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Analysis of Coenzymes and Antioxidants in Tissue and Blood Using 1D 1H NMR Spectroscopy.

Nagana Gowda GA, Raftery D.

Methods Mol Biol. 2019;2037:97-110. doi: 10.1007/978-1-4939-9690-2_6.


Analysis of Plasma, Serum, and Whole Blood Metabolites Using 1H NMR Spectroscopy.

Nagana Gowda GA, Raftery D.

Methods Mol Biol. 2019;2037:17-34. doi: 10.1007/978-1-4939-9690-2_2.


Overview of NMR Spectroscopy-Based Metabolomics: Opportunities and Challenges.

Nagana Gowda GA, Raftery D.

Methods Mol Biol. 2019;2037:3-14. doi: 10.1007/978-1-4939-9690-2_1.


Plasma metabolomics profiles suggest beneficial effects of a low-glycemic load dietary pattern on inflammation and energy metabolism.

Navarro SL, Tarkhan A, Shojaie A, Randolph TW, Gu H, Djukovic D, Osterbauer KJ, Hullar MA, Kratz M, Neuhouser ML, Lampe PD, Raftery D, Lampe JW.

Am J Clin Nutr. 2019 Aug 20. pii: nqz169. doi: 10.1093/ajcn/nqz169. [Epub ahead of print]


Perspective: Dietaryiomarkers of Intake and Exposure-Exploration with Omics Approaches.

Maruvada P, Lampe JW, Wishart DS, Barupal D, Chester DN, Dodd D, Djoumbou-Feunang Y, Dorrestein PC, Dragsted LO, Draper J, Duffy LC, Dwyer JT, Emenaker NJ, Fiehn O, Gerszten RE, B Hu F, Karp RW, Klurfeld DM, Laughlin MR, Little AR, Lynch CJ, Moore SC, Nicastro HL, O'Brien DM, Ordovás JM, Osganian SK, Playdon M, Prentice R, Raftery D, Reisdorph N, Roche HM, Ross SA, Sang S, Scalbert A, Srinivas PR, Zeisel SH.

Adv Nutr. 2019 Aug 6. pii: nmz075. doi: 10.1093/advances/nmz075. [Epub ahead of print]


Measuring cognitive insight in people with problematic substance use: An exploration of the factor validity of the Beck Cognitive Insight Scale.

Raftery D, Kelly PJ, Deane FP, Mcketin R, Baker AL, Turner A, Dean OM.

Drug Alcohol Rev. 2019 Jul 23. doi: 10.1111/dar.12966. [Epub ahead of print]


Characterization of aporphine alkaloids by electrospray ionization tandem mass spectrometry and DFT calculations.

Carnevale Neto F, Andreo MA, Raftery D, Lopes JLC, Lopes NP, Castro-Gamboa I, Lameiro de Noronha Sales Maia BH, Costa EV, Vessecchi R.

Rapid Commun Mass Spectrom. 2019 Jul 22. doi: 10.1002/rcm.8533. [Epub ahead of print]


Mass Spectral Similarity Networking and Gas-Phase Fragmentation Reactions in the Structural Analysis of Flavonoid Glycoconjugates.

Pilon AC, Gu H, Raftery D, Bolzani VDS, Lopes NP, Castro-Gamboa I, Carnevale Neto F.

Anal Chem. 2019 Aug 20;91(16):10413-10423. doi: 10.1021/acs.analchem.8b05479. Epub 2019 Jul 31.


Proteomic Analysis of Plasma Reveals Fat Mass Influences Cancer-Related Pathways in Healthy Humans Fed Controlled Diets Differing in Glycemic Load.

Garrison CB, Zhang Y, Navarro SL, Randolph TW, Hullar MAJ, Kratz M, Neuhouser ML, Raftery D, Lampe PD, Lampe JW.

Cancer Prev Res (Phila). 2019 Sep;12(9):567-578. doi: 10.1158/1940-6207.CAPR-19-0175. Epub 2019 Jul 2.


NMR Spectroscopy for Metabolomics Research.

Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS.

Metabolites. 2019 Jun 27;9(7). pii: E123. doi: 10.3390/metabo9070123. Review.


