Professor Elaine Holmes

Publications


Journals

  • Fonville JM; Carter C; Cloarec O; Nicholson JK; Lindon JC; Bunch J; Holmes E. (10 Jan 2012). Robust Data Processing and Normalization Strategy for MALDI Mass Spectrometric Imaging. Anal Chem. DOI.
  • Heinzmann SS; Merrifield CA; Rezzi S; Kochhar S; Lindon JC; Holmes E; Nicholson JK. (3 Feb 2012). Stability and robustness of human metabolic phenotypes in response to sequential food challenges. J Proteome Res. 11:643-655. DOI.
  • Mirnezami R; Kinross JM; Vorkas PA; Goldin R; Holmes E; Nicholson J; Darzi A. (8 Dec 2011). Implementation of Molecular Phenotyping Approaches in the Personalized Surgical Patient Journey. Ann Surg. DOI.
  • Mestdagh R; Dumas ME; Rezzi S; Kochhar S; Holmes E; Claus SP; Nicholson JK. (3 Feb 2012). Gut microbiota modulate the metabolism of brown adipose tissue in mice. J Proteome Res. 11:620-630. DOI.
  • Li JV; Saric J; Wang YL; Keiser J; Utzinger J; Holmes E. (19 Sep 2011). Chemometric analysis of biofluids from mice experimentally infected with Schistosoma mansoni. PARASITE VECTOR. 4. DOI.
  • Fonville JM; Bylesjö M; Coen M; Nicholson JK; Holmes E; Lindon JC; Rantalainen M. (31 Oct 2011). Non-linear modeling of 1H NMR metabonomic data using kernel-based orthogonal projections to latent structures optimized by simulated annealing. Anal Chim Acta. 705:72-80. DOI.
  • Holmes E; Li JV; Athanasiou T; Ashrafian H; Nicholson JK. (Jul 2011). Understanding the role of gut microbiome-host metabolic signal disruption in health and disease. Trends Microbiol. 19:349-359. DOI.
  • Li JV; Reshat R; Wu Q; Ashrafian H; Bueter M; le Roux CW; Darzi A; Athanasiou T; et alMarchesi JR; Nicholson JK; Holmes E; Gooderham NJ. (2011). Experimental bariatric surgery in rats generates a cytotoxic chemical environment in the gut contents. Front Microbiol. 2:183. DOI.
  • Edmands WM; Beckonert OP; Stella C; Campbell A; Lake BG; Lindon JC; Holmes E; Gooderham NJ. (7 Oct 2011). Identification of human urinary biomarkers of cruciferous vegetable consumption by metabonomic profiling. J Proteome Res. 10:4513-4521. DOI.
  • Thomas EL; Parkinson JR; Hyde MJ; Yap IK; Holmes E; Doré CJ; Bell JD; Modi N. (Nov 2011). Aberrant adiposity and ectopic lipid deposition characterize the adult phenotype of the preterm infant. Pediatr Res. 70:507-512. DOI.
  • Merrifield CA; Lewis M; Claus SP; Beckonert OP; Dumas ME; Duncker S; Kochhar S; Rezzi S; et alLindon JC; Bailey M; Holmes E; Nicholson JK. (Sep 2011). A metabolic system-wide characterisation of the pig: a model for human physiology. Mol Biosyst. 7:2577-2588. DOI.
  • Ashrafian H; Ahmed K; Rowland SP; Patel VM; Gooderham NJ; Holmes E; Darzi A; Athanasiou T. (1 May 2011). Metabolic surgery and cancer: protective effects of bariatric procedures. Cancer. 117:1788-1799. DOI.
  • Legido-Quigley C; McDermott L; Vilca-Melendez H; Murphy GM; Heaton N; Lindon JC; Nicholson JK; Holmes E. (Aug 2011). Bile UPLC-MS fingerprinting and bile acid fluxes during human liver transplantation. Electrophoresis. 32:2063-2070. DOI.
  • Veselkov KA; Vingara LK; Masson P; Robinette SL; Want E; Li JV; Barton RH; Boursier-Neyret C; et alWalther B; Ebbels TM; Pelczer I; Holmes E; Lindon JC; Nicholson JK. (1 Aug 2011). Optimized preprocessing of ultra-performance liquid chromatography/mass spectrometry urinary metabolic profiles for improved information recovery. Anal Chem. 83:5864-5872. DOI.
  • Swann JR; Tuohy KM; Lindfors P; Brown DT; Gibson GR; Wilson ID; Sidaway J; Nicholson JK; et alHolmes E. (5 Aug 2011). Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats. J Proteome Res. 10:3590-3603. DOI.
  • Li JV; Ashrafian H; Bueter M; Kinross J; Sands C; le Roux CW; Bloom SR; Darzi A; et alAthanasiou T; Marchesi JR; Nicholson JK; Holmes E. (Sep 2011). Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut. 60:1214-1223. DOI.
  • Li J; Holmes E. (May 2011). Bioanalysis young investigator: jia li. Bioanalysis. 3:1077-1079. DOI.
  • Claus SP; Ellero SL; Berger B; Krause L; Bruttin A; Molina J; Paris A; Want EJ; et alde Waziers I; Cloarec O; Richards SE; Wang Y; Dumas ME; Ross A; Rezzi S; Kochhar S; Van Bladeren P; Lindon JC; Holmes E; Nicholson JK. (2011). Colonization-induced host-gut microbial metabolic interaction. MBio. 2:e00271-e00210. DOI.
  • Sands CJ; Coen M; Ebbels TM; Holmes E; Lindon JC; Nicholson JK. (15 Mar 2011). Data-driven approach for metabolite relationship recovery in biological 1H NMR data sets using iterative statistical total correlation spectroscopy. Anal Chem. 83:2075-2082. DOI.
  • Li JV; Saric J; Wang Y; Utzinger J; Holmes E; Balmer O. (Jan 2011). Metabonomic investigation of single and multiple strain Trypanosoma brucei brucei infections. Am J Trop Med Hyg. 84:91-98. DOI.
  • Chadeau-Hyam M; Ebbels TM; Brown IJ; Chan Q; Stamler J; Huang CC; Daviglus ML; Ueshima H; et alZhao L; Holmes E; Nicholson JK; Elliott P; De Iorio M. (3 Sep 2010). Metabolic profiling and the metabolome-wide association study: significance level for biomarker identification. J Proteome Res. 9:4620-4627. DOI.
  • Spagou K; Wilson ID; Masson P; Theodoridis G; Raikos N; Coen M; Holmes E; Lindon JC; et alPlumb RS; Nicholson JK; Want EJ. (1 Jan 2011). HILIC-UPLC-MS for exploratory urinary metabolic profiling in toxicological studies. Anal Chem. 83:382-390. DOI.
  • Kinross JM; Alkhamesi N; Barton RH; Silk DB; Yap IK; Darzi AW; Holmes E; Nicholson JK. (7 Jan 2011). Global metabolic phenotyping in an experimental laparotomy model of surgical trauma. J Proteome Res. 10:277-287. DOI.
  • Chadeau-Hyam M; Athersuch TJ; Keun HC; De Iorio M; Ebbels TM; Jenab M; Sacerdote C; Bruce SJ; et alHolmes E; Vineis P. (Feb 2011). Meeting-in-the-middle using metabolic profiling - a strategy for the identification of intermediate biomarkers in cohort studies. Biomarkers. 16:83-88. DOI.
