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Metabolomic and Lipidomic Biomarkers for Premalignant Liver Disease Diagnosis and Therapy.

Beyoğlu D, Idle JR.

Metabolites. 2020 Jan 28;10(2). pii: E50. doi: 10.3390/metabo10020050. Review.


Mass isotopomer-guided decluttering of metabolomic data to visualize endogenous biomarkers of drug toxicity.

Beyoğlu D, Zhou Y, Chen C, Idle JR.

Biochem Pharmacol. 2018 Oct;156:491-500. doi: 10.1016/j.bcp.2018.09.022. Epub 2018 Sep 20. Review.


Robust Regression Analysis of GCMS Data Reveals Differential Rewiring of Metabolic Networks in Hepatitis B and C Patients.

Simillion C, Semmo N, Idle JR, Beyoğlu D.

Metabolites. 2017 Oct 8;7(4). pii: E51. doi: 10.3390/metabo7040051.


A Novel Anti-Hepatitis C Virus and Antiproliferative Agent Alters Metabolic Networks in HepG2 and Hep3B Cells.

Keogh A, Şenkardeş S, Idle JR, Küçükgüzel ŞG, Beyoğlu D.

Metabolites. 2017 Jun 2;7(2). pii: E23. doi: 10.3390/metabo7020023.


Metabolic profiling by gas chromatography-mass spectrometry of energy metabolism in high-fat diet-fed obese mice.

Patel DP, Krausz KW, Xie C, Beyoğlu D, Gonzalez FJ, Idle JR.

PLoS One. 2017 May 16;12(5):e0177953. doi: 10.1371/journal.pone.0177953. eCollection 2017.


Metabolomic Analysis of Mice Exposed to Gamma Radiation Reveals a Systemic Understanding of Total-Body Exposure.

Golla S, Golla JP, Krausz KW, Manna SK, Simillion C, Beyoğlu D, Idle JR, Gonzalez FJ.

Radiat Res. 2017 May;187(5):612-629. doi: 10.1667/RR14592.1. Epub 2017 Mar 9.


The plasma lipidome in acute myeloid leukemia at diagnosis in relation to clinical disease features.

Pabst T, Kortz L, Fiedler GM, Ceglarek U, Idle JR, Beyoğlu D.

BBA Clin. 2017 Mar 8;7:105-114. doi: 10.1016/j.bbacli.2017.03.002. eCollection 2017 Jun.


The metabolomic profile of gamma-irradiated human hepatoma and muscle cells reveals metabolic changes consistent with the Warburg effect.

Wang M, Keogh A, Treves S, Idle JR, Beyoğlu D.

PeerJ. 2016 Jan 26;4:e1624. doi: 10.7717/peerj.1624. eCollection 2016.


Metabolomics reveals that aldose reductase activity due to AKR1B10 is upregulated in hepatitis C virus infection.

Semmo N, Weber T, Idle JR, Beyoğlu D.

J Viral Hepat. 2015 Jul;22(7):617-24. doi: 10.1111/jvh.12376. Epub 2014 Dec 9.


Disruption of tumor suppressor gene Hint1 leads to remodeling of the lipid metabolic phenotype of mouse liver.

Beyoğlu D, Krausz KW, Martin J, Maurhofer O, Dorow J, Ceglarek U, Gonzalez FJ, Dufour JF, Idle JR.

J Lipid Res. 2014 Nov;55(11):2309-19. doi: 10.1194/jlr.M050682. Epub 2014 Sep 5.


Metabolic profiling of praziquantel enantiomers.

Wang H, Fang ZZ, Zheng Y, Zhou K, Hu C, Krausz KW, Sun D, Idle JR, Gonzalez FJ.

Biochem Pharmacol. 2014 Jul 15;90(2):166-78. doi: 10.1016/j.bcp.2014.05.001. Epub 2014 May 10.


Noninvasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer.

Mathé EA, Patterson AD, Haznadar M, Manna SK, Krausz KW, Bowman ED, Shields PG, Idle JR, Smith PB, Anami K, Kazandjian DG, Hatzakis E, Gonzalez FJ, Harris CC.

Cancer Res. 2014 Jun 15;74(12):3259-70. doi: 10.1158/0008-5472.CAN-14-0109. Epub 2014 Apr 15.


Painting the liver with lasers: the future of liver histology?

