Weber RJM.

Nat Commun. 2019 Jul 10;10(1):3041. doi: 10.1038/s41467-019-10900-y. Review.


Multiple metabolic pathways are predictive of ricin intoxication in a rat model.

D'Elia RV, Goodchild SA, Winder CL, Southam AD, Weber RJM, Stahl FM, Docx C, Patel V, Green AC, Viant MR, Lukaszewski RA, Dunn WB.

Metabolomics. 2019 Jul 3;15(7):102. doi: 10.1007/s11306-019-1547-9.


Metabolomic method to detect a metabolite corona on amino-functionalized polystyrene nanoparticles.

Grintzalis K, Lawson TN, Nasser F, Lynch I, Viant MR.

Nanotoxicology. 2019 Aug;13(6):783-794. doi: 10.1080/17435390.2019.1577510. Epub 2019 May 16.


Improved Algal Toxicity Test System for Robust Omics-Driven Mode-of-Action Discovery in Chlamydomonas reinhardtii.

Schade S, Butler E, Gutsell S, Hodges G, Colbourne JK, Viant MR.

Metabolites. 2019 May 10;9(5). pii: E94. doi: 10.3390/metabo9050094.


Pulmonary toxicity of inhaled nano-sized cerium oxide aerosols in Sprague-Dawley rats.

Guo C, Robertson S, Weber RJM, Buckley A, Warren J, Hodgson A, Rappoport JZ, Ignatyev K, Meldrum K, Römer I, Macchiarulo S, Chipman JK, Marczylo T, Leonard MO, Gant TW, Viant MR, Smith R.

Nanotoxicology. 2019 Aug;13(6):733-750. doi: 10.1080/17435390.2018.1554751. Epub 2019 Feb 1.


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.


Comparison of modified Matyash method to conventional solvent systems for polar metabolite and lipid extractions.

Sostare J, Di Guida R, Kirwan J, Chalal K, Palmer E, Dunn WB, Viant MR.

Anal Chim Acta. 2018 Dec 11;1037:301-315. doi: 10.1016/j.aca.2018.03.019. Epub 2018 Apr 5. Erratum in: Anal Chim Acta. 2019 Dec 24;1091:169.


Quantitative Lipoprotein Subclass and Low Molecular Weight Metabolite Analysis in Human Serum and Plasma by 1H NMR Spectroscopy in a Multilaboratory Trial.

Jiménez B, Holmes E, Heude C, Tolson RF, Harvey N, Lodge SL, Chetwynd AJ, Cannet C, Fang F, Pearce JTM, Lewis MR, Viant MR, Lindon JC, Spraul M, Schäfer H, Nicholson JK.

Anal Chem. 2018 Oct 16;90(20):11962-11971. doi: 10.1021/acs.analchem.8b02412. Epub 2018 Sep 27.


Terahertz VRT Spectroscopy of the Water Hexamer-h12 Cage: Dramatic Libration-Induced Enhancement of Hydrogen Bond Tunneling Dynamics.

Cole WTS, Yönder Ö, Sheikh AA, Fellers RS, Viant MR, Saykally RJ, Farrell JD, Wales DJ.

J Phys Chem A. 2018 Sep 20;122(37):7421-7426. doi: 10.1021/acs.jpca.8b05777. Epub 2018 Sep 10.


Metabolomics Discovers Early-Response Metabolic Biomarkers that Can Predict Chronic Reproductive Fitness in Individual Daphnia magna.

Taylor NS, Gavin A, Viant MR.

Metabolites. 2018 Jul 23;8(3). pii: E42. doi: 10.3390/metabo8030042.


Use of 5-azacytidine in a proof-of-concept study to evaluate the impact of pre-natal and post-natal exposures, as well as within generation persistent DNA methylation changes in Daphnia.

Athanasio CG, Sommer U, Viant MR, Chipman JK, Mirbahai L.

Ecotoxicology. 2018 Jul;27(5):556-568. doi: 10.1007/s10646-018-1927-3. Epub 2018 Apr 5.


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.

Version 2. F1000Res. 2017 Sep 6 [revised 2017 Jan 1];6. pii: ELIXIR-1649. doi: 10.12688/f1000research.12342.2. eCollection 2017.


nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S.

Anal Chem. 2018 Jan 2;90(1):649-656. doi: 10.1021/acs.analchem.7b02795. Epub 2017 Dec 14.


Automated assembly of species metabolomes through data submission into a public repository.

Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C.

Gigascience. 2017 Aug 1;6(8):1-4. doi: 10.1093/gigascience/gix062.


ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G.

F1000Res. 2017 Jun 21;6. pii: ELIXIR-952. doi: 10.12688/f1000research.11837.1. eCollection 2017.


mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM.

