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Bile Acid Profile and its Changes in Response to Cefoperazone Treatment in MR1 Deficient Mice.

Sun J, Cao Z, Smith AD, Carlson PE Jr, Coryell M, Chen H, Beger RD.

Metabolites. 2020 Mar 26;10(4). pii: E127. doi: 10.3390/metabo10040127.


Hepatic Transcript Profiles of Cytochrome P450 Genes Predict Sex Differences in Drug Metabolism.

Fuscoe JC, Vijay V, Hanig JP, Han T, Ren L, Greenhaw JJ, Beger RD, Pence LM, Shi Q.

Drug Metab Dispos. 2020 Mar 19. pii: dmd.119.089367. doi: 10.1124/dmd.119.089367. [Epub ahead of print]


Determination of structural factors affecting binding to mu, kappa and delta opioid receptors.

Slavov S, Mattes W, Beger RD.

Arch Toxicol. 2020 Feb 27. doi: 10.1007/s00204-020-02684-8. [Epub ahead of print]


Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite.

Bearden DW, Sheen DA, Simón-Manso Y, Benner BA Jr, Rocha WFC, Blonder N, Lippa KA, Beger RD, Schnackenberg LK, Sun J, Mehta KY, Cheema AK, Gu H, Marupaka R, Nagana Gowda GA, Raftery D.

Metabolites. 2019 Nov 7;9(11). pii: E270. doi: 10.3390/metabo9110270.


Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection.

Smith AD, Foss ED, Zhang I, Hastie JL, Giordano NP, Gasparyan L, VinhNguyen LP, Schubert AM, Prasad D, McMichael HL, Sun J, Beger RD, Simonyan V, Cowley SC, Carlson PE Jr.

PLoS One. 2019 Sep 27;14(9):e0223025. doi: 10.1371/journal.pone.0223025. eCollection 2019.


Stability of the Human Plasma Proteome to Pre-analytical Variability as Assessed by an Aptamer-Based Approach.

Daniels JR, Cao Z, Maisha M, Schnackenberg LK, Sun J, Pence L, Schmitt TC, Kamlage B, Rogstad S, Beger RD, Yu LR.

J Proteome Res. 2019 Oct 4;18(10):3661-3670. doi: 10.1021/acs.jproteome.9b00320. Epub 2019 Sep 12.


Metabolomics-based pathway changes in testis fragments treated with ethinylestradiol in vitro.

Sun J, Beger RD, Sloper DT, Nakamura N.

Birth Defects Res. 2019 Dec 1;111(20):1643-1654. doi: 10.1002/bdr2.1560. Epub 2019 Jul 26. Review.


Pharmacometabolomic Pathway Response of Effective Anticancer Agents on Different Diets in Rats with Induced Mammary Tumors.

Cao Z, Miller MS, Lubet RA, Grubbs CJ, Beger RD.

Metabolites. 2019 Jul 22;9(7). pii: E149. doi: 10.3390/metabo9070149.


Evaluation of the Performance of Lipidyzer Platform and Its Application in the Lipidomics Analysis in Mouse Heart and Liver.

Cao Z, Schmitt TC, Varma V, Sloper D, Beger RD, Sun J.

J Proteome Res. 2019 Jul 26. doi: 10.1021/acs.jproteome.9b00289. [Epub ahead of print]


Use cases, best practice and reporting standards for metabolomics in regulatory toxicology.

Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT, Kamp H, Leonards PEG, Loizou GD, MacRae JI, van Ravenzwaay B, Rocca-Serra P, Salek RM, Walk T, Weber RJM.

Nat Commun. 2019 Jul 10;10(1):3041. doi: 10.1038/s41467-019-10900-y. Review.


An Integrated Analysis of Metabolites, Peptides, and Inflammation Biomarkers for Assessment of Preanalytical Variability of Human Plasma.

Cao Z, Kamlage B, Wagner-Golbs A, Maisha M, Sun J, Schnackenberg LK, Pence L, Schmitt TC, Daniels JR, Rogstad S, Beger RD, Yu LR.

J Proteome Res. 2019 Jun 7;18(6):2411-2421. doi: 10.1021/acs.jproteome.8b00903. Epub 2019 May 22.


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.


Testicular function in cultured postnatal mouse testis fragments is similar to that of animals during the first wave of spermatogenesis.

Pence LM, Schmitt TC, Beger RD, Del Valle PL, Nakamura N.

Birth Defects Res. 2019 Mar 15;111(5):270-280. doi: 10.1002/bdr2.1451. Epub 2019 Jan 31.


Comparison of Effects of Diet on Mammary Cancer: Efficacy of Various Preventive Agents and Metabolomic Changes of Different Diets and Agents.

