Nicholson, J. K. Molecular Phenomic Approaches to Deconvolving the Systemic Effects of SARS-CoV-2 Infection and Post-acute COVID-19 Syndrome, Phenomics. (2021). https://doi.org/10.1007/s43657-021-00020-3.

Gray, N. et al.  Diagnostic Potential of the Plasma Lipidome in Infectious Disease: Application to Acute SARS-CoV-2 Infection, Metabolites. 11 (2021) 467. https://dx.doi.org/10.3390%2Fmetabo11070467.

Masuda, R. et al. Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts, J. Proteome Res. (2021). https://doi.org/10.1021/acs.jproteome.1c00458.

Holmes E. et al. Incomplete Systemic Recovery and Metabolic Phenoreversion in Post-Acute-Phase Nonhospitalized COVID-19 Patients: Implications for Assessment of Post-Acute COVID-19 Syndrome, J. Proteome Res. (2021). https://doi.org/10.1021/acs.jproteome.1c00224.

Lawler, NG. et al Systemic Perturbations in Amine and Kynurenine Metabolism Associated with Acute SARS-CoV-2 Infection and Inflammatory Cytokine Responses, J. Proteome Res. (2021). https://doi.org/10.1021/acs.jproteome.1c00052.

Lodge S, et al. Diffusion and Relaxation Edited Proton NMR Spectroscopy of Plasma Reveals a High-Fidelity Supramolecular Biomarker Signature of SARS-CoV-2 Infection. Anal Chem. 2021 Mar 2;93(8):3976-3986. doi: 10.1021/acs.analchem.0c04952.

Lodge S. et al. NMR Spectroscopic Windows on the Systemic Effects of SARS-CoV-2 Infection on Plasma Lipoproteins and Metabolites in Relation to Circulating Cytokines. J. Proteome Res. 2021 Jan 11:acs.jproteome.0c00876. DOI: 10.1021/acs.jproteome.0c00876.

Lodge S, et al. Low Volume in Vitro Diagnostic Proton NMR Spectroscopy of Human Blood Plasma for Lipoprotein and Metabolite Analysis: Application to SARS-CoV-2 Biomarkers. J Proteome Res. 2021 Jan 23. DOI: 10.1021/acs.jproteome.0c00815.

Kimhofer T. et al. Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection. Journal of proteome research, 2020: 19, 4442-4454. DOI:10.1021/acs.jproteome.0c00519

Loo RL. et al. Quantitative In-Vitro Diagnostic NMR Spectroscopy for Lipoprotein and Metabolite Measurements in Plasma and Serum: Recommendations for Analytical Artifact Minimization with Special Reference to COVID-19/SARS-CoV-2 Samples. Journal of proteome research, 2020; 19, 4428-4441. DOI: 10.1021/acs.jproteome.0c00537

NMR Spectroscopy Methods

Garcia Perez I. et al. Identifying unknown metabolites using NMR-based metabolic profiling techniques. Nature protocols, 2020; 15, 2538-2567. DOI:10.1038/s41596-020-0343-3

Vonhof EV. Et al. Improved Spatial Resolution of Metabolites in Tissue Biopsies Using High-Resolution Magic-Angle-Spinning Slice Localization NMR Spectroscopy. Analytical chemistry, 2020; 92, 11516-11519. DOI:10.1021/acs.analchem.0c02377

Loo RL. et al. A feasibility study of metabolic phenotyping of dried blood spot specimens in rural Chinese women exposed to household air pollution. J Expo Sci Environ Epidemiol. 2020; DOI: 10.1038/s41370-020-0252-0

Mass Spectrometry Methods

Barbas-Bernardos, C. et al. Development and validation of a high performance liquid chromatography-tandem mass spectrometry method for the absolute analysis of 17 alpha D-amino acids in cooked meals. Journal of chromatography A, 2020; 1611: 460598. DOI:10.1016/j.chroma.2019.460598