  • Legido-Quigley C; Cloarec O; Parker DA; Murphy GM; Holmes E; Lindon JC; Nicholson JK; Mitry RR; et alVilca-Melendez H; Rela M; Dhawan A; Heaton N. (2009). First example of hepatocyte transplantation to alleviate ornithine transcarbamylase deficiency, monitored by NMR-based metabonomics. Bioanalysis. 1:1527-1535.
  • Yap IK; Brown IJ; Chan Q; Wijeyesekera A; Garcia-Perez I; Bictash M; Loo RL; Chadeau-Hyam M; et alEbbels T; De Iorio M; Maibaum E; Zhao L; Kesteloot H; Daviglus ML; Stamler J; Nicholson JK; Elliott P; Holmes E. (3 Dec 2010). Metabolome-wide association study identifies multiple biomarkers that discriminate north and south Chinese populations at differing risks of cardiovascular disease: INTERMAP study. J Proteome Res. 9:6647-6654. DOI.
  • Ashrafian H; Athanasiou T; Li JV; Bueter M; Ahmed K; Nagpal K; Holmes E; Darzi A; et alBloom SR. (May 2011). Diabetes resolution and hyperinsulinaemia after metabolic Roux-en-Y gastric bypass. Obes Rev. 12:e257-e272. DOI.
  • Swann JR; Want EJ; Geier FM; Spagou K; Wilson ID; Sidaway JE; Nicholson JK; Holmes E. (15 Mar 2011). Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A. 108 Suppl 1:4523-4530. DOI.
  • Heinzmann SS; Brown IJ; Chan Q; Bictash M; Dumas ME; Kochhar S; Stamler J; Holmes E; et alElliott P; Nicholson JK. (Aug 2010). Metabolic profiling strategy for discovery of nutritional biomarkers: proline betaine as a marker of citrus consumption. Am J Clin Nutr. 92:436-443. DOI.
  • Saric J; Li JV; Utzinger J; Wang Y; Keiser J; Dirnhofer S; Beckonert O; Sharabiani MT; et alFonville JM; Nicholson JK; Holmes E. (Jul 2010). Systems parasitology: effects of Fasciola hepatica on the neurochemical profile in the rat brain. Mol Syst Biol. 6:396. DOI.
  • Beckonert O; Coen M; Keun HC; Wang Y; Ebbels TM; Holmes E; Lindon JC; Nicholson JK. (2010). High-resolution magic-angle-spinning NMR spectroscopy for metabolic profiling of intact tissues. Nat Protoc. 5:1019-1032. DOI.
  • Veselkov KA; Pahomov VI; Lindon JC; Volynkin VS; Crockford D; Osipenko GS; Davies DB; Barton RH; et alBang JW; Holmes E; Nicholson JK. (2 Jul 2010). A metabolic entropy approach for measurements of systemic metabolic disruptions in patho-physiological States. J Proteome Res. 9:3537-3544. DOI.
  • Want EJ; Coen M; Masson P; Keun HC; Pearce JT; Reily MD; Robertson DG; Rohde CM; et alHolmes E; Lindon JC; Plumb RS; Nicholson JK. (15 Jun 2010). Ultra performance liquid chromatography-mass spectrometry profiling of bile acid metabolites in biofluids: application to experimental toxicology studies. Anal Chem. 82:5282-5289. DOI.
  • Want EJ; Wilson ID; Gika H; Theodoridis G; Plumb RS; Shockcor J; Holmes E; Nicholson JK. (2010). Global metabolic profiling procedures for urine using UPLC-MS. Nat Protoc. 5:1005-1018. DOI.
  • Yap IK; Angley M; Veselkov KA; Holmes E; Lindon JC; Nicholson JK. (4 Jun 2010). Urinary metabolic phenotyping differentiates children with autism from their unaffected siblings and age-matched controls. J Proteome Res. 9:2996-3004. DOI.
  • Holmes E. (Aug 2010). The evolution of metabolic profiling in parasitology. Parasitology. 137:1437-1449. DOI.
  • Saric J; Li JV; Swann JR; Utzinger J; Calvert G; Nicholson JK; Dirnhofer S; Dallman MJ; et alBictash M; Holmes E. (7 May 2010). Integrated cytokine and metabolic analysis of pathological responses to parasite exposure in rodents. J Proteome Res. 9:2255-2264. DOI.
  • Barton RH; Waterman D; Bonner FW; Holmes E; Clarke R; Procardis Consortium; Nicholson JK; Lindon JC. (Jan 2010). The influence of EDTA and citrate anticoagulant addition to human plasma on information recovery from NMR-based metabolic profiling studies. Mol Biosyst. 6:215-224. DOI.
  • Fonville JM; Maher AD; Coen M; Holmes E; Lindon JC; Nicholson JK. (1 Mar 2010). Evaluation of full-resolution J-resolved 1H NMR projections of biofluids for metabonomics information retrieval and biomarker identification. Anal Chem. 82:1811-1821. DOI.
  • Bictash M; Ebbels TM; Chan Q; Loo RL; Yap IK; Brown IJ; de Iorio M; Daviglus ML; et alHolmes E; Stamler J; Nicholson JK; Elliott P. (Sep 2010). Opening up the "Black Box": metabolic phenotyping and metabolome-wide association studies in epidemiology. J Clin Epidemiol. 63:970-979. DOI.
  • Garcia-Perez I; Couto Alves A; Angulo S; Li JV; Utzinger J; Ebbels TM; Legido-Quigley C; Nicholson JK; et alHolmes E; Barbas C. (1 Jan 2010). Bidirectional correlation of NMR and capillary electrophoresis fingerprints: a new approach to investigating Schistosoma mansoni infection in a mouse model. Anal Chem. 82:203-210. DOI.
  • Legido-Quigley C; Stella C; Perez-Jimenez F; Lopez-Miranda J; Ordovas J; Powell J; van-der-Ouderaa F; Ware L; et alLindon JC; Nicholson JK; Holmes E. (Jul 2010). Liquid chromatography-mass spectrometry methods for urinary biomarker detection in metabonomic studies with application to nutritional studies. Biomed Chromatogr. 24:737-743. DOI.
  • Wang Y; Xiao SH; Xue J; Singer BH; Utzinger J; Holmes E. (Dec 2009). Systems metabolic effects of a necator americanus infection in Syrian hamster. J Proteome Res. 8:5442-5450. DOI.
  • Hong YS; Coen M; Rhode CM; Reily MD; Robertson DG; Holmes E; Lindon JC; Nicholson JK. (Dec 2009). Chemical shift calibration of 1H MAS NMR liver tissue spectra exemplified using a study of glycine protection of galactosamine toxicity. Magn Reson Chem. 47 Suppl 1:S47-S53. DOI.
  • Coen M; Want EJ; Clayton TA; Rhode CM; Hong YS; Keun HC; Cantor GH; Metz AL; et alRobertson DG; Reily MD; Holmes E; Lindon JC; Nicholson JK. (Nov 2009). Mechanistic aspects and novel biomarkers of responder and non-responder phenotypes in galactosamine-induced hepatitis. J Proteome Res. 8:5175-5187. DOI.