Beyoğlu D, Idle JR.

Hepatology. 2014 Mar;59(3):757-60. doi: 10.1002/hep.26734. Epub 2013 Dec 4. No abstract available.


Identification of 2-piperidone as a biomarker of CYP2E1 activity through metabolomic phenotyping.

Cheng J, Chen C, Kristopher KW, Manna SK, Scerba M, Friedman FK, Luecke H, Idle JR, Gonzalez FJ.

Toxicol Sci. 2013 Sep;135(1):37-47. doi: 10.1093/toxsci/kft143. Epub 2013 Jun 28.


The metabolomic window into hepatobiliary disease.

Beyoğlu D, Idle JR.

J Hepatol. 2013 Oct;59(4):842-58. doi: 10.1016/j.jhep.2013.05.030. Epub 2013 May 25. Review.


Potential role of CYP2D6 in the central nervous system.

Cheng J, Zhen Y, Miksys S, Beyoğlu D, Krausz KW, Tyndale RF, Yu A, Idle JR, Gonzalez FJ.

Xenobiotica. 2013 Nov;43(11):973-84. doi: 10.3109/00498254.2013.791410. Epub 2013 Apr 25.


Metabolomics reveals aging-associated attenuation of noninvasive radiation biomarkers in mice: potential role of polyamine catabolism and incoherent DNA damage-repair.

Manna SK, Krausz KW, Bonzo JA, Idle JR, Gonzalez FJ.

J Proteome Res. 2013 May 3;12(5):2269-81. doi: 10.1021/pr400161k. Epub 2013 Apr 24.


Metabolomics reveals trichloroacetate as a major contributor to trichloroethylene-induced metabolic alterations in mouse urine and serum.

Fang ZZ, Krausz KW, Tanaka N, Li F, Qu A, Idle JR, Gonzalez FJ.

Arch Toxicol. 2013 Nov;87(11):1975-1987. doi: 10.1007/s00204-013-1053-1. Epub 2013 Apr 11.


Tissue metabolomics of hepatocellular carcinoma: tumor energy metabolism and the role of transcriptomic classification.

Beyoğlu D, Imbeaud S, Maurhofer O, Bioulac-Sage P, Zucman-Rossi J, Dufour JF, Idle JR.

Hepatology. 2013 Jul;58(1):229-38. doi: 10.1002/hep.26350. Epub 2013 May 8.


Cytochrome P450 regulation by α-tocopherol in Pxr-null and PXR-humanized mice.

Johnson CH, Bonzo JA, Cheng J, Krausz KW, Kang DW, Luecke H, Idle JR, Gonzalez FJ.

Drug Metab Dispos. 2013 Feb;41(2):406-13. doi: 10.1124/dmd.112.048009. Epub 2012 Nov 16.


Radiation metabolomics. 5. Identification of urinary biomarkers of ionizing radiation exposure in nonhuman primates by mass spectrometry-based metabolomics.

Johnson CH, Patterson AD, Krausz KW, Kalinich JF, Tyburski JB, Kang DW, Luecke H, Gonzalez FJ, Blakely WF, Idle JR.

Radiat Res. 2012 Oct;178(4):328-40. Epub 2012 Sep 6.


Novel metabolites and roles for α-tocopherol in humans and mice discovered by mass spectrometry-based metabolomics.

Johnson CH, Slanař O, Krausz KW, Kang DW, Patterson AD, Kim JH, Luecke H, Gonzalez FJ, Idle JR.

Am J Clin Nutr. 2012 Oct;96(4):818-30. Epub 2012 Sep 5.


Metabolomic markers for intestinal ischemia in a mouse model.

Fahrner R, Beyoğlu D, Beldi G, Idle JR.

J Surg Res. 2012 Dec;178(2):879-87. doi: 10.1016/j.jss.2012.08.011. Epub 2012 Aug 25.


Metabolomics and its potential in drug development.

Beyoğlu D, Idle JR.

Biochem Pharmacol. 2013 Jan 1;85(1):12-20. doi: 10.1016/j.bcp.2012.08.013. Epub 2012 Aug 23.


The glycine deportation system and its pharmacological consequences.

Beyoğlu D, Idle JR.

Pharmacol Ther. 2012 Aug;135(2):151-67. doi: 10.1016/j.pharmthera.2012.05.003. Epub 2012 May 11. Review.