Letertre M. et al. Metabolic Phenotyping Using UPLC–MS and Rapid Microbore UPLC–IM–MS: Determination of the Effect of Different Dietary Regimes on the Urinary Metabolome of the Rat. Chromatographia, 2020;  83, 853–861. DOI:10.1007/s10337-020-03900-4

Whiley L, et al. 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. Anal Chem. 2019; 91(8):5207-5216. DOI: 10.1021/acs.analchem.8b05884

Barbas-Bernardos C, et al. Development and validation of a high performance liquid chromatography-tandem mass spectrometry method for the absolute analysis of 17 α D-amino acids in cooked meals. J Chromatogr A. 2019: 1611, 460598. DOI:10.1016/j.chroma.2019.460598

Nye LC, et al. 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 J Chromatogr A. 2019; 1602:386-396. DOI: 10.1016/j.chroma.2019.06.056

Gray N, et al. A validated UPLC-MS/MS assay for the quantification of amino acids and biogenicamines in rat urine. J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Feb 1;1106-1107:50-57. DOI:10.1016/j.jchromb.2018.12.028

King AM, et al Rapid profiling method for the analysis of lipids in human plasma using ion mobility enabled-reversed phase-ultra high performance liquid chromatography/ mass spectrometry. J Chromatogr A. 2020, 1611; 460597. DOI: 10.1016/j.chroma.2019.460597


Loo RL. et al. Strategy for improved characterisation of human metabolic phenotypes using a COmbined Multiblock Principal components Analysis with Statistical Spectroscopy (COMPASS). Bioinformatics, 2020. 1-8. DOI:10.1093/bioinformatics/btaa649


Garcia Perez I et al. Dietary metabotype modelling predicts individual responses to dietary interventions. Nat Food 2020; 1, 355–364. DOI: 10.1038/s43016-020-0092-z

Posma JM. Et al. Nutriome-metabolome relationships provide insights into dietary intake and metabolism. Nature food, 2020; 1, 426-436. DOI: 10.1038/s43016-020-0093-y

Petropoulou K. et al. A natural mutation in Pisum sativum L. (pea) alters starch assembly and improves glucose homeostasis in humans. Nat Food, 2020; 1, 693–704. DOI: 10.1038/s43016-020-00159-8

Eriksen R. et al. Dietary metabolite profiling brings new insight into the relationship between nutrition and metabolic risk: An IMI DIRECT study. EBioMedicine, 2020; 58, 102932. DOI:10.1016/j.ebiom.2020.102932

Gibson R, et al The association of fish consumption and its urinary metabolites with cardiovascular risk factors. Am J Clin Nutr. 2019, 111, 280-290. DOI: 10.1093/ajcn/nqz293

Byrne CS, et al. Effects of Inulin Propionate Ester Incorporated into Palatable Food Products on Appetite and Resting Energy Expenditure: A Randomised Crossover Study. Nutrients. 2019; 11(4). pii: E861. DOI: 10.3390/nu11040861


West KA et al. Longitudinal metabolic and gut bacterial profiling of pregnant women with previous bariatric surgery. Gut, 2020; 69, 1452-1459. DOI:10.1136/gutjnl-2019-319620

Ding NS. Et al. Metabonomics and the Gut Microbiome Associated With Primary Response to Anti-TNF Therapy in Crohn’s Disease. Journal of Crohn’s & colitis, 2020; 14, 1090-1102. DOI: 10.1093/ecco-jcc/jjaa039

Letertre MPM. Et al. A Two-Way Interaction between Methotrexate and the Gut Microbiota of Male Sprague-Dawley Rats. J Proteome Res, 2020; 19, 3326-3339. DOI:10.1021/acs.jproteome.0c00230

Martinez-Gili L. et al. Understanding the mechanisms of efficacy of fecal microbiota transplant in treating recurrent Clostridioides difficile infection and beyond: the contribution of gut microbial-derived metabolites. Gut microbes, 2020; 12, 1810531. DOI:10.1080/19490976.2020.1810531