Metabolomic Characterization of Human Model of Liver Rejection Identifies Aberrancies Linked to Cyclooxygenase (COX) and Nitric Oxide Synthase (NOS).

Skill NJ, Elliott CM, Ceballos B, Saxena R, Pepin R, Bettcher L, Ellensberg M, Raftery D, Malucio MA, Ekser B, Mangus RS, Kubal CA.

Ann Transplant. 2019 Jun 11;24:341-349. doi: 10.12659/AOT.913800.


A study protocol for the N-ICE trial: A randomised double-blind placebo-controlled study of the safety and efficacy of N-acetyl-cysteine (NAC) as a pharmacotherapy for methamphetamine ("ice") dependence.

McKetin R, Dean OM, Turner A, Kelly PJ, Quinn B, Lubman DI, Dietze P, Carter G, Higgs P, Baker AL, Sinclair B, Reid D, Manning V, Te Pas N, Liang W, Thomas T, Bathish R, Kent M, Raftery D, Arunogiri S, Cordaro F, Hill H, Berk M.

Trials. 2019 Jun 4;20(1):325. doi: 10.1186/s13063-019-3450-0.


Polybrominated Diphenyl Ethers and Gut Microbiome Modulate Metabolic Syndrome-Related Aqueous Metabolites in Mice.

Scoville DK, Li CY, Wang D, Dempsey JL, Raftery D, Mani S, Gu H, Cui JY.

Drug Metab Dispos. 2019 Aug;47(8):928-940. doi: 10.1124/dmd.119.086538. Epub 2019 May 23.


PPARα contributes to protection against metabolic and inflammatory derangements associated with acute kidney injury in experimental sepsis.

Iwaki T, Bennion BG, Stenson EK, Lynn JC, Otinga C, Djukovic D, Raftery D, Fei L, Wong HR, Liles WC, Standage SW.

Physiol Rep. 2019 May;7(10):e14078. doi: 10.14814/phy2.14078.


Extractive Ratio Analysis NMR Spectroscopy for Metabolite Identification in Complex Biological Mixtures.

Paudel L, Nagana Gowda GA, Raftery D.

Anal Chem. 2019 Jun 4;91(11):7373-7378. doi: 10.1021/acs.analchem.9b01235. Epub 2019 May 14.


Towards quality assurance and quality control in untargeted metabolomics studies.

Beger RD, Dunn WB, Bandukwala A, Bethan B, Broadhurst D, Clish CB, Dasari S, Derr L, Evans A, Fischer S, Flynn T, Hartung T, Herrington D, Higashi R, Hsu PC, Jones C, Kachman M, Karuso H, Kruppa G, Lippa K, Maruvada P, Mosley J, Ntai I, O'Donovan C, Playdon M, Raftery D, Shaughnessy D, Souza A, Spaeder T, Spalholz B, Tayyari F, Ubhi B, Verma M, Walk T, Wilson I, Witkin K, Bearden DW, Zanetti KA.

Metabolomics. 2019 Jan 3;15(1):4. doi: 10.1007/s11306-018-1460-7.


Combining NMR and MS with Chemical Derivatization for Absolute Quantification with Reduced Matrix Effects.

Fei Q, Wang D, Jasbi P, Zhang P, Nagana Gowda GA, Raftery D, Gu H.

Anal Chem. 2019 Mar 19;91(6):4055-4062. doi: 10.1021/acs.analchem.8b05611. Epub 2019 Mar 11.


Metabolic profiling identifies phospholipids as potential serum biomarkers for schizophrenia.

Wang D, Cheng SL, Fei Q, Gu H, Raftery D, Cao B, Sun X, Yan J, Zhang C, Wang J.

Psychiatry Res. 2019 Feb;272:18-29. doi: 10.1016/j.psychres.2018.12.008. Epub 2018 Dec 7.


Breast cancer detection using targeted plasma metabolomics.

Jasbi P, Wang D, Cheng SL, Fei Q, Cui JY, Liu L, Wei Y, Raftery D, Gu H.

J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Jan 15;1105:26-37. doi: 10.1016/j.jchromb.2018.11.029. Epub 2018 Dec 3.


Dynamic Metabolic Response to Adriamycin-Induced Senescence in Breast Cancer Cells.

