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A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry: Application to the characterisation of metabolites in rat urine.

Nye LC, Williams JP, Munjoma NC, Letertre MPM, Coen M, Bouwmeester R, Martens L, Swann JR, Nicholson JK, Plumb RS, McCullagh M, Gethings LA, Lai S, Langridge JI, Vissers JPC, Wilson ID.

J Chromatogr A. 2019 Jun 27. pii: S0021-9673(19)30665-X. doi: 10.1016/j.chroma.2019.06.056. [Epub ahead of print]


Application of novel solid phase extraction-NMR protocols for metabolic profiling of human urine.

McGill D, Chekmeneva E, Lindon JC, Takats Z, Nicholson JK.

Faraday Discuss. 2019 May 22. doi: 10.1039/c8fd00220g. [Epub ahead of print]


Serum metabolic signatures of coronary and carotid atherosclerosis and subsequent cardiovascular disease.

Tzoulaki I, Castagné R, Boulangé CL, Karaman I, Chekmeneva E, Evangelou E, Ebbels TMD, Kaluarachchi MR, Chadeau-Hyam M, Mosen D, Dehghan A, Moayyeri A, Ferreira DLS, Guo X, Rotter JI, Taylor KD, Kavousi M, de Vries PS, Lehne B, Loh M, Hofman A, Nicholson JK, Chambers J, Gieger C, Holmes E, Tracy R, Kooner J, Greenland P, Franco OH, Herrington D, Lindon JC, Elliott P.

Eur Heart J. 2019 May 18. pii: ehz235. doi: 10.1093/eurheartj/ehz235. [Epub ahead of print]


Differences in Fecal Gut Microbiota, Short-Chain Fatty Acids and Bile Acids Link Colorectal Cancer Risk to Dietary Changes Associated with Urbanization Among Zimbabweans.

Katsidzira L, Ocvirk S, Wilson A, Li J, Mahachi CB, Soni D, DeLany J, Nicholson JK, Zoetendal EG, O'Keefe SJD.

Nutr Cancer. 2019 Apr 22:1-12. doi: 10.1080/01635581.2019.1602659. [Epub ahead of print]


Obesity and Cage Environment Modulate Metabolism in the Zucker Rat: A Multiple Biological Matrix Approach to Characterizing Metabolic Phenomena.

Lees HJ, Swann JR, Poucher S, Holmes E, Wilson ID, Nicholson JK.

J Proteome Res. 2019 May 3;18(5):2160-2174. doi: 10.1021/acs.jproteome.9b00040. Epub 2019 Apr 18.


Ultrahigh-Performance Liquid Chromatography Tandem Mass Spectrometry with Electrospray Ionization Quantification of Tryptophan Metabolites and Markers of Gut Health in Serum and Plasma-Application to Clinical and Epidemiology Cohorts.

Whiley L, Nye LC, Grant I, Andreas N, Chappell KE, Sarafian MH, Misra R, Plumb RS, Lewis MR, Nicholson JK, Holmes E, Swann JR, Wilson ID.

Anal Chem. 2019 Apr 16;91(8):5207-5216. doi: 10.1021/acs.analchem.8b05884. Epub 2019 Mar 25.


Systems Genetics of Hepatic Metabolome Reveals Octopamine as a Target for Non-Alcoholic Fatty Liver Disease Treatment.

Brial F, Le Lay A, Hedjazi L, Tsang T, Fearnside JF, Otto GW, Alzaid F, Wilder SP, Venteclef N, Cazier JB, Nicholson JK, Day C, Burt AD, Gut IG, Lathrop M, Dumas ME, Gauguier D.

Sci Rep. 2019 Mar 6;9(1):3656. doi: 10.1038/s41598-019-40153-0.


Untargeted Mass Spectrometry Lipidomics identifies correlation between serum sphingomyelins and plasma cholesterol.

Zalloua P, Kadar H, Hariri E, Abi Farraj L, Brial F, Hedjazi L, Le Lay A, Colleu A, Dubus J, Touboul D, Matsuda F, Lathrop M, Nicholson JK, Dumas ME, Gauguier D.

Lipids Health Dis. 2019 Feb 2;18(1):38. doi: 10.1186/s12944-018-0948-5.


A validated UPLC-MS/MS assay for the quantification of amino acids and biogenic amines in rat urine.