Metabolomics reveals the metabolic map of procainamide in humans and mice.

Li F, Patterson AD, Krausz KW, Dick B, Frey FJ, Gonzalez FJ, Idle JR.

Biochem Pharmacol. 2012 May 15;83(10):1435-44. doi: 10.1016/j.bcp.2012.02.013. Epub 2012 Feb 24.


Dog bites man or man bites dog? The enigma of the amino acid conjugations.

Beyoğlu D, Smith RL, Idle JR.

Biochem Pharmacol. 2012 May 15;83(10):1331-9. doi: 10.1016/j.bcp.2011.12.031. Epub 2011 Dec 29.


Aberrant lipid metabolism in hepatocellular carcinoma revealed by plasma metabolomics and lipid profiling.

Patterson AD, Maurhofer O, Beyoglu D, Lanz C, Krausz KW, Pabst T, Gonzalez FJ, Dufour JF, Idle JR.

Cancer Res. 2011 Nov 1;71(21):6590-600. doi: 10.1158/0008-5472.CAN-11-0885. Epub 2011 Sep 7.


Xenobiotic metabolomics: major impact on the metabolome.

Johnson CH, Patterson AD, Idle JR, Gonzalez FJ.

Annu Rev Pharmacol Toxicol. 2012;52:37-56. doi: 10.1146/annurev-pharmtox-010611-134748. Epub 2011 Aug 3. Review.


UPLC-MS-based urine metabolomics reveals indole-3-lactic acid and phenyllactic acid as conserved biomarkers for alcohol-induced liver disease in the Ppara-null mouse model.

Manna SK, Patterson AD, Yang Q, Krausz KW, Idle JR, Fornace AJ, Gonzalez FJ.

J Proteome Res. 2011 Sep 2;10(9):4120-33. doi: 10.1021/pr200310s. Epub 2011 Jul 28.


Racemates revisited: heterochiral assemblies and the example of DL-thalidomide.

Hague DE, Idle JR, Mitchell SC, Smith RL.

Xenobiotica. 2011 Oct;41(10):837-43. doi: 10.3109/00498254.2011.590547. Epub 2011 Jul 5.


Metabolomics reveals attenuation of the SLC6A20 kidney transporter in nonhuman primate and mouse models of type 2 diabetes mellitus.

Patterson AD, Bonzo JA, Li F, Krausz KW, Eichler GS, Aslam S, Tigno X, Weinstein JN, Hansen BC, Idle JR, Gonzalez FJ.

J Biol Chem. 2011 Jun 3;286(22):19511-22. doi: 10.1074/jbc.M111.221739. Epub 2011 Apr 12.


Radiation metabolomics. 4. UPLC-ESI-QTOFMS-Based metabolomics for urinary biomarker discovery in gamma-irradiated rats.

Johnson CH, Patterson AD, Krausz KW, Lanz C, Kang DW, Luecke H, Gonzalez FJ, Idle JR.

Radiat Res. 2011 Apr;175(4):473-84. doi: 10.1667/RR2437.1. Epub 2011 Feb 10.


A comprehensive understanding of thioTEPA metabolism in the mouse using UPLC-ESI-QTOFMS-based metabolomics.

Li F, Patterson AD, Höfer CC, Krausz KW, Gonzalez FJ, Idle JR.

Biochem Pharmacol. 2011 Apr 15;81(8):1043-53. doi: 10.1016/j.bcp.2011.01.024. Epub 2011 Feb 12.


The production and composition of rat sebum is unaffected by 3 Gy gamma radiation.

Lanz C, Ledermann M, Slavík J, Idle JR.

Int J Radiat Biol. 2011 Apr;87(4):360-71. doi: 10.3109/09553002.2010.537432. Epub 2010 Dec 15.


Analysis of N1-acetyl-N2-formyl-5-methoxykynuramine/N1-acetyl-5-methoxy-kynuramine formation from melatonin in mice.

Niu S, Li F, Tan DX, Zhang L, Idle JR, Gonzalez FJ, Ma X.

J Pineal Res. 2010 Sep;49(2):106-14. doi: 10.1111/j.1600-079X.2010.00771.x. Epub 2010 May 27.


Comparative metabolism of cyclophosphamide and ifosfamide in the mouse using UPLC-ESI-QTOFMS-based metabolomics.