You R, Dai J, Zhang P, Barding GA Jr, Raftery D.

Metabolites. 2018 Dec 15;8(4). pii: E95. doi: 10.3390/metabo8040095.


Correction to "15N-Cholamine-A Smart Isotope Tag for Combining NMR- and MS-Based Metabolite Profiling".

Tayyari F, Gowda GAN, Gu H, Raftery D.

Anal Chem. 2019 Jan 2;91(1):1211. doi: 10.1021/acs.analchem.8b05631. Epub 2018 Dec 13. No abstract available.


Pharmacological Activation of PXR and CAR Downregulates Distinct Bile Acid-Metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis.

Dempsey JL, Wang D, Siginir G, Fei Q, Raftery D, Gu H, Yue Cui J.

Toxicol Sci. 2019 Mar 1;168(1):40-60. doi: 10.1093/toxsci/kfy271.


Age- and Genotype-Specific Effects of the Angiotensin-Converting Enzyme Inhibitor Lisinopril on Mitochondrial and Metabolic Parameters in Drosophila melanogaster.

Ederer KA, Jin K, Bouslog S, Wang L, Gorman GS, Rowe GC, Abadir P, Raftery D, Moellering D, Promislow D, Jumbo-Lucioni P, De Luca M.

Int J Mol Sci. 2018 Oct 26;19(11). pii: E3351. doi: 10.3390/ijms19113351.


Loneliness in Treatment-Seeking Substance-Dependent Populations: Validation of the Social and Emotional Loneliness Scale for Adults-Short Version.

Ingram I, Kelly PJ, Deane FP, Baker AL, Raftery DK.

J Dual Diagn. 2018 Oct-Dec;14(4):211-219. doi: 10.1080/15504263.2018.1498565. Epub 2018 Sep 28.


Salivary metabolite profiling distinguishes patients with oral cavity squamous cell carcinoma from normal controls.

Lohavanichbutr P, Zhang Y, Wang P, Gu H, Nagana Gowda GA, Djukovic D, Buas MF, Raftery D, Chen C.

PLoS One. 2018 Sep 20;13(9):e0204249. doi: 10.1371/journal.pone.0204249. eCollection 2018.


Chronic kidney disease attenuates the plasma metabolome response to insulin.

Roshanravan B, Zelnick LR, Djucovic D, Gu H, Alvarez JA, Ziegler TR, Gamboa JL, Utzschneider K, Kestenbaum B, Himmelfarb J, Kahn SE, Raftery D, de Boer IH.

JCI Insight. 2018 Aug 23;3(16). pii: 122219. doi: 10.1172/jci.insight.122219. eCollection 2018 Aug 23.


Glucose promotes cell growth by suppressing branched-chain amino acid degradation.

Shao D, Villet O, Zhang Z, Choi SW, Yan J, Ritterhoff J, Gu H, Djukovic D, Christodoulou D, Kolwicz SC Jr, Raftery D, Tian R.

Nat Commun. 2018 Jul 26;9(1):2935. doi: 10.1038/s41467-018-05362-7.


Detection of Succinate by Intestinal Tuft Cells Triggers a Type 2 Innate Immune Circuit.

Nadjsombati MS, McGinty JW, Lyons-Cohen MR, Jaffe JB, DiPeso L, Schneider C, Miller CN, Pollack JL, Nagana Gowda GA, Fontana MF, Erle DJ, Anderson MS, Locksley RM, Raftery D, von Moltke J.

Immunity. 2018 Jul 17;49(1):33-41.e7. doi: 10.1016/j.immuni.2018.06.016.


Loss of Fnip1 alters kidney developmental transcriptional program and synergizes with TSC1 loss to promote mTORC1 activation and renal cyst formation.

Centini R, Tsang M, Iwata T, Park H, Delrow J, Margineantu D, Iritani BM, Gu H, Liggitt HD, Kang J, Kang L, Hockenbery DM, Raftery D, Iritani BM.

PLoS One. 2018 Jun 13;13(6):e0197973. doi: 10.1371/journal.pone.0197973. eCollection 2018.


A Metabolomics Study of BPTES Altered Metabolism in Human Breast Cancer Cell Lines.