Lubet RA, Beger RD, Miller MS, Luster J, Seifried HE, Grubbs CJ.

Cancer Prev Res (Phila). 2018 Dec;11(12):831-840. doi: 10.1158/1940-6207.CAPR-18-0116. Epub 2018 Nov 20.


Aptamer-Based Proteomics Identifies Mortality-Associated Serum Biomarkers in Dialysis-Dependent AKI Patients.

Yu LR, Sun J, Daniels JR, Cao Z, Schnackenberg L, Choudhury D, Palevsky PM, Ma JZ, Beger RD, Portilla D.

Kidney Int Rep. 2018 May 3;3(5):1202-1213. doi: 10.1016/j.ekir.2018.04.012. eCollection 2018 Sep.


Computational identification of structural factors affecting the mutagenic potential of aromatic amines: study design and experimental validation.

Slavov SH, Stoyanova-Slavova I, Mattes W, Beger RD, Brüschweiler BJ.

Arch Toxicol. 2018 Jul;92(7):2369-2384. doi: 10.1007/s00204-018-2216-x. Epub 2018 May 19.


Immune response proteins as predictive biomarkers of doxorubicin-induced cardiotoxicity in breast cancer patients.

Yu LR, Cao Z, Makhoul I, Daniels JR, Klimberg S, Wei JY, Bai JP, Li J, Lathrop JT, Beger RD, Todorova VK.

Exp Biol Med (Maywood). 2018 Feb;243(3):248-255. doi: 10.1177/1535370217746383. Epub 2017 Dec 9.


Multiple microRNAs function as self-protective modules in acetaminophen-induced hepatotoxicity in humans.

Yu D, Wu L, Gill P, Tolleson WH, Chen S, Sun J, Knox B, Jin Y, Xiao W, Hong H, Wang Y, Ren Z, Guo L, Mei N, Guo Y, Yang X, Shi L, Chen Y, Zeng L, Dreval K, Tryndyak V, Pogribny I, Fang H, Shi T, McCullough S, Bhattacharyya S, Schnackenberg L, Mattes W, Beger RD, James L, Tong W, Ning B.

Arch Toxicol. 2018 Feb;92(2):845-858. doi: 10.1007/s00204-017-2090-y. Epub 2017 Oct 24.


Targeted metabolomic profiling indicates structure-based perturbations in serum phospholipids in children with acetaminophen overdose.

Bhattacharyya S, Pence L, Yan K, Gill P, Luo C, Letzig LG, Simpson PM, Kearns GL, Beger RD, James LP.

Toxicol Rep. 2016 Aug 23;3:747-755. doi: 10.1016/j.toxrep.2016.08.004. eCollection 2016.


Metabolomics Analysis of Urine Samples from Children after Acetaminophen Overdose.

Schnackenberg LK, Sun J, Bhattacharyya S, Gill P, James LP, Beger RD.

Metabolites. 2017 Sep 6;7(3). pii: E46. doi: 10.3390/metabo7030046.


Evaluation of metabolism of azo dyes and their effects on Staphylococcus aureus metabolome.

Sun J, Jin J, Beger RD, Cerniglia CE, Chen H.

J Ind Microbiol Biotechnol. 2017 Oct;44(10):1471-1481. doi: 10.1007/s10295-017-1970-8. Epub 2017 Aug 7.


Dose-response analysis of epigenetic, metabolic, and apical endpoints after short-term exposure to experimental hepatotoxicants.

Miousse IR, Murphy LA, Lin H, Schisler MR, Sun J, Chalbot MG, Sura R, Johnson K, LeBaron MJ, Kavouras IG, Schnackenberg LK, Beger RD, Rasoulpour RJ, Koturbash I.

Food Chem Toxicol. 2017 Nov;109(Pt 1):690-702. doi: 10.1016/j.fct.2017.05.013. Epub 2017 May 8.


3D-SDAR modeling of hERG potassium channel affinity: A case study in model design and toxicophore identification.

Stoyanova-Slavova IB, Slavov SH, Buzatu DA, Beger RD, Wilkes JG.

J Mol Graph Model. 2017 Mar;72:246-255. doi: 10.1016/j.jmgm.2017.01.012. Epub 2017 Jan 16.


Proteomic analysis of acetaminophen-induced hepatotoxicity and identification of heme oxygenase 1 as a potential plasma biomarker of liver injury.

Gao Y, Cao Z, Yang X, Abdelmegeed MA, Sun J, Chen S, Beger RD, Davis K, Salminen WF, Song BJ, Mendrick DL, Yu LR.

Proteomics Clin Appl. 2017 Jan;11(1-2). doi: 10.1002/prca.201600123. Epub 2016 Oct 28.