Bioinformatics. 2017 Aug 15;33(16):2598-2600. doi: 10.1093/bioinformatics/btx169.


Defining the Baseline and Oxidant Perturbed Lipidomic Profiles of Daphnia magna.

Taylor NS, White TA, Viant MR.

Metabolites. 2017 Mar 15;7(1). pii: E11. doi: 10.3390/metabo7010011.


Application of Passive Sampling to Characterise the Fish Exometabolome.

Viant MR, Elphinstone Davis J, Duffy C, Engel J, Stenton C, Sebire M, Katsiadaki I.

Metabolites. 2017 Feb 14;7(1). pii: E8. doi: 10.3390/metabo7010008.


msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry-Based Fragmentation in Metabolomics.

Lawson TN, Weber RJ, Jones MR, Chetwynd AJ, Rodrı Guez-Blanco G, Di Guida R, Viant MR, Dunn WB.

Anal Chem. 2017 Feb 21;89(4):2432-2439. doi: 10.1021/acs.analchem.6b04358. Epub 2017 Feb 8.


Miniaturising acute toxicity and feeding rate measurements in Daphnia magna.

Grintzalis K, Dai W, Panagiotidis K, Belavgeni A, Viant MR.

Ecotoxicol Environ Saf. 2017 May;139:352-357. doi: 10.1016/j.ecoenv.2017.02.002. Epub 2017 Feb 23.


How close are we to complete annotation of metabolomes?

Viant MR, Kurland IJ, Jones MR, Dunn WB.

Curr Opin Chem Biol. 2017 Feb;36:64-69. doi: 10.1016/j.cbpa.2017.01.001. Epub 2017 Jan 21. Review.


Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.

Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR.

Metabolomics. 2017;13(2):12. doi: 10.1007/s11306-016-1147-x. Epub 2016 Dec 27. No abstract available.


A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics.

Southam AD, Weber RJ, Engel J, Jones MR, Viant MR.

Nat Protoc. 2016 Feb;12(2):310–328. doi: 10.1038/nprot.2016.156. Epub 2017 Jan 12.


Regional adaptation defines sensitivity to future ocean acidification.

Calosi P, Melatunan S, Turner LM, Artioli Y, Davidson RL, Byrne JJ, Viant MR, Widdicombe S, Rundle SD.

Nat Commun. 2017 Jan 9;8:13994. doi: 10.1038/ncomms13994.


Hydrogen bond breaking dynamics in the water pentamer: Terahertz VRT spectroscopy of a 20 μm libration.

Cole WT, Fellers RS, Viant MR, Saykally RJ.

J Chem Phys. 2017 Jan 7;146(1):014306. doi: 10.1063/1.4973418.


Mass Spectrometry Based Metabolomics Comparison of Liver Grafts from Donors after Circulatory Death (DCD) and Donors after Brain Death (DBD) Used in Human Orthotopic Liver Transplantation.

Hrydziuszko O, Perera MT, Laing R, Kirwan J, Silva MA, Richards DA, Murphy N, Mirza DF, Viant MR.

PLoS One. 2016 Nov 11;11(11):e0165884. doi: 10.1371/journal.pone.0165884. eCollection 2016.


Protein Corona Modulates Uptake and Toxicity of Nanoceria via Clathrin-Mediated Endocytosis.

Mazzolini J, Weber RJ, Chen HS, Khan A, Guggenheim E, Shaw RK, Chipman JK, Viant MR, Rappoport JZ.

Biol Bull. 2016 Aug;231(1):40-60.


Biodiversity in marine invertebrate responses to acute warming revealed by a comparative multi-omics approach.

Clark MS, Sommer U, Sihra JK, Thorne MA, Morley SA, King M, Viant MR, Peck LS.

Glob Chang Biol. 2017 Jan;23(1):318-330. doi: 10.1111/gcb.13357. Epub 2016 Jun 17.


Optimisation of DNA extraction from the crustacean Daphnia.

Athanasio CG, Chipman JK, Viant MR, Mirbahai L.

PeerJ. 2016 May 10;4:e2004. doi: 10.7717/peerj.2004. eCollection 2016.


Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling.

Di Guida R, Engel J, Allwood JW, Weber RJ, Jones MR, Sommer U, Viant MR, Dunn WB.

Metabolomics. 2016;12:93. Epub 2016 Apr 15.


Metabolomics reveals an involvement of pantothenate for male production responding to the short-day stimulus in the water flea, Daphnia pulex.

Toyota K, Gavin A, Miyagawa S, Viant MR, Iguchi T.

Sci Rep. 2016 Apr 26;6:25125. doi: 10.1038/srep25125.


Wolbachia Modulates Lipid Metabolism in Aedes albopictus Mosquito Cells.

Molloy JC, Sommer U, Viant MR, Sinkins SP.