  • McLoughlin GA; Ma D; Tsang TM; Jones DN; Cilia J; Hill MD; Robbins MJ; Benzel IM; et alMaycox PR; Holmes E; Bahn S. (Apr 2009). Analyzing the effects of psychotropic drugs on metabolite profiles in rat brain using 1H NMR spectroscopy. J Proteome Res. 8:1943-1952.
  • Saric J; Li JV; Wang Y; Keiser J; Veselkov K; Dirnhofer S; Yap IK; Nicholson JK; et alHolmes E; Utzinger J. (Aug 2009). Panorganismal metabolic response modeling of an experimental Echinostoma caproni infection in the mouse. J Proteome Res. 8:3899-3911. DOI Open Access copy.
  • Kinross J; von Roon AC; Penney N; Holmes E; Silk D; Nicholson JK; Darzi A. (2009). The gut microbiota as a target for improved surgical outcome and improved patient care. Curr Pharm Des. 15:1537-1545.
  • Sands CJ; Coen M; Maher AD; Ebbels TM; Holmes E; Lindon JC; Nicholson JK. (1 Aug 2009). Statistical total correlation spectroscopy editing of 1H NMR spectra of biofluids: application to drug metabolite profile identification and enhanced information recovery. Anal Chem. 81:6458-6466. DOI.
  • Loo RL; Coen M; Ebbels T; Cloarec O; Maibaum E; Bictash M; Yap I; Elliott P; et alStamler J; Nicholson JK; Holmes E; INTERMAP Research Group. (1 Jul 2009). Metabolic profiling and population screening of analgesic usage in nuclear magnetic resonance spectroscopy-based large-scale epidemiologic studies. Anal Chem. 81:5119-5129. DOI.
  • Martin FP; Wang Y; Yap IK; Sprenger N; Lindon JC; Rezzi S; Kochhar S; Holmes E; et alNicholson JK. (Jul 2009). Topographical variation in murine intestinal metabolic profiles in relation to microbiome speciation and functional ecological activity. J Proteome Res. 8:3464-3474. DOI.
  • Smith LM; Maher AD; Want EJ; Elliott P; Stamler J; Hawkes GE; Holmes E; Lindon JC; et alNicholson JK. (15 Jun 2009). Large-scale human metabolic phenotyping and molecular epidemiological studies via 1H NMR spectroscopy of urine: investigation of borate preservation. Anal Chem. 81:4847-4856. DOI.
  • Swann J; Wang Y; Abecia L; Costabile A; Tuohy K; Gibson G; Roberts D; Sidaway J; et alJones H; Wilson ID; Nicholson J; Holmes E. (Apr 2009). Gut microbiome modulates the toxicity of hydrazine: a metabonomic study. Mol Biosyst. 5:351-355. DOI.
  • Waldram A; Holmes E; Wang Y; Rantalainen M; Wilson ID; Tuohy KM; McCartney AL; Gibson GR; et alNicholson JK. (May 2009). Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents. J Proteome Res. 8:2361-2375. DOI.
  • Martin FP; Sprenger N; Yap IK; Wang Y; Bibiloni R; Rochat F; Rezzi S; Cherbut C; et alKochhar S; Lindon JC; Holmes E; Nicholson JK. (Apr 2009). Panorganismal gut microbiome-host metabolic crosstalk. J Proteome Res. 8:2090-2105. DOI.
  • Alves AC; Rantalainen M; Holmes E; Nicholson JK; Ebbels TM. (15 Mar 2009). Analytic properties of statistical total correlation spectroscopy based information recovery in 1H NMR metabolic data sets. Anal Chem. 81:2075-2084. DOI.
  • Maher AD; Cloarec O; Patki P; Craggs M; Holmes E; Lindon JC; Nicholson JK. (1 Jan 2009). Dynamic biochemical information recovery in spontaneous human seminal fluid reactions via 1H NMR kinetic statistical total correlation spectroscopy. Anal Chem. 81:288-295. DOI.
  • Tsang TM; Haselden JN; Holmes E. (Jul 2009). Metabonomic characterization of the 3-nitropropionic acid rat model of Huntington's disease. Neurochem Res. 34:1261-1271. DOI.
  • Li JV; Holmes E; Saric J; Keiser J; Dirnhofer S; Utzinger J; Wang Y. (Apr 2009). Metabolic profiling of a Schistosoma mansoni infection in mouse tissues using magic angle spinning-nuclear magnetic resonance spectroscopy. Int J Parasitol. 39:547-558. DOI.
  • Veselkov KA; Lindon JC; Ebbels TM; Crockford D; Volynkin VV; Holmes E; Davies DB; Nicholson JK. (1 Jan 2009). Recursive segment-wise peak alignment of biological (1)h NMR spectra for improved metabolic biomarker recovery. Anal Chem. 81:56-66. DOI.
  • Cavill R; Keun HC; Holmes E; Lindon JC; Nicholson JK; Ebbels TM. (1 Jan 2009). Genetic algorithms for simultaneous variable and sample selection in metabonomics. Bioinformatics. 25:112-118. DOI.
  • Claus SP; Tsang TM; Wang Y; Cloarec O; Skordi E; Martin FP; Rezzi S; Ross A; et alKochhar S; Holmes E; Nicholson JK. (Oct 2008). Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Molecular Systems Biology. 4.
  • Maher AD; Patki P; Lindon JC; Want EJ; Holmes E; Craggs M; Nicholson JK. (Dec 2008). Seminal oligouridinosis: low uridine secretion as a biomarker for infertility in spinal neurotrauma. Clin Chem. 54:2063-2066. DOI.
  • Holmes E; Nicholson JK. (2007). Human metabolic phenotyping and metabolome wide association studies. Ernst Schering Found Symp Proc. 227-249.
  • Holmes E; Wilson ID; Nicholson JK. (5 Sep 2008). Metabolic phenotyping in health and disease. Cell. 134:714-717. DOI.
  • Maher AD; Crockford D; Toft H; Malmodin D; Faber JH; McCarthy MI; Barrett A; Allen M; et alWalker M; Holmes E; Lindon JC; Nicholson JK. (1 Oct 2008). Optimization of human plasma 1H NMR spectroscopic data processing for high-throughput metabolic phenotyping studies and detection of insulin resistance related to type 2 diabetes. Anal Chem. 80:7354-7362. DOI.
  • Bohus E; Coen M; Keun HC; Ebbels TM; Beckonert O; Lindon JC; Holmes E; Noszál B; et alNicholson JK. (Oct 2008). Temporal metabonomic modeling of l-arginine-induced exocrine pancreatitis. J Proteome Res. 7:4435-4445. DOI.
  • Kinross JM; von Roon AC; Holmes E; Darzi A; Nicholson JK. (Aug 2008). The human gut microbiome: implications for future health care. Curr Gastroenterol Rep. 10:396-403.
  • Martin FP; Wang Y; Sprenger N; Yap IK; Rezzi S; Ramadan Z; Peré-Trepat E; Rochat F; et alCherbut C; van Bladeren P; Fay LB; Kochhar S; Lindon JC; Holmes E; Nicholson JK. (2008). Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model. Mol Syst Biol. 4:205. DOI.