Metabolomics enables precision medicine: "A White Paper, Community Perspective".

Beger RD, Dunn W, Schmidt MA, Gross SS, Kirwan JA, Cascante M, Brennan L, Wishart DS, Oresic M, Hankemeier T, Broadhurst DI, Lane AN, Suhre K, Kastenmüller G, Sumner SJ, Thiele I, Fiehn O, Kaddurah-Daouk R; for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative.

Metabolomics. 2016;12(10):149. Epub 2016 Sep 2.


Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena.

Sun J, Jin J, Beger RD, Cerniglia CE, Yang M, Chen H.

Toxicol In Vitro. 2016 Oct;36:133-141. doi: 10.1016/j.tiv.2016.07.020. Epub 2016 Jul 30.


Early metabolomics changes in heart and plasma during chronic doxorubicin treatment in B6C3F1 mice.

Schnackenberg LK, Pence L, Vijay V, Moland CL, George N, Cao Z, Yu LR, Fuscoe JC, Beger RD, Desai VG.

J Appl Toxicol. 2016 Nov;36(11):1486-95. doi: 10.1002/jat.3307. Epub 2016 Mar 2.


CERAPP: Collaborative Estrogen Receptor Activity Prediction Project.

Mansouri K, Abdelaziz A, Rybacka A, Roncaglioni A, Tropsha A, Varnek A, Zakharov A, Worth A, Richard AM, Grulke CM, Trisciuzzi D, Fourches D, Horvath D, Benfenati E, Muratov E, Wedebye EB, Grisoni F, Mangiatordi GF, Incisivo GM, Hong H, Ng HW, Tetko IV, Balabin I, Kancherla J, Shen J, Burton J, Nicklaus M, Cassotti M, Nikolov NG, Nicolotti O, Andersson PL, Zang Q, Politi R, Beger RD, Todeschini R, Huang R, Farag S, Rosenberg SA, Slavov S, Hu X, Judson RS.

Environ Health Perspect. 2016 Jul;124(7):1023-33. doi: 10.1289/ehp.1510267. Epub 2016 Feb 23.


Circulating mitochondrial biomarkers for drug-induced liver injury.

Shi Q, Yang X, Mattes WB, Mendrick DL, Harrill AH, Beger RD.

Biomark Med. 2015;9(11):1215-23. doi: 10.2217/bmm.15.59. Epub 2015 Oct 28. Review.


Fructose Alters Intermediary Metabolism of Glucose in Human Adipocytes and Diverts Glucose to Serine Oxidation in the One-Carbon Cycle Energy Producing Pathway.

Varma V, Boros LG, Nolen GT, Chang CW, Wabitsch M, Beger RD, Kaput J.

Metabolites. 2015 Jun 16;5(2):364-85. doi: 10.3390/metabo5020364.


Translational biomarkers of acetaminophen-induced acute liver injury.

Beger RD, Bhattacharyya S, Yang X, Gill PS, Schnackenberg LK, Sun J, James LP.

Arch Toxicol. 2015 Sep;89(9):1497-522. doi: 10.1007/s00204-015-1519-4. Epub 2015 May 17. Review.


Metabolic fate of fructose in human adipocytes: a targeted 13C tracer fate association study.

Varma V, Boros LG, Nolen GT, Chang CW, Wabitsch M, Beger RD, Kaput J.

Metabolomics. 2015;11(3):529-544. Epub 2014 Aug 3.


Potential of extracellular microRNAs as biomarkers of acetaminophen toxicity in children.

Yang X, Salminen WF, Shi Q, Greenhaw J, Gill PS, Bhattacharyya S, Beger RD, Mendrick DL, Mattes WB, James LP.

Toxicol Appl Pharmacol. 2015 Apr 15;284(2):180-7. doi: 10.1016/j.taap.2015.02.013. Epub 2015 Feb 21.


Computational identification of a phospholipidosis toxicophore using (13)C and (15)N NMR-distance based fingerprints.

Slavov SH, Wilkes JG, Buzatu DA, Kruhlak NL, Willard JM, Hanig JP, Beger RD.

Bioorg Med Chem. 2014 Dec 1;22(23):6706-6714. doi: 10.1016/j.bmc.2014.08.021. Epub 2014 Aug 27.


Neuroprotective effect of the chemical chaperone, trehalose in a chronic MPTP-induced Parkinson's disease mouse model.

Sarkar S, Chigurupati S, Raymick J, Mann D, Bowyer JF, Schmitt T, Beger RD, Hanig JP, Schmued LC, Paule MG.

Neurotoxicology. 2014 Sep;44:250-62. doi: 10.1016/j.neuro.2014.07.006. Epub 2014 Jul 23.


Genetic associations with micronutrient levels identified in immune and gastrointestinal networks.