Appl Environ Microbiol. 2016 May 2;82(10):3109-3120. doi: 10.1128/AEM.00275-16. Print 2016 May 15.


Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.

Davidson RL, Weber RJ, Liu H, Sharma-Oates A, Viant MR.

Gigascience. 2016 Feb 23;5:10. doi: 10.1186/s13742-016-0115-8. eCollection 2016.


The Time Is Right to Focus on Model Organism Metabolomes.

Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR.

Metabolites. 2016 Feb 15;6(1). pii: E8. doi: 10.3390/metabo6010008.


Predicting chronic copper and nickel reproductive toxicity to Daphnia pulex-pulicaria from whole-animal metabolic profiles.

Taylor NS, Kirwan JA, Johnson C, Yan ND, Viant MR, Gunn JM, McGeer JC.

Environ Pollut. 2016 May;212:325-329. doi: 10.1016/j.envpol.2016.01.074. Epub 2016 Feb 6.


Statistical Correlations between NMR Spectroscopy and Direct Infusion FT-ICR Mass Spectrometry Aid Annotation of Unknowns in Metabolomics.

Hao J, Liebeke M, Sommer U, Viant MR, Bundy JG, Ebbels TM.

Anal Chem. 2016 Mar 1;88(5):2583-9. doi: 10.1021/acs.analchem.5b02889. Epub 2016 Feb 10.


Omega-3 and alpha-tocopherol provide more protection against contaminants in novel feeds for Atlantic salmon (Salmo salar L.) than omega-6 and gamma tocopherol.

Søfteland L, Berntssen MHG, Kirwan JA, Størseth TR, Viant MR, Torstensen BE, Waagbø R, Olsvik PA.

Toxicol Rep. 2016 Jan 14;3:211-224. doi: 10.1016/j.toxrep.2016.01.008. eCollection 2016.


Data standards can boost metabolomics research, and if there is a will, there is a way.

Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S.

Metabolomics. 2016;12:14. doi: 10.1007/s11306-015-0879-3. Epub 2015 Nov 17. Review.


Gene expression and metabolic responses of HepG2/C3A cells exposed to flame retardants and dust extracts at concentrations relevant to indoor environmental exposures.

Zhang J, Abdallah MA, Williams TD, Harrad S, Chipman JK, Viant MR.

Chemosphere. 2016 Feb;144:1996-2003. doi: 10.1016/j.chemosphere.2015.10.014. Epub 2015 Nov 11.


Far-infrared VRT spectroscopy of the water dimer: Characterization of the 20 μm out-of-plane librational vibration.

Cole WT, Fellers RS, Viant MR, Leforestier C, Saykally RJ.

J Chem Phys. 2015 Oct 21;143(15):154306. doi: 10.1063/1.4933116.


COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C.

Metabolomics. 2015;11(6):1587-1597. Epub 2015 May 26.


The metabolic response of marine copepods to environmental warming and ocean acidification in the absence of food.

Mayor DJ, Sommer U, Cook KB, Viant MR.

Sci Rep. 2015 Sep 14;5:13690. doi: 10.1038/srep13690.


Transcriptomic and metabolomic approaches to investigate the molecular responses of human cell lines exposed to the flame retardant hexabromocyclododecane (HBCD).

Zhang J, Williams TD, Abdallah MA, Harrad S, Chipman JK, Viant MR.

Toxicol In Vitro. 2015 Dec;29(8):2116-23. doi: 10.1016/j.tiv.2015.08.017. Epub 2015 Aug 28.


Metabolomics confirms that dissolved organic carbon mitigates copper toxicity.

Taylor NS, Kirwan JA, Yan ND, Viant MR, Gunn JM, McGeer JC.

Environ Toxicol Chem. 2016 Mar;35(3):635-44. doi: 10.1002/etc.3206. Epub 2016 Feb 3.


Systems Biology Approach Reveals a Calcium-Dependent Mechanism for Basal Toxicity in Daphnia magna.

Antczak P, White TA, Giri A, Michelangeli F, Viant MR, Cronin MT, Vulpe C, Falciani F.

Environ Sci Technol. 2015 Sep 15;49(18):11132-40. doi: 10.1021/acs.est.5b02707. Epub 2015 Aug 24.


Defensive and adverse energy-related molecular responses precede tris (1, 3-dichloro-2-propyl) phosphate cytotoxicity.

Zhang J, Williams TD, Chipman JK, Viant MR.

J Appl Toxicol. 2016 May;36(5):649-58. doi: 10.1002/jat.3194. Epub 2015 Jul 15.


Training needs in metabolomics.

Weber RJ, Winder CL, Larcombe LD, Dunn WB, Viant MR.

Metabolomics. 2015;11(4):784-786. Epub 2015 May 29. No abstract available.

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