  • Li JV; Wang Y; Saric J; Nicholson JK; Dirnhofer S; Singer BH; Tanner M; Wittlin S; et alHolmes E; Utzinger J. (Sep 2008). Global metabolic responses of NMRI mice to an experimental Plasmodium berghei infection. J Proteome Res. 7:3948-3956. DOI.
  • Richards SE; Wang Y; Lawler D; Kochhar S; Holmes E; Lindon JC; Nicholson JK. (1 Jul 2008). Self-modeling curve resolution recovery of temporal metabolite signal modulation in NMR spectroscopic data sets: application to a life-long caloric restriction study in dogs. Anal Chem. 80:4876-4885. DOI.
  • Wang Y; Cloarec O; Tang H; Lindon JC; Holmes E; Kochhar S; Nicholson JK. (15 Feb 2008). Magic angle spinning NMR and 1H-31P heteronuclear statistical total correlation spectroscopy of intact human gut biopsies. Anal Chem. 80:1058-1066. DOI.
  • Rantalainen M; Cloarec O; Ebbels TM; Lundstedt T; Nicholson JK; Holmes E; Trygg J. (2008). Piecewise multivariate modelling of sequential metabolic profiling data. BMC Bioinformatics. 9:105. DOI.
  • Holmes E; Loo RL; Stamler J; Bictash M; Yap IK; Chan Q; Ebbels T; De Iorio M; et alBrown IJ; Veselkov KA; Daviglus ML; Kesteloot H; Ueshima H; Zhao L; Nicholson JK; Elliott P. (15 May 2008). Human metabolic phenotype diversity and its association with diet and blood pressure. Nature. 453:396-400. DOI.
  • Wang Y; Utzinger J; Saric J; Li JV; Burckhardt J; Dirnhofer S; Nicholson JK; Singer BH; et alBrun R; Holmes E. (22 Apr 2008). Global metabolic responses of mice to Trypanosoma brucei brucei infection. Proc Natl Acad Sci U S A. 105:6127-6132. DOI.
  • Barton RH; Nicholson JK; Elliott P; Holmes E. (Apr 2008). High-throughput 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study. Int J Epidemiol. 37 Suppl 1:i31-i40. DOI.
  • Coen M; Holmes E; Lindon JC; Nicholson JK. (Jan 2008). NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chem Res Toxicol. 21:9-27. DOI.
  • Keun HC; Athersuch TJ; Beckonert O; Wang Y; Saric J; Shockcor JP; Lindon JC; Wilson ID; et alHolmes E; Nicholson JK. (15 Feb 2008). Heteronuclear 19F-1H statistical total correlation spectroscopy as a tool in drug metabolism: study of flucloxacillin biotransformation. Anal Chem. 80:1073-1079. DOI.
  • Bang JW; Crockford DJ; Holmes E; Pazos F; Sternberg MJ; Muggleton SH; Nicholson JK. (Feb 2008). Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods. J Proteome Res. 7:497-503. DOI.
  • Martin FP; Wang Y; Sprenger N; Yap IK; Lundstedt T; Lek P; Rezzi S; Ramadan Z; et alvan Bladeren P; Fay LB; Kochhar S; Lindon JC; Holmes E; Nicholson JK. (2008). Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol Syst Biol. 4:157. DOI.
  • Faber J; Malmodin D; Toft H; Maher A; Crockford D; Holmes E; Nicholson J; Dumas M; et alBaunsgaard D. Metabonomics in Diabetes Research. J Diabetes Sci Technol. 1:549-557.
  • Beckonert O; Keun HC; Ebbels TM; Bundy J; Holmes E; Lindon JC; Nicholson JK. (2007). Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc. 2:2692-2703. DOI.
  • Skordi E; Yap IK; Claus SP; Martin FP; Cloarec O; Lindberg J; Schuppe-Koistinen I; Holmes E; et alNicholson JK. (Dec 2007). Analysis of time-related metabolic fluctuations induced by ethionine in the rat. J Proteome Res. 6:4572-4581. DOI.
  • Coen M; Hong YS; Cloarec O; Rhode CM; Reily MD; Robertson DG; Holmes E; Lindon JC; et alNicholson JK. (1 Dec 2007). Heteronuclear 1H-31P statistical total correlation NMR spectroscopy of intact liver for metabolic biomarker assignment: application to galactosamine-induced hepatotoxicity. Anal Chem. 79:8956-8966. DOI.
  • Ebbels TM; Keun HC; Beckonert OP; Bollard ME; Lindon JC; Holmes E; Nicholson JK. (Nov 2007). Prediction and classification of drug toxicity using probabilistic modeling of temporal metabolic data: the consortium on metabonomic toxicology screening approach. J Proteome Res. 6:4407-4422. DOI.
  • Wang Y; Holmes E; Comelli EM; Fotopoulos G; Dorta G; Tang H; Rantalainen MJ; Lindon JC; et alCorthésy-Theulaz IE; Fay LB; Kochhar S; Nicholson JK. (Oct 2007). Topographical variation in metabolic signatures of human gastrointestinal biopsies revealed by high-resolution magic-angle spinning 1H NMR spectroscopy. J Proteome Res. 6:3944-3951. DOI.
  • Li J; Wang Y; Fenwick A; Clayton TA; Lau YY; Legido-Quigley C; Lindon JC; Utzinger J; et alHolmes E. (18 Oct 2007). A high-performance liquid chromatography and nuclear magnetic resonance spectroscopy-based analysis of commercially available praziquantel tablets. J Pharm Biomed Anal. 45:263-267. DOI.
  • Keun HC; Ebbels TMD; Antti H; Bollard ME; Beckonert O; Holmes E; Lindon JC; Nicholson JK. (25 Aug 2003). Improved analysis of multivariate data by variable stability scaling: application to NMR-based metabolic profiling. ANAL CHIM ACTA. 490:265-276.
  • Beckonert O; Bollard ME; Ebbels TMD; Keun HC; Antti H; Holmes E; Lindon JC; Nicholson JK. (25 Aug 2003). NMR-based metabonomic toxicity classification: hierarchical cluster analysis and k-nearest-neighbour approaches. ANAL CHIM ACTA. 490:3-15.
  • Antti H; Ebbels TMD; Keun HC; Bollard ME; Beckonert O; Lindon JC; Nicholson JK; Holmes E. (28 Sep 2004). Statistical experimental design and partial least squares regression analysis of biofluid metabonomic NMR and clinical chemistry data for screening of adverse drug effects. CHEMOMETR INTELL LAB. 73:139-149.
  • Holmes E; Tsang TM; Huang JT; Leweke FM; Koethe D; Gerth CW; Nolden BM; Gross S; et alSchreiber D; Nicholson JK; Bahn, S. (22 Aug 2006). Metabolic profiling of CSF: evidence that early intervention may impact on disease progression and outcome in schizophrenia. PLoS Med. 8, 3:1420-1428.
  • Lindon JC; Holmes E; Nicholson JK. (2001). Pattern recognition methods and applications in biomedical magnetic resonance. Prog Nucl Magn Reson Spectroscop. 1, 39:1-4.
  • Espina JR; Shockcor JP; Herron WJ; Car BD; Contel NR; Ciaccio PJ; Lindon JC; Holmes E; et alNicholson JK. (2001). Detection of in vivo biomarkers of phospholipidosis using NMR-based metabonomic approaches. Magn Reson Chem. 39:559-565.