Gray N, Plumb RS, Wilson ID, Nicholson JK.

J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Feb 1;1106-1107:50-57. doi: 10.1016/j.jchromb.2018.12.028. Epub 2018 Dec 29.


The metabolic fate and effects of 2-Bromophenol in male Sprague-Dawley rats.

Adesina-Georgiadis KN, Gray N, Plumb RS, Thompson DF, Holmes E, Nicholson JK, Wilson ID.

Xenobiotica. 2018 Dec 17:1-8. doi: 10.1080/00498254.2018.1559376. [Epub ahead of print]


Reduced plasma levels of small HDL particles transporting fibrinolytic proteins in pulmonary arterial hypertension.

Harbaum L, Ghataorhe P, Wharton J, Jiménez B, Howard LSG, Gibbs JSR, Nicholson JK, Rhodes CJ, Wilkins MR.

Thorax. 2019 Apr;74(4):380-389. doi: 10.1136/thoraxjnl-2018-212144. Epub 2018 Nov 26.


pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra.

Rodriguez-Martinez A, Ayala R, Posma JM, Harvey N, Jiménez B, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME.

Bioinformatics. 2019 Jun 1;35(11):1916-1922. doi: 10.1093/bioinformatics/bty837.


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.


Ultra-Performance Liquid Chromatography-High-Resolution Mass Spectrometry and Direct Infusion-High-Resolution Mass Spectrometry for Combined Exploratory and Targeted Metabolic Profiling of Human Urine.

Chekmeneva E, Dos Santos Correia G, Gómez-Romero M, Stamler J, Chan Q, Elliott P, Nicholson JK, Holmes E.

J Proteome Res. 2018 Oct 5;17(10):3492-3502. doi: 10.1021/acs.jproteome.8b00413. Epub 2018 Sep 19.


XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules.

Domingo-Almenara X, Montenegro-Burke JR, Ivanisevic J, Thomas A, Sidibé J, Teav T, Guijas C, Aisporna AE, Rinehart D, Hoang L, Nordström A, Gómez-Romero M, Whiley L, Lewis MR, Nicholson JK, Benton HP, Siuzdak G.

Nat Methods. 2018 Sep;15(9):681-684. doi: 10.1038/s41592-018-0110-3. Epub 2018 Aug 27.


Publisher Correction: Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.

Hoyles L, Fernández-Real JM, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, Chilloux J, Myridakis A, Martinez-Gili L, Moreno-Navarrete JM, Benhamed F, Azalbert V, Blasco-Baque V, Puig J, Xifra G, Ricart W, Tomlinson C, Woodbridge M, Cardellini M, Davato F, Cardolini I, Porzio O, Gentileschi P, Lopez F, Foufelle F, Butcher SA, Holmes E, Nicholson JK, Postic C, Burcelin R, Dumas ME.

Nat Med. 2018 Oct;24(10):1628. doi: 10.1038/s41591-018-0169-5.


Paracetamol metabolism, hepatotoxicity, biomarkers and therapeutic interventions: a perspective.

Athersuch TJ, Antoine DJ, Boobis AR, Coen M, Daly AK, Possamai L, Nicholson JK, Wilson ID.

Toxicol Res (Camb). 2018 Mar 6;7(3):347-357. doi: 10.1039/c7tx00340d. eCollection 2018 May 8. Review.


SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data.

Inglese P, Correia G, Takats Z, Nicholson JK, Glen RC.

Bioinformatics. 2019 Jan 1;35(1):178-180. doi: 10.1093/bioinformatics/bty622.


The effects of kisspeptin on β-cell function, serum metabolites and appetite in humans.

Izzi-Engbeaya C, Comninos AN, Clarke SA, Jomard A, Yang L, Jones S, Abbara A, Narayanaswamy S, Eng PC, Papadopoulou D, Prague JK, Bech P, Godsland IF, Bassett P, Sands C, Camuzeaux S, Gomez-Romero M, Pearce JTM, Lewis MR, Holmes E, Nicholson JK, Tan T, Ratnasabapathy R, Hu M, Carrat G, Piemonti L, Bugliani M, Marchetti P, Johnson PR, Hughes SJ, James Shapiro AM, Rutter GA, Dhillo WS.