Morine MJ, Monteiro JP, Wise C, Teitel C, Pence L, Williams A, Ning B, McCabe-Sellers B, Champagne C, Turner J, Shelby B, Bogle M, Beger RD, Priami C, Kaput J.

Genes Nutr. 2014 Jul;9(4):408. doi: 10.1007/s12263-014-0408-4. Epub 2014 May 31.


Methylation potential associated with diet, genotype, protein, and metabolite levels in the Delta Obesity Vitamin Study.

Monteiro JP, Wise C, Morine MJ, Teitel C, Pence L, Williams A, McCabe-Sellers B, Champagne C, Turner J, Shelby B, Ning B, Oguntimein J, Taylor L, Toennessen T, Priami C, Beger RD, Bogle M, Kaput J.

Genes Nutr. 2014 May;9(3):403. doi: 10.1007/s12263-014-0403-9. Epub 2014 Apr 24.


Targeted liquid chromatography-mass spectrometry analysis of serum acylcarnitines in acetaminophen toxicity in children.

Bhattacharyya S, Yan K, Pence L, Simpson PM, Gill P, Letzig LG, Beger RD, Sullivan JE, Kearns GL, Reed MD, Marshall JD, Van Den Anker JN, James LP.

Biomark Med. 2014;8(2):147-59. doi: 10.2217/bmm.13.150.


Partial least square and k-nearest neighbor algorithms for improved 3D quantitative spectral data-activity relationship consensus modeling of acute toxicity.

Stoyanova-Slavova IB, Slavov SH, Pearce B, Buzatu DA, Beger RD, Wilkes JG.

Environ Toxicol Chem. 2014 Jun;33(6):1271-82. doi: 10.1002/etc.2534. Epub 2014 Apr 9.


Complementary PLS and KNN algorithms for improved 3D-QSDAR consensus modeling of AhR binding.

Slavov SH, Pearce BA, Buzatu DA, Wilkes JG, Beger RD.

J Cheminform. 2013 Nov 21;5(1):47. doi: 10.1186/1758-2946-5-47.


Metabolomics evaluation of the effects of green tea extract on acetaminophen-induced hepatotoxicity in mice.

Lu Y, Sun J, Petrova K, Yang X, Greenhaw J, Salminen WF, Beger RD, Schnackenberg LK.

Food Chem Toxicol. 2013 Dec;62:707-21. doi: 10.1016/j.fct.2013.09.025. Epub 2013 Sep 27.


Evaluating effects of penicillin treatment on the metabolome of rats.

Sun J, Schnackenberg LK, Khare S, Yang X, Greenhaw J, Salminen W, Mendrick DL, Beger RD.

J Chromatogr B Analyt Technol Biomed Life Sci. 2013 Aug 1;932:134-43. doi: 10.1016/j.jchromb.2013.05.030. Epub 2013 Jun 7.


Metabolomics as a tool for personalizing medicine: 2012 update.

Sun J, Beger RD, Schnackenberg LK.

Per Med. 2013 Mar;10(2):149-161. doi: 10.2217/pme.13.8.


A review of applications of metabolomics in cancer.

Beger RD.

Metabolites. 2013 Jul 5;3(3):552-74. doi: 10.3390/metabo3030552.


Metabolomics techniques in nanotoxicology studies.

Schnackenberg LK, Sun J, Beger RD.

Methods Mol Biol. 2012;926:141-56. doi: 10.1007/978-1-62703-002-1_10. Review.


Erratum: (13)C NMR-Distance Matrix Descriptors: Optimal Abstract 3D Space Granularity for Predicting Estrogen Binding.

Slavov SH, Geesaman EL, Pearce BA, Schnackenberg LK, Buzatu DA, Wilkes JG, Beger RD.

J Chem Inf Model. 2012 Sep 24;52(9):2484. Epub 2012 Aug 24. No abstract available.


Metabolomics evaluation of hydroxyproline as a potential marker of melamine and cyanuric acid nephrotoxicity in male and female Fischer F344 rats.

Schnackenberg LK, Sun J, Pence LM, Bhattacharyya S, Gamboa da Costa G, Beger RD.

Food Chem Toxicol. 2012 Nov;50(11):3978-83. doi: 10.1016/j.fct.2012.08.010. Epub 2012 Aug 10.


¹³C NMR-distance matrix descriptors: optimal abstract 3D space granularity for predicting estrogen binding.

Slavov SH, Geesaman EL, Pearce BA, Schnackenberg LK, Buzatu DA, Wilkes JG, Beger RD.

J Chem Inf Model. 2012 Jul 23;52(7):1854-64. doi: 10.1021/ci3001698. Epub 2012 Jun 22.


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