  • Antti H; Bollard ME; Ebbels TM; Keun H; Lindon JC; Nicholson JK; Holmes E. (2002). Batch statistical processing of H NMR-derived urinary spectral data. J Chemometrics. 08-Oct, 16:461-468.
  • Smith LM; Maher AD; Cloarec O; Rantalainen M; Tang H; Elliott P; Stamler J; Lindon JC; et alHolmes E; Nicholson JK. (1 Aug 2007). Statistical correlation and projection methods for improved information recovery from diffusion-edited NMR spectra of biological samples. Anal Chem. 79:5682-5689. DOI.
  • Coen M; Hong YS; Clayton TA; Rohde CM; Pearce JT; Reily MD; Robertson DG; Holmes E; et alLindon JC; Nicholson JK. (Jul 2007). The mechanism of galactosamine toxicity revisited; a metabonomic study. J Proteome Res. 6:2711-2719. DOI.
  • Maher AD; Zirah SF; Holmes E; Nicholson JK. (15 Jul 2007). Experimental and analytical variation in human urine in 1H NMR spectroscopy-based metabolic phenotyping studies. Anal Chem. 79:5204-5211. DOI.
  • Martin FP; Dumas ME; Wang Y; Legido-Quigley C; Yap IK; Tang H; Zirah S; Murphy GM; et alCloarec O; Lindon JC; Sprenger N; Fay LB; Kochhar S; van Bladeren P; Holmes E; Nicholson JK. (2007). A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol. 3:112. DOI.
  • Teague CR; Dhabhar FS; Barton RH; Beckwith-Hall B; Powell J; Cobain M; Singer B; McEwen BS; et alLindon JC; Nicholson JK; Holmes E. (Jun 2007). Metabonomic studies on the physiological effects of acute and chronic psychological stress in Sprague-Dawley rats. J Proteome Res. 6:2080-2093. DOI.
  • Wang Y; Lawler D; Larson B; Ramadan Z; Kochhar S; Holmes E; Nicholson JK. (May 2007). Metabonomic investigations of aging and caloric restriction in a life-long dog study. J Proteome Res. 6:1846-1854. DOI.
  • Lindon JC; Holmes E; Nicholson JK. (Mar 2007). Metabonomics in pharmaceutical R&D. FEBS J. 274:1140-1151. DOI.
  • Martin FP; Wang Y; Sprenger N; Holmes E; Lindon JC; Kochhar S; Nicholson JK. (Apr 2007). Effects of probiotic Lactobacillus paracasei treatment on the host gut tissue metabolic profiles probed via magic-angle-spinning NMR spectroscopy. J Proteome Res. 6:1471-1481. DOI.
  • Holmes E; Loo RL; Cloarec O; Coen M; Tang H; Maibaum E; Bruce S; Chan Q; et alElliott P; Stamler J; Wilson ID; Lindon JC; Nicholson JK. (1 Apr 2007). Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy. Anal Chem. 79:2629-2640. DOI.
  • Marchesi JR; Holmes E; Khan F; Kochhar S; Scanlan P; Shanahan F; Wilson ID; Wang Y. (Feb 2007). Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 6:546-551. DOI.
  • Nicholson JK; Holmes E. (Apr 2006). Global systems biology and personalized healthcare solutions. Discov Med. 6:63-70.
  • Rantalainen M; Cloarec O; Beckonert O; Wilson ID; Jackson D; Tonge R; Rowlinson R; Rayner S; et alNickson J; Wilkinson RW; Mills JD; Trygg J; Nicholson JK; Holmes E. (Oct 2006). Statistically integrated metabonomic-proteomic studies on a human prostate cancer xenograft model in mice. J Proteome Res. 5:2642-2655. DOI.
  • Holmes E; Tang H; Wang Y; Seger C. (Jul 2006). The assessment of plant metabolite profiles by NMR-based methodologies. Planta Med. 72:771-785. DOI.
  • Holmes E; Tsang TM; Huang JT; Leweke FM; Koethe D; Gerth CW; Nolden BM; Gross S; et alSchreiber D; Nicholson JK; Bahn S. (Aug 2006). Metabolic profiling of CSF: evidence that early intervention may impact on disease progression and outcome in schizophrenia. PLoS Med. 3:e327. DOI.
  • Stella C; Beckwith-Hall B; Cloarec O; Holmes E; Lindon JC; Powell J; van der Ouderaa F; Bingham S; et alCross AJ; Nicholson JK. (Oct 2006). Susceptibility of human metabolic phenotypes to dietary modulation. J Proteome Res. 5:2780-2788. DOI.
  • Martin FP; Verdu EF; Wang Y; Dumas ME; Yap IK; Cloarec O; Bergonzelli GE; Corthesy-Theulaz I; et alKochhar S; Holmes E; Lindon JC; Collins SM; Nicholson JK. (Sep 2006). Transgenomic metabolic interactions in a mouse disease model: interactions of Trichinella spiralis infection with dietary Lactobacillus paracasei supplementation. J Proteome Res. 5:2185-2193. DOI.
  • Dumas ME; Barton RH; Toye A; Cloarec O; Blancher C; Rothwell A; Fearnside J; Tatoud R; et alBlanc V; Lindon JC; Mitchell SC; Holmes E; McCarthy MI; Scott J; Gauguier D; Nicholson JK. (15 Aug 2006). Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A. 103:12511-12516. DOI.
  • Wang Y; Holmes E; Tang H; Lindon JC; Sprenger N; Turini ME; Bergonzelli G; Fay LB; et alKochhar S; Nicholson JK. (Jul 2006). Experimental metabonomic model of dietary variation and stress interactions. J Proteome Res. 5:1535-1542. DOI.
  • Craig A; Sidaway J; Holmes E; Orton T; Jackson D; Rowlinson R; Nickson J; Tonge R; et alWilson I; Nicholson J. (Jul 2006). Systems toxicology: integrated genomic, proteomic and metabonomic analysis of methapyrilene induced hepatotoxicity in the rat. J Proteome Res. 5:1586-1601. DOI.
  • Teahan O; Gamble S; Holmes E; Waxman J; Nicholson JK; Bevan C; Keun HC. (1 Jul 2006). Impact of analytical bias in metabonomic studies of human blood serum and plasma. Anal Chem. 78:4307-4318. DOI.
  • Crockford DJ; Lindon JC; Cloarec O; Plumb RS; Bruce SJ; Zirah S; Rainville P; Stumpf CL; et alJohnson K; Holmes E; Nicholson JK. (1 Jul 2006). Statistical search space reduction and two-dimensional data display approaches for UPLC-MS in biomarker discovery and pathway analysis. Anal Chem. 78:4398-4408. DOI.
  • Holmes E; Tsang TM; Tabrizi SJ. (Jul 2006). The application of NMR-based metabonomics in neurological disorders. NeuroRx. 3:358-372. DOI.
  • Holmes E; Cloarec O; Nicholson JK. (Jun 2006). Probing latent biomarker signatures and in vivo pathway activity in experimental disease states via statistical total correlation spectroscopy (STOCSY) of biofluids: application to HgCl2 toxicity. J Proteome Res. 5:1313-1320. DOI.