Nagana Gowda GA, Barding GA Jr, Dai J, Gu H, Margineantu DH, Hockenbery DM, Raftery D.

Front Mol Biosci. 2018 May 15;5:49. doi: 10.3389/fmolb.2018.00049. eCollection 2018.


PBDEs Altered Gut Microbiome and Bile Acid Homeostasis in Male C57BL/6 Mice.

Li CY, Dempsey JL, Wang D, Lee S, Weigel KM, Fei Q, Bhatt DK, Prasad B, Raftery D, Gu H, Cui JY.

Drug Metab Dispos. 2018 Aug;46(8):1226-1240. doi: 10.1124/dmd.118.081547. Epub 2018 May 16.


Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism.

Davis RJ, Gönen M, Margineantu DH, Handeli S, Swanger J, Hoellerbauer P, Paddison PJ, Gu H, Raftery D, Grim JE, Hockenbery DM, Margolin AA, Clurman BE.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):5462-5467. doi: 10.1073/pnas.1718338115. Epub 2018 May 7.


Multiplatform Metabolomics Investigation of Antiadipogenic Effects on 3T3-L1 Adipocytes by a Potent Diarylheptanoid.

Du D, Gu H, Djukovic D, Bettcher L, Gong M, Zheng W, Hu L, Zhang X, Zhang R, Wang D, Raftery D.

J Proteome Res. 2018 Jun 1;17(6):2092-2101. doi: 10.1021/acs.jproteome.8b00028. Epub 2018 May 3.


Colorectal Cancer Detection Using Targeted LC-MS Metabolic Profiling.

Djukovic D, Zhang J, Raftery D.

Methods Mol Biol. 2018;1765:229-240. doi: 10.1007/978-1-4939-7765-9_15.


Metabolic profiles of triple-negative and luminal A breast cancer subtypes in African-American identify key metabolic differences.

Tayyari F, Gowda GAN, Olopade OF, Berg R, Yang HH, Lee MP, Ngwa WF, Mittal SK, Raftery D, Mohammed SI.

Oncotarget. 2018 Feb 7;9(14):11677-11690. doi: 10.18632/oncotarget.24433. eCollection 2018 Feb 20.


Circulating bile acids in healthy adults respond differently to a dietary pattern characterized by whole grains, legumes and fruits and vegetables compared to a diet high in refined grains and added sugars: A randomized, controlled, crossover feeding study.

Ginos BNR, Navarro SL, Schwarz Y, Gu H, Wang D, Randolph TW, Shojaie A, Hullar MAJ, Lampe PD, Kratz M, Neuhouser ML, Raftery D, Lampe JW.

Metabolism. 2018 Jun;83:197-204. doi: 10.1016/j.metabol.2018.02.006. Epub 2018 Feb 17.


Transcriptome and DNA Methylome Analysis in a Mouse Model of Diet-Induced Obesity Predicts Increased Risk of Colorectal Cancer.

Li R, Grimm SA, Mav D, Gu H, Djukovic D, Shah R, Merrick BA, Raftery D, Wade PA.

Cell Rep. 2018 Jan 16;22(3):624-637. doi: 10.1016/j.celrep.2017.12.071.


Biomarker profiling for breast cancer detection: translational research to determine acceptance of a novel breast cancer screening technique.

Carcioppolo N, Christy KR, Jensen JD, King AJ, Goonewardene J, Raftery D.

Health Syst (Basingstoke). 2018 Jan 4;8(1):44-51. doi: 10.1080/20476965.2017.1414740. eCollection 2019.


NMR-Guided Mass Spectrometry for Absolute Quantitation of Human Blood Metabolites.

Nagana Gowda GA, Djukovic D, Bettcher LF, Gu H, Raftery D.

Anal Chem. 2018 Feb 6;90(3):2001-2009. doi: 10.1021/acs.analchem.7b04089. Epub 2018 Jan 9.


An open-label, non-randomized study of the pharmacokinetics of the nutritional supplement nicotinamide riboside (NR) and its effects on blood NAD+ levels in healthy volunteers.

Airhart SE, Shireman LM, Risler LJ, Anderson GD, Nagana Gowda GA, Raftery D, Tian R, Shen DD, O'Brien KD.