Diabetes Obes Metab. 2018 Dec;20(12):2800-2810. doi: 10.1111/dom.13460. Epub 2018 Aug 16.


Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.

Hoyles L, Fernández-Real JM, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, Chilloux J, Myridakis A, Martinez-Gili L, Moreno-Navarrete JM, Benhamed F, Azalbert V, Blasco-Baque V, Puig J, Xifra G, Ricart W, Tomlinson C, Woodbridge M, Cardellini M, Davato F, Cardolini I, Porzio O, Gentileschi P, Lopez F, Foufelle F, Butcher SA, Holmes E, Nicholson JK, Postic C, Burcelin R, Dumas ME.

Nat Med. 2018 Jul;24(7):1070-1080. doi: 10.1038/s41591-018-0061-3. Epub 2018 Jun 25. Erratum in: Nat Med. 2018 Aug 9;:.


Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota.

Hoyles L, Jiménez-Pranteda ML, Chilloux J, Brial F, Myridakis A, Aranias T, Magnan C, Gibson GR, Sanderson JD, Nicholson JK, Gauguier D, McCartney AL, Dumas ME.

Microbiome. 2018 Apr 20;6(1):73. doi: 10.1186/s40168-018-0461-0.


Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier.

Hoyles L, Snelling T, Umlai UK, Nicholson JK, Carding SR, Glen RC, McArthur S.

Microbiome. 2018 Mar 21;6(1):55. doi: 10.1186/s40168-018-0439-y.


BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology.

Veselkov K, Sleeman J, Claude E, Vissers JPC, Galea D, Mroz A, Laponogov I, Towers M, Tonge R, Mirnezami R, Takats Z, Nicholson JK, Langridge JI.

Sci Rep. 2018 Mar 6;8(1):4053. doi: 10.1038/s41598-018-22499-z.


Optimized Phenotypic Biomarker Discovery and Confounder Elimination via Covariate-Adjusted Projection to Latent Structures from Metabolic Spectroscopy Data.

Posma JM, Garcia-Perez I, Ebbels TMD, Lindon JC, Stamler J, Elliott P, Holmes E, Nicholson JK.

J Proteome Res. 2018 Apr 6;17(4):1586-1595. doi: 10.1021/acs.jproteome.7b00879. Epub 2018 Feb 27.


Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin.

Brown RG, Marchesi JR, Lee YS, Smith A, Lehne B, Kindinger LM, Terzidou V, Holmes E, Nicholson JK, Bennett PR, MacIntyre DA.

BMC Med. 2018 Jan 24;16(1):9. doi: 10.1186/s12916-017-0999-x.


The pathophysiology of human obstructive cholestasis is mimicked in cholestatic Gold Syrian hamsters.

van Golen RF, Olthof PB, de Haan LR, Coelen RJ, Pechlivanis A, de Keijzer MJ, Weijer R, de Waart DR, van Kuilenburg ABP, Roelofsen J, Gilijamse PW, Maas MA, Lewis MR, Nicholson JK, Verheij J, Heger M.

Biochim Biophys Acta Mol Basis Dis. 2018 Mar;1864(3):942-951. doi: 10.1016/j.bbadis.2017.11.022. Epub 2017 Nov 28.


MWASTools: an R/bioconductor package for metabolome-wide association studies.

Rodriguez-Martinez A, Posma JM, Ayala R, Neves AL, Anwar M, Petretto E, Emanueli C, Gauguier D, Nicholson JK, Dumas ME.

Bioinformatics. 2018 Mar 1;34(5):890-892. doi: 10.1093/bioinformatics/btx477.


Urinary Metabolic Phenotyping of Women with Lower Urinary Tract Symptoms.

Bray R, Cacciatore S, Jiménez B, Cartwright R, Digesu A, Fernando R, Holmes E, Nicholson JK, Bennett PR, MacIntyre DA, Khullar V.

J Proteome Res. 2017 Nov 3;16(11):4208-4216. doi: 10.1021/acs.jproteome.7b00568. Epub 2017 Oct 4.


J-Resolved 1H NMR 1D-Projections for Large-Scale Metabolic Phenotyping Studies: Application to Blood Plasma Analysis.

Rodriguez-Martinez A, Posma JM, Ayala R, Harvey N, Jimenez B, Neves AL, Lindon JC, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME.