  • Waters NJ; Waterfield CJ; Farrant RD; Holmes E; Nicholson JK. (Jun 2006). Integrated metabonomic analysis of bromobenzene-induced hepatotoxicity: novel induction of 5-oxoprolinosis. J Proteome Res. 5:1448-1459. DOI.
  • Lindon JC; Holmes E; Nicholson JK. (Jun 2006). Metabonomics techniques and applications to pharmaceutical research & development. Pharm Res. 23:1075-1088. DOI.
  • Tsang TM; Huang JT; Holmes E; Bahn S. (Apr 2006). Metabolic profiling of plasma from discordant schizophrenia twins: correlation between lipid signals and global functioning in female schizophrenia patients. J Proteome Res. 5:756-760. DOI.
  • Dumas ME; Maibaum EC; Teague C; Ueshima H; Zhou B; Lindon JC; Nicholson JK; Stamler J; et alElliott P; Chan Q; Holmes E. (1 Apr 2006). Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study. Anal Chem. 78:2199-2208. DOI.
  • Craig A; Cloarec O; Holmes E; Nicholson JK; Lindon JC. (1 Apr 2006). Scaling and normalization effects in NMR spectroscopic metabonomic data sets. Anal Chem. 78:2262-2267. DOI.
  • Tsang TM; Woodman B; McLoughlin GA; Griffin JL; Tabrizi SJ; Bates GP; Holmes E. (Mar 2006). Metabolic characterization of the R6/2 transgenic mouse model of Huntington's disease by high-resolution MAS 1H NMR spectroscopy. J Proteome Res. 5:483-492. DOI.
  • Crockford DJ; Holmes E; Lindon JC; Plumb RS; Zirah S; Bruce SJ; Rainville P; Stumpf CL; et alNicholson JK. (15 Jan 2006). Statistical heterospectroscopy, an approach to the integrated analysis of NMR and UPLC-MS data sets: application in metabonomic toxicology studies. Anal Chem. 78:363-371. DOI.
  • Wang Y; Utzinger J; Xiao SH; Xue J; Nicholson JK; Tanner M; Singer BH; Holmes E. (Mar 2006). System level metabolic effects of a Schistosoma japonicum infection in the Syrian hamster. Mol Biochem Parasitol. 146:1-9. DOI.
  • Azmi J; Connelly J; Holmes E; Nicholson JK; Shore RF; Griffin JL. (Nov 2005). Characterization of the biochemical effects of 1-nitronaphthalene in rats using global metabolic profiling by NMR spectroscopy and pattern recognition. Biomarkers. 10:401-416. DOI.
  • Lindon JC; Keun HC; Ebbels TM; Pearce JM; Holmes E; Nicholson JK. (Oct 2005). The Consortium for Metabonomic Toxicology (COMET): aims, activities and achievements. Pharmacogenomics. 6:691-699. DOI.
  • Wang Y; Bollard ME; Nicholson JK; Holmes E. (13 Feb 2006). Exploration of the direct metabolic effects of mercury II chloride on the kidney of Sprague-Dawley rats using high-resolution magic angle spinning 1H NMR spectroscopy of intact tissue and pattern recognition. J Pharm Biomed Anal. 40:375-381. DOI.
  • Holmes E; Nicholson J. (Sep 2005). Variation in gut microbiota strongly influences individual rodent phenotypes. Toxicol Sci. 87:1-2.
  • Stanley EG; Bailey NJ; Bollard ME; Haselden JN; Waterfield CJ; Holmes E; Nicholson JK. (15 Aug 2005). Sexual dimorphism in urinary metabolite profiles of Han Wistar rats revealed by nuclear-magnetic-resonance-based metabonomics. Anal Biochem. 343:195-202. DOI.
  • Azmi J; Griffin JL; Shore RF; Holmes E; Nicholson JK. (Aug 2005). Chemometric analysis of biofluids following toxicant induced hepatotoxicity: a metabonomic approach to distinguish the effects of 1-naphthylisothiocyanate from its products. Xenobiotica. 35:839-852. DOI.
  • Crockford DJ; Keun HC; Smith LM; Holmes E; Nicholson JK. (15 Jul 2005). Curve-fitting method for direct quantitation of compounds in complex biological mixtures using 1H NMR: application in metabonomic toxicology studies. Anal Chem. 77:4556-4562. DOI.
  • Wang Y; Tang H; Holmes E; Lindon JC; Turini ME; Sprenger N; Bergonzelli G; Fay LB; et alKochhar S; Nicholson JK. (Jul 2005). Biochemical characterization of rat intestine development using high-resolution magic-angle-spinning 1H NMR spectroscopy and multivariate data analysis. J Proteome Res. 4:1324-1329. DOI.
  • Lindon JC; Nicholson JK; Holmes E; Keun HC; Craig A; Pearce JT; Bruce SJ; Hardy N; et alSansone SA; Antti H; Jonsson P; Daykin C; Navarange M; Beger RD; Verheij ER; Amberg A; Baunsgaard D; Cantor GH; Lehman-McKeeman L; Earll M; Wold S; Johansson E; Haselden JN; Kramer K; Thomas C; Lindberg J; Schuppe-Koistinen I; Wilson ID; Reily MD; Robertson DG; Senn H; Krotzky A; Kochhar S; Powell J; van der Ouderaa F; Plumb R; Schaefer H; Spraul M; Standard Metabolic Reporting Structures working group. (Jul 2005). Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol. 23:833-838. DOI.
  • Nicholson JK; Holmes E; Wilson ID. (May 2005). Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol. 3:431-438. DOI.
  • Tsang TM; Griffin JL; Haselden J; Fish C; Holmes E. (May 2005). Metabolic characterization of distinct neuroanatomical regions in rats by magic angle spinning 1H nuclear magnetic resonance spectroscopy. Magn Reson Med. 53:1018-1024. DOI.
  • Bollard ME; Stanley EG; Lindon JC; Nicholson JK; Holmes E. (May 2005). NMR-based metabonomic approaches for evaluating physiological influences on biofluid composition. NMR Biomed. 18:143-162. DOI.
  • Bollard ME; Keun HC; Beckonert O; Ebbels TM; Antti H; Nicholls AW; Shockcor JP; Cantor GH; et alStevens G; Lindon JC; Holmes E; Nicholson JK. (15 Apr 2005). Comparative metabonomics of differential hydrazine toxicity in the rat and mouse. Toxicol Appl Pharmacol. 204:135-151. DOI.
  • Solanky KS; Bailey NJ; Beckwith-Hall BM; Bingham S; Davis A; Holmes E; Nicholson JK; Cassidy A. (Apr 2005). Biofluid 1H NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans. J Nutr Biochem. 16:236-244. DOI.
  • Waters NJ; Waterfield CJ; Farrant RD; Holmes E; Nicholson JK. (Apr 2005). Metabonomic deconvolution of embedded toxicity: application to thioacetamide hepato- and nephrotoxicity. Chem Res Toxicol. 18:639-654. DOI.
  • Cloarec O; Dumas ME; Craig A; Barton RH; Trygg J; Hudson J; Blancher C; Gauguier D; et alLindon JC; Holmes E; Nicholson J. (1 Mar 2005). Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. Anal Chem. 77:1282-1289. DOI.