PLoS One. 2017 Dec 6;12(12):e0186459. doi: 10.1371/journal.pone.0186459. eCollection 2017.


Metabolomics and Gene Expression Analysis Reveal Down-regulation of the Citric Acid (TCA) Cycle in Non-diabetic CKD Patients.

Hallan S, Afkarian M, Zelnick LR, Kestenbaum B, Sharma S, Saito R, Darshi M, Barding G, Raftery D, Ju W, Kretzler M, Sharma K, de Boer IH.

EBioMedicine. 2017 Dec;26:68-77. doi: 10.1016/j.ebiom.2017.10.027. Epub 2017 Oct 31.


Altered metabolite levels and correlations in patients with colorectal cancer and polyps detected using seemingly unrelated regression analysis.

Chen C, Gowda GAN, Zhu J, Deng L, Gu H, Chiorean EG, Zaid MA, Harrison M, Zhang D, Zhang M, Raftery D.

Metabolomics. 2017 Nov;13(11). pii: 125. doi: 10.1007/s11306-017-1265-0. Epub 2017 Sep 15.


Plasma metabolite abundances are associated with urinary enterolactone excretion in healthy participants on controlled diets.

Miles FL, Navarro SL, Schwarz Y, Gu H, Djukovic D, Randolph TW, Shojaie A, Kratz M, Hullar MAJ, Lampe PD, Neuhouser ML, Raftery D, Lampe JW.

Food Funct. 2017 Sep 20;8(9):3209-3218. doi: 10.1039/c7fo00684e.


Human retinal pigment epithelial cells prefer proline as a nutrient and transport metabolic intermediates to the retinal side.

Chao JR, Knight K, Engel AL, Jankowski C, Wang Y, Manson MA, Gu H, Djukovic D, Raftery D, Hurley JB, Du J.

J Biol Chem. 2017 Aug 4;292(31):12895-12905. doi: 10.1074/jbc.M117.788422. Epub 2017 Jun 14.


Whole Blood Metabolomics by 1H NMR Spectroscopy Provides a New Opportunity To Evaluate Coenzymes and Antioxidants.

Nagana Gowda GA, Raftery D.

Anal Chem. 2017 Apr 18;89(8):4620-4627. doi: 10.1021/acs.analchem.7b00171. Epub 2017 Mar 30.


Candidate serum metabolite biomarkers for differentiating gastroesophageal reflux disease, Barrett's esophagus, and high-grade dysplasia/esophageal adenocarcinoma.

Buas MF, Gu H, Djukovic D, Zhu J, Onstad L, Reid BJ, Raftery D, Vaughan TL.

Metabolomics. 2017 Mar;13(3). pii: 23. doi: 10.1007/s11306-016-1154-y. Epub 2017 Jan 20.


Defective Branched-Chain Amino Acid Catabolism Disrupts Glucose Metabolism and Sensitizes the Heart to Ischemia-Reperfusion Injury.

Li T, Zhang Z, Kolwicz SC Jr, Abell L, Roe ND, Kim M, Zhou B, Cao Y, Ritterhoff J, Gu H, Raftery D, Sun H, Tian R.

Cell Metab. 2017 Feb 7;25(2):374-385. doi: 10.1016/j.cmet.2016.11.005.


Parenteral and enteral nutrition in surgical critical care: Plasma metabolomics demonstrates divergent effects on nitrogen, fatty-acid, ribonucleotide, and oxidative metabolism.

Parent BA, Seaton M, Djukovic D, Gu H, Wheelock B, Navarro SL, Raftery D, O'Keefe GE.

J Trauma Acute Care Surg. 2017 Apr;82(4):704-713. doi: 10.1097/TA.0000000000001381.


Recent Advances in NMR-Based Metabolomics.

Nagana Gowda GA, Raftery D.

Anal Chem. 2017 Jan 3;89(1):490-510. doi: 10.1021/acs.analchem.6b04420. Epub 2016 Dec 2. Review. No abstract available.


Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish.

Rabinowitz JS, Robitaille AM, Wang Y, Ray CA, Thummel R, Gu H, Djukovic D, Raftery D, Berndt JD, Moon RT.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E717-E726. doi: 10.1073/pnas.1620755114. Epub 2017 Jan 17.

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