Anal Chem. 2017 Nov 7;89(21):11405-11412. doi: 10.1021/acs.analchem.7b02374. Epub 2017 Oct 13.


Ion mobility spectrometry combined with ultra performance liquid chromatography/mass spectrometry for metabolic phenotyping of urine: Effects of column length, gradient duration and ion mobility spectrometry on metabolite detection.

Rainville PD, Wilson ID, Nicholson JK, Isaac G, Mullin L, Langridge JI, Plumb RS.

Anal Chim Acta. 2017 Aug 22;982:1-8. doi: 10.1016/j.aca.2017.06.020. Epub 2017 Jun 19.


Early intervention with Bifidobacterium lactis NCC2818 modulates the host-microbe interface independent of the sustained changes induced by the neonatal environment.

Lewis MC, Merrifield CA, Berger B, Cloarec O, Duncker S, Mercenier A, Nicholson JK, Holmes E, Bailey M.

Sci Rep. 2017 Jul 13;7(1):5310. doi: 10.1038/s41598-017-05689-z.


Microbial-Host Co-metabolites Are Prodromal Markers Predicting Phenotypic Heterogeneity in Behavior, Obesity, and Impaired Glucose Tolerance.

Dumas ME, Rothwell AR, Hoyles L, Aranias T, Chilloux J, Calderari S, Noll EM, Péan N, Boulangé CL, Blancher C, Barton RH, Gu Q, Fearnside JF, Deshayes C, Hue C, Scott J, Nicholson JK, Gauguier D.

Cell Rep. 2017 Jul 5;20(1):136-148. doi: 10.1016/j.celrep.2017.06.039.


Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism.

Swann JR, Garcia-Perez I, Braniste V, Wilson ID, Sidaway JE, Nicholson JK, Pettersson S, Holmes E.

J Pharm Biomed Anal. 2017 Sep 5;143:141-146. doi: 10.1016/j.jpba.2017.05.040. Epub 2017 May 31.


Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer.

Inglese P, McKenzie JS, Mroz A, Kinross J, Veselkov K, Holmes E, Takats Z, Nicholson JK, Glen RC.

Chem Sci. 2017 May 1;8(5):3500-3511. doi: 10.1039/c6sc03738k. Epub 2017 Feb 21.


Longitudinal analysis of serum oxylipin profile as a novel descriptor of the inflammatory response to surgery.

Wolfer AM, Scott AJ, Rueb C, Gaudin M, Darzi A, Nicholson JK, Holmes E, Kinross JM.

J Transl Med. 2017 Apr 26;15(1):83. doi: 10.1186/s12967-017-1171-2.


Gut microbiota modulation of chemotherapy efficacy and toxicity.

Alexander JL, Wilson ID, Teare J, Marchesi JR, Nicholson JK, Kinross JM.

Nat Rev Gastroenterol Hepatol. 2017 Jun;14(6):356-365. doi: 10.1038/nrgastro.2017.20. Epub 2017 Mar 8. Review.


Optimization and Application of Direct Infusion Nanoelectrospray HRMS Method for Large-Scale Urinary Metabolic Phenotyping in Molecular Epidemiology.

Chekmeneva E, Dos Santos Correia G, Chan Q, Wijeyesekera A, Tin A, Young JH, Elliott P, Nicholson JK, Holmes E.

J Proteome Res. 2017 Apr 7;16(4):1646-1658. doi: 10.1021/acs.jproteome.6b01003. Epub 2017 Mar 14.


Integrated Analytical and Statistical Two-Dimensional Spectroscopy Strategy for Metabolite Identification: Application to Dietary Biomarkers.

Posma JM, Garcia-Perez I, Heaton JC, Burdisso P, Mathers JC, Draper J, Lewis M, Lindon JC, Frost G, Holmes E, Nicholson JK.

Anal Chem. 2017 Mar 21;89(6):3300-3309. doi: 10.1021/acs.analchem.6b03324. Epub 2017 Mar 10.


High-Speed Quantitative UPLC-MS Analysis of Multiple Amines in Human Plasma and Serum via Precolumn Derivatization with 6-Aminoquinolyl-N-hydroxysuccinimidyl Carbamate: Application to Acetaminophen-Induced Liver Failure.