  • Garrod S; Bollard ME; Nicholls AW; Connor SC; Connelly J; Nicholson JK; Holmes E. (Feb 2005). Integrated metabonomic analysis of the multiorgan effects of hydrazine toxicity in the rat. Chem Res Toxicol. 18:115-122. DOI.
  • Wang Y; Tang H; Nicholson JK; Hylands PJ; Sampson J; Holmes E. (26 Jan 2005). A metabonomic strategy for the detection of the metabolic effects of chamomile (Matricaria recutita L.) ingestion. J Agric Food Chem. 53:191-196. DOI.
  • Cloarec O; Dumas ME; Trygg J; Craig A; Barton RH; Lindon JC; Nicholson JK; Holmes E. (15 Jan 2005). Evaluation of the orthogonal projection on latent structure model limitations caused by chemical shift variability and improved visualization of biomarker changes in 1H NMR spectroscopic metabonomic studies. Anal Chem. 77:517-526. DOI.
  • Ebbels TM; Holmes E; Lindon JC; Nicholson JK. (19 Nov 2004). Evaluation of metabolic variation in normal rat strains from a statistical analysis of 1H NMR spectra of urine. J Pharm Biomed Anal. 36:823-833. DOI.
  • Nicholson JK; Holmes E; Lindon JC; Wilson ID. (Oct 2004). The challenges of modeling mammalian biocomplexity. Nat Biotechnol. 22:1268-1274. DOI.
  • Wang Y; Holmes E; Nicholson JK; Cloarec O; Chollet J; Tanner M; Singer BH; Utzinger J. (24 Aug 2004). Metabonomic investigations in mice infected with Schistosoma mansoni: an approach for biomarker identification. Proc Natl Acad Sci U S A. 101:12676-12681. DOI.
  • Lindon JC; Holmes E; Nicholson JK. (Jun 2004). Metabonomics: systems biology in pharmaceutical research and development. Curr Opin Mol Ther. 6:265-272.
  • Keun HC; Ebbels TM; Bollard ME; Beckonert O; Antti H; Holmes E; Lindon JC; Nicholson JK. (May 2004). Geometric trajectory analysis of metabolic responses to toxicity can define treatment specific profiles. Chem Res Toxicol. 17:579-587. DOI.
  • Teague C; Holmes E; Maibaum E; Nicholson J; Tang H; Chan Q; Elliott P; Stamler J; et alUeshima H; Zhou B; Wilson I. (Mar 2004). Ethyl glucoside in human urine following dietary exposure: detection by 1H NMR spectroscopy as a result of metabonomic screening of humans. Analyst. 129:259-264. DOI.
  • Wang Y; Tang H; Nicholson JK; Hylands PJ; Sampson J; Whitcombe I; Stewart CG; Caiger S; et alOru I; Holmes E. (Mar 2004). Metabolomic strategy for the classification and quality control of phytomedicine: a case study of chamomile flower (Matricaria recutita L.). Planta Med. 70:250-255. DOI.
  • Lindon JC; Holmes E; Nicholson JK. (Mar 2004). Metabonomics and its role in drug development and disease diagnosis. Expert Rev Mol Diagn. 4:189-199. DOI.
  • Lindon JC; Holmes E; Bollard ME; Stanley EG; Nicholson JK. (Jan 2004). Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis. Biomarkers. 9:1-31. DOI.
  • Solanky KS; Bailey NJ; Beckwith-Hall BM; Davis A; Bingham S; Holmes E; Nicholson JK; Cassidy A. (15 Dec 2003). Application of biofluid 1H nuclear magnetic resonance-based metabonomic techniques for the analysis of the biochemical effects of dietary isoflavones on human plasma profile. Anal Biochem. 323:197-204.
  • Wang Y; Bollard ME; Keun H; Antti H; Beckonert O; Ebbels TM; Lindon JC; Holmes E; et alTang H; Nicholson JK. (1 Dec 2003). Spectral editing and pattern recognition methods applied to high-resolution magic-angle spinning 1H nuclear magnetic resonance spectroscopy of liver tissues. Anal Biochem. 323:26-32.
  • Lindon JC; Holmes E; Nicholson JK. (1 Sep 2003). So what's the deal with metabonomics?. Anal Chem. 75:384A-391A.
  • Solanky KS; Bailey NJ; Holmes E; Lindon JC; Davis AL; Mulder TP; Van Duynhoven JP; Nicholson JK. (2 Jul 2003). NMR-based metabonomic studies on the biochemical effects of epicatechin in the rat. J Agric Food Chem. 51:4139-4145. DOI.
  • Beckwith-Hall BM; Thompson NA; Nicholson JK; Lindon JC; Holmes E. (Jul 2003). A metabonomic investigation of hepatotoxicity using diffusion-edited 1H NMR spectroscopy of blood serum. Analyst. 128:814-818.
  • Lindon JC; Nicholson JK; Holmes E; Antti H; Bollard ME; Keun H; Beckonert O; Ebbels TM; et alReily MD; Robertson D; Stevens GJ; Luke P; Breau AP; Cantor GH; Bible RH; Niederhauser U; Senn H; Schlotterbeck G; Sidelmann UG; Laursen SM; Tymiak A; Car BD; Lehman-McKeeman L; Colet JM; Loukaci A; Thomas C. (15 Mar 2003). Contemporary issues in toxicology the role of metabonomics in toxicology and its evaluation by the COMET project. Toxicol Appl Pharmacol. 187:137-146.
  • Bailey NJ; Oven M; Holmes E; Nicholson JK; Zenk MH. (Mar 2003). Metabolomic analysis of the consequences of cadmium exposure in Silene cucubalus cell cultures via 1H NMR spectroscopy and chemometrics. Phytochemistry. 62:851-858.
  • Brindle JT; Nicholson JK; Schofield PM; Grainger DJ; Holmes E. (Jan 2003). Application of chemometrics to 1H NMR spectroscopic data to investigate a relationship between human serum metabolic profiles and hypertension. Analyst. 128:32-36.
  • Connelly JC; Connor SC; Monte S; Bailey NJ; Borgeaud N; Holmes E; Troke J; Nicholson JK; et alGavaghan CL. (Dec 2002). Application of directly coupled high performance liquid chromatography-NMR-mass spectometry and 1H NMR spectroscopic studies to the investigation of 2,3-benzofuran metabolism in Sprague-Dawley rats. Drug Metab Dispos. 30:1357-1363.
  • Holmes E; Antti H. (Dec 2002). Chemometric contributions to the evolution of metabonomics: mathematical solutions to characterising and interpreting complex biological NMR spectra. Analyst. 127:1549-1557.
  • Brindle JT; Antti H; Holmes E; Tranter G; Nicholson JK; Bethell HW; Clarke S; Schofield PM; et alMcKilligin E; Mosedale DE; Grainger DJ. (Dec 2002). Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics. Nat Med. 8:1439-1444. DOI.
  • Keun HC; Ebbels TM; Antti H; Bollard ME; Beckonert O; Schlotterbeck G; Senn H; Niederhauser U; et alHolmes E; Lindon JC; Nicholson JK. (Nov 2002). Analytical reproducibility in (1)H NMR-based metabonomic urinalysis. Chem Res Toxicol. 15:1380-1386.