Li F, Patterson AD, Höfer CC, Krausz KW, Gonzalez FJ, Idle JR.

Biochem Pharmacol. 2010 Oct 1;80(7):1063-74. doi: 10.1016/j.bcp.2010.06.002. Epub 2010 Jun 10.


Identification of noninvasive biomarkers for alcohol-induced liver disease using urinary metabolomics and the Ppara-null mouse.

Manna SK, Patterson AD, Yang Q, Krausz KW, Li H, Idle JR, Fornace AJ Jr, Gonzalez FJ.

J Proteome Res. 2010 Aug 6;9(8):4176-88. doi: 10.1021/pr100452b.


Xenobiotic metabolism: a view through the metabolometer.

Patterson AD, Gonzalez FJ, Idle JR.

Chem Res Toxicol. 2010 May 17;23(5):851-60. doi: 10.1021/tx100020p. Review.


Control of steroid 21-oic acid synthesis by peroxisome proliferator-activated receptor alpha and role of the hypothalamic-pituitary-adrenal axis.

Wang T, Shah YM, Matsubara T, Zhen Y, Tanabe T, Nagano T, Fotso S, Krausz KW, Zabriskie TM, Idle JR, Gonzalez FJ.

J Biol Chem. 2010 Mar 5;285(10):7670-85. doi: 10.1074/jbc.M109.090175. Epub 2009 Dec 23.


Urinary metabolomics in Fxr-null mice reveals activated adaptive metabolic pathways upon bile acid challenge.

Cho JY, Matsubara T, Kang DW, Ahn SH, Krausz KW, Idle JR, Luecke H, Gonzalez FJ.

J Lipid Res. 2010 May;51(5):1063-74. doi: 10.1194/jlr.M002923. Epub 2009 Nov 9.


The role of mass spectrometry-based metabolomics in medical countermeasures against radiation.

Patterson AD, Lanz C, Gonzalez FJ, Idle JR.

Mass Spectrom Rev. 2010 May-Jun;29(3):503-21. doi: 10.1002/mas.20272. Review.


Radiation metabolomics. 2. Dose- and time-dependent urinary excretion of deaminated purines and pyrimidines after sublethal gamma-radiation exposure in mice.

Tyburski JB, Patterson AD, Krausz KW, Slavík J, Fornace AJ Jr, Gonzalez FJ, Idle JR.

Radiat Res. 2009 Jul;172(1):42-57. doi: 10.1667/RR1703.1.


Human urinary metabolomic profile of PPARalpha induced fatty acid beta-oxidation.

Patterson AD, Slanar O, Krausz KW, Li F, Höfer CC, Perlík F, Gonzalez FJ, Idle JR.

J Proteome Res. 2009 Sep;8(9):4293-300. doi: 10.1021/pr9004103.


Rifampicin-activated human pregnane X receptor and CYP3A4 induction enhance acetaminophen-induced toxicity.

Cheng J, Ma X, Krausz KW, Idle JR, Gonzalez FJ.

Drug Metab Dispos. 2009 Aug;37(8):1611-21. doi: 10.1124/dmd.109.027565. Epub 2009 May 21.


Fenofibrate metabolism in the cynomolgus monkey using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry-based metabolomics.

Liu A, Patterson AD, Yang Z, Zhang X, Liu W, Qiu F, Sun H, Krausz KW, Idle JR, Gonzalez FJ, Dai R.

Drug Metab Dispos. 2009 Jun;37(6):1157-63. doi: 10.1124/dmd.108.025817. Epub 2009 Feb 27.


Metabolomics reveals a novel vitamin E metabolite and attenuated vitamin E metabolism upon PXR activation.

Cho JY, Kang DW, Ma X, Ahn SH, Krausz KW, Luecke H, Idle JR, Gonzalez FJ.

J Lipid Res. 2009 May;50(5):924-37. doi: 10.1194/jlr.M800647-JLR200. Epub 2009 Jan 13.


A double transgenic mouse model expressing human pregnane X receptor and cytochrome P450 3A4.

Ma X, Cheung C, Krausz KW, Shah YM, Wang T, Idle JR, Gonzalez FJ.

Drug Metab Dispos. 2008 Dec;36(12):2506-12. doi: 10.1124/dmd.108.022723. Epub 2008 Sep 17.

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