Gray N, Zia R, King A, Patel VC, Wendon J, McPhail MJ, Coen M, Plumb RS, Wilson ID, Nicholson JK.

Anal Chem. 2017 Feb 21;89(4):2478-2487. doi: 10.1021/acs.analchem.6b04623. Epub 2017 Feb 7.


The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk.

Kindinger LM, Bennett PR, Lee YS, Marchesi JR, Smith A, Cacciatore S, Holmes E, Nicholson JK, Teoh TG, MacIntyre DA.

Microbiome. 2017 Jan 19;5(1):6. doi: 10.1186/s40168-016-0223-9.


Objective assessment of dietary patterns by use of metabolic phenotyping: a randomised, controlled, crossover trial.

Garcia-Perez I, Posma JM, Gibson R, Chambers ES, Hansen TH, Vestergaard H, Hansen T, Beckmann M, Pedersen O, Elliott P, Stamler J, Nicholson JK, Draper J, Mathers JC, Holmes E, Frost G.

Lancet Diabetes Endocrinol. 2017 Mar;5(3):184-195. doi: 10.1016/S2213-8587(16)30419-3. Epub 2017 Jan 13.


MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways.

Rodriguez-Martinez A, Ayala R, Posma JM, Neves AL, Gauguier D, Nicholson JK, Dumas ME.

Bioinformatics. 2017 Mar 1;33(5):773-775. doi: 10.1093/bioinformatics/btw697.


Metabolic phenotyping for discovery of urinary biomarkers of diet, xenobiotics and blood pressure in the INTERMAP Study: an overview.

Chan Q, Loo RL, Ebbels TM, Van Horn L, Daviglus ML, Stamler J, Nicholson JK, Holmes E, Elliott P.

Hypertens Res. 2017 Apr;40(4):336-345. doi: 10.1038/hr.2016.164. Epub 2016 Dec 22. Review.


Metabolic Phenotype of Obesity in a Saudi Population.

Ahmad MS, Alsaleh M, Kimhofer T, Ahmad S, Jamal W, Wali SO, Nicholson JK, Damanhouri ZA, Holmes E.

J Proteome Res. 2017 Feb 3;16(2):635-644. doi: 10.1021/acs.jproteome.6b00710. Epub 2017 Jan 20.


Correction to 2-Furoylglycine as a Candidate Biomarker of Coffee Consumption.

Heinzmann SS, Holmes E, Kochhar S, Nicholson JK, Schmitt-Kopplin P.

J Agric Food Chem. 2016 Nov 23;64(46):8958. Epub 2016 Nov 11. No abstract available.


Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series.

Dumas ME, Domange C, Calderari S, Martínez AR, Ayala R, Wilder SP, Suárez-Zamorano N, Collins SC, Wallis RH, Gu Q, Wang Y, Hue C, Otto GW, Argoud K, Navratil V, Mitchell SC, Lindon JC, Holmes E, Cazier JB, Nicholson JK, Gauguier D.

Genome Med. 2016 Sep 30;8(1):101.


Gut microbiome interactions with drug metabolism, efficacy, and toxicity.

Wilson ID, Nicholson JK.

Transl Res. 2017 Jan;179:204-222. doi: 10.1016/j.trsl.2016.08.002. Epub 2016 Aug 13. Review.


Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage.

Kindinger LM, MacIntyre DA, Lee YS, Marchesi JR, Smith A, McDonald JA, Terzidou V, Cook JR, Lees C, Israfil-Bayli F, Faiza Y, Toozs-Hobson P, Slack M, Cacciatore S, Holmes E, Nicholson JK, Teoh TG, Bennett PR.

Sci Transl Med. 2016 Aug 3;8(350):350ra102. doi: 10.1126/scitranslmed.aag1026.


Development and Application of Ultra-Performance Liquid Chromatography-TOF MS for Precision Large Scale Urinary Metabolic Phenotyping.

Lewis MR, Pearce JT, Spagou K, Green M, Dona AC, Yuen AH, David M, Berry DJ, Chappell K, Horneffer-van der Sluis V, Shaw R, Lovestone S, Elliott P, Shockcor J, Lindon JC, Cloarec O, Takats Z, Holmes E, Nicholson JK.

Anal Chem. 2016 Sep 20;88(18):9004-13. doi: 10.1021/acs.analchem.6b01481. Epub 2016 Aug 26.

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