  • Bollard ME; Xu J; Purcell W; Griffin JL; Quirk C; Holmes E; Nicholson JK. (Nov 2002). Metabolic profiling of the effects of D-galactosamine in liver spheroids using (1)H NMR and MAS-NMR spectroscopy. Chem Res Toxicol. 15:1351-1359.
  • Beckwith-Hall BM; Brindle JT; Barton RH; Coen M; Holmes E; Nicholson JK; Antti H. (Oct 2002). Application of orthogonal signal correction to minimise the effects of physical and biological variation in high resolution 1H NMR spectra of biofluids. Analyst. 127:1283-1288.
  • Mitchell S; Holmes E; Carmichael P. (Oct 2002). Metabonomics and medicine: the Biochemical Oracle. Biologist (London). 49:217-221.
  • Beckwith-Hall BM; Holmes E; Lindon JC; Gounarides J; Vickers A; Shapiro M; Nicholson JK. (Sep 2002). NMR-based metabonomic studies on the biochemical effects of commonly used drug carrier vehicles in the rat. Chem Res Toxicol. 15:1136-1141.
  • Bailey NJ; Sampson J; Hylands PJ; Nicholson JK; Holmes E. (Aug 2002). Multi-component metabolic classification of commercial feverfew preparations via high-field 1H-NMR spectroscopy and chemometrics. Planta Med. 68:734-738. DOI.
  • Waters NJ; Holmes E; Waterfield CJ; Farrant RD; Nicholson JK. (1 Jul 2002). NMR and pattern recognition studies on liver extracts and intact livers from rats treated with alpha-naphthylisothiocyanate. Biochem Pharmacol. 64:67-77.
  • Scarfe GB; Wilson ID; Warne MA; Holmes E; Nicholson JK; Lindon JC. (Apr 2002). Structure-metabolism relationships of substituted anilines: prediction of N-acetylation and N-oxanilic acid formation using computational chemistry. Xenobiotica. 32:267-277. DOI.
  • Azmi J; Griffin JL; Antti H; Shore RF; Johansson E; Nicholson JK; Holmes E. (Feb 2002). Metabolic trajectory characterisation of xenobiotic-induced hepatotoxic lesions using statistical batch processing of NMR data. Analyst. 127:271-276.
  • Nicholson JK; Connelly J; Lindon JC; Holmes E. (Feb 2002). Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov. 1:153-161. DOI.
  • Talbert AM; Tranter GE; Holmes E; Francis PL. (15 Jan 2002). Determination of drug-plasma protein binding kinetics and equilibria by chromatographic profiling: exemplification of the method using L-tryptophan and albumin. Anal Chem. 74:446-452.
  • Shockcor JP; Holmes E. (Jan 2002). Metabonomic applications in toxicity screening and disease diagnosis. Curr Top Med Chem. 2:35-51.
  • Waters NJ; Holmes E; Williams A; Waterfield CJ; Farrant RD; Nicholson JK. (Oct 2001). NMR and pattern recognition studies on the time-related metabolic effects of alpha-naphthylisothiocyanate on liver, urine, and plasma in the rat: an integrative metabonomic approach. Chem Res Toxicol. 14:1401-1412.
  • Bollard ME; Holmes E; Lindon JC; Mitchell SC; Branstetter D; Zhang W; Nicholson JK. (15 Aug 2001). Investigations into biochemical changes due to diurnal variation and estrus cycle in female rats using high-resolution (1)H NMR spectroscopy of urine and pattern recognition. Anal Biochem. 295:194-202. DOI.
  • Nicholls AW; Holmes E; Lindon JC; Shockcor JP; Farrant RD; Haselden JN; Damment SJ; Waterfield CJ; et alNicholson JK. (Aug 2001). Metabonomic investigations into hydrazine toxicity in the rat. Chem Res Toxicol. 14:975-987.
  • Garrod S; Humpher E; Connor SC; Connelly JC; Spraul M; Nicholson JK; Holmes E. (May 2001). High-resolution (1)H NMR and magic angle spinning NMR spectroscopic investigation of the biochemical effects of 2-bromoethanamine in intact renal and hepatic tissue. Magn Reson Med. 45:781-790.
  • Coen M; Lindon JC; Gavaghan C; Holmes E; Humpfer E; Wilson ID; Stanley PD; Nicholson JK. (May 2001). Investigation of water environments in a C18 bonded silica phase using 1H magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. Analyst. 126:548-550.
  • Gavaghan CL; Nicholson JK; Connor SC; Wilson ID; Wright B; Holmes E. (15 Apr 2001). Directly coupled high-performance liquid chromatography and nuclear magnetic resonance spectroscopic with chemometric studies on metabolic variation in Sprague--Dawley rats. Anal Biochem. 291:245-252. DOI.
  • Holmes E; Nicholson JK; Tranter G. (Feb 2001). Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks. Chem Res Toxicol. 14:182-191.
  • Gavaghan CL; Holmes E; Lenz E; Wilson ID; Nicholson JK. (10 Nov 2000). An NMR-based metabonomic approach to investigate the biochemical consequences of genetic strain differences: application to the C57BL10J and Alpk:ApfCD mouse. FEBS Lett. 484:169-174.
  • Griffin JL; Walker LA; Garrod S; Holmes E; Shore RF; Nicholson JK. (Nov 2000). NMR spectroscopy based metabonomic studies on the comparative biochemistry of the kidney and urine of the bank vole (Clethrionomys glareolus), wood mouse (Apodemus sylvaticus), white toothed shrew (Crocidura suaveolens) and the laboratory rat. Comp Biochem Physiol B Biochem Mol Biol. 127:357-367.

Chapters in books

  • Robertson DG; Reily M; Lindon JC; Holmes E; Nicholson JK. Metabonomic technology as a tool for rapid throughput in vivo toxicity screening. In Comprehensive Toxicology Vol. XIV: Cellular and molecular toxicology. 583-610. (2002).

Conferences

  • Solanky KS; Bailey NJC; Holmes E; Lindon JC; Nicholson JK; Davis AL; Mulder TPJ; Van Duynhoven J. NMR and pattern recognition studies on the biochemistry of black tea-derived polyphenolic compounds in the rat. 11th Eurofoodchem Meeting on Biologically-Active Phytochemicals in Food. 140-142. (2001).
  • Ebbels T; Keun H; Beckonert O; Antti H; Bollard M; Holmes E; Lindon J; Nicholson J. Toxicity classification from metabonomic data using a density superposition approach: 'CLOUDS'. 8th International Conference on Chemometrics in Analytical Chemistry (CAC 2002). 490:109-122. (25 Aug 2003).
  • Bailey NJC; Oven M; Holmes E; Zenk MH; Nicholson JK. An NMR-based metabolomic approach to the analysis of the effects of xenobiotics on endogenous metabolite levels in plants. 2nd International Conference on Biomedical Spectroscopy. 18:279-287. (2004).

Patents

  • Methods for spectral analysis and their applications: spectral replacement. Patent number: US 6,683,455 (USA). Application: US20010029380 20011220, US2002145425. Awarded: 2004.
  • Methods for Analysis of Spectral Data and Their Applications: Atherosclerosis and Coronary Heart Disease. Application: PCT/GB02/01854. Filed: 2002.
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