Kundu P, et al. Neurogenesis and prolongevity signaling in young germ-free mice transplanted with the gut microbiota of old mice. Sci Transl Med. 2019; 11(518). pii: eaau4760. DOI: 10.1126/scitranslmed.aau4760

James K, et al. Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal. Sci Rep. 2019; 9(1):15427. DOI: 10.1038/s41598-019-51901-7

Lahiri S, et al. The gut microbiota influences skeletal muscle mass and function in mice. Sci Transl Med. 2019 Jul 24;11(502). pii: eaan5662. DOI: 10.1126/scitranslmed.aan5662

Barton W. et al. The effects of sustained fitness improvement on the gut microbiome: A longitudinal, repeated measures case-study approach. medRxiv 2020.06.04.20046292. DOI: 10.1002/tsm2.215

Cardiometabolic Disease

Lau, CHE. Et al. Metabolic Signatures of Gestational Weight Gain and Postpartum Weight Loss in a Lifestyle Intervention Study of Overweight and Obese Women. Metabolites, 2020; 10(12), 498. DOI: 10.3390/metabo10120498

Gray N. et al. UHPLC-MS-Based Lipidomic and Metabonomic Investigation of the Metabolic Phenotypes of Wild Type and Hepatic CYP Reductase Null (HRN) Mice. J Pharm Biomed Anal, 2020; 186, 113318. DOI: 10.1016/j.jpba.2020.113318

Onida S, et al. Metabolic Phenotyping in Venous Disease: The Need for Standardization. J Proteome Res. 2019 Nov 1;18(11):3809-3820. DOI: 10.1021/acs.jproteome.9b00460

Brial F, et al. Systems Genetics of Hepatic Metabolome Reveals Octopamine as a Target for Non-Alcoholic Fatty Liver Disease Treatment. Sci Rep. 2019; 9(1):3656. DOI:10.1038/s41598-019-40153-0

West K, et al. Longitudinal metabolic and gut bacterial profiling of pregnant women with previous bariatric surgery. Gut 2019; 69:1452-1459. DOI: 10.1136/gutjnl-2019-319620


Jiménez B, et al.  Neuroendocrine Neoplasms: Identification of Novel Metabolic Circuits of Potential Diagnostic Utility.Cancers (Basel). 2021; 13(3):E374. DOI: 10.3390/cancers13030374.

Koundouros N. et al. Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids. Cell, 2020; 181, 1596-1611 e27. DOI: 10.1016/j.cell.2020.05.053

Ocvirk S. et al. A prospective cohort analysis of gut microbial co-metabolism in Alaska Native and rural African people at high and low risk of colorectal cancer. Am J Clin Nutr, 2020; 111, 406-419. DOI: 10.1093/ajcn/nqz301

Dumennci OE, et al. Exploring Metabolic Consequences of CPS1 and CAD Dysregulation in Hepatocellular Carcinoma by Network Reconstruction. Journal of hepatocellular carcinoma, 2020; 7, 1-9. DOI: 10.2147/JHC.S239039

Seow WJ, et al. Association of Untargeted Urinary Metabolomics and Lung Cancer Risk Among Never-Smoking Women in China. JAMA Netw Open. 2019 Sep 4;2(9):e1911970. DOI:10.1001/jamanetworkopen.2019.11970


Whiley L, et al. Metabolic phenotyping reveals a reduction in the bioavailability of serotonin and kynurenine pathway metabolites in both the urine and serum of individuals living with Alzheimer’s disease. Alzheimers Res Ther. 2021; 13(1):20. DOI: 10.1186/s13195-020-00741-z.

Kurbatova N. et al. Urinary metabolic phenotyping for Alzheimer’s disease. Scientific reports, 2020; 10, 21745. DOI:10.1038/s41598-020-78031-9

Gastrointestinal Diseases

Gallagher K. et al. Metabolomic Analysis in Inflammatory Bowel Disease: A Systematic Review. Journal of Crohn’s & colitis. 2020; DOI: 10.1093/ecco-jcc/jjaa227