Metabolomics – Publications


  1. Hsu PC, Lan RS, Brasky TM, Marian C, Cheema AK, Ressom HW, Loffredo CA, Pickworth WB, Shields PG.2017.Menthol Smokers: Metabolomic Profiling and Smoking Behavior.Cancer Epidemiol Biomarkers Prev.PubMed:27628308
  2. Hsu PC, Lan RS, Brasky TM, Marian C, Cheema AK, Ressom HW, Loffredo CA, Pickworth WB, Shields PG.2017.Metabolomic profiles of current cigarette smokers.Mol Carcinog. PubMed:27341184
  3. Mapstone M, Lin F, Nalls MA, Cheema AK, Singleton AB, Fiandaca MS, Federoff HJ.2017.What success can teach us about failure: the plasma metabolome of older adults with superior memory and lessons for Alzheimer’s disease.Neurobiol Aging. PubMed:27939698
  4. Pannkuk EL, Fornace AJ Jr, Laiakis EC.2017.Metabolomic applications in radiation biodosimetry: exploring radiation effects through small molecules.Int J Radiat Biol. PubMed:28067089


  1. Altadill T, Campoy I, Lanau L, Gill K, Rigau M, Gil-Moreno A, Reventos J, Byers S, Colas E, Cheema AK.2016.Enabling Metabolomics Based Biomarker Discovery Studies Using Molecular Phenotyping of Exosome-Like Vesicles. PLoS One.PMCID:PMC4790956
  2. Bhuvaneshwar K, Belouali A, Singh V, Johnson RM, Song L, Alaoui A, Harris MA, Clarke R, Weiner LM, Gusev Y, Madhavan S.2016.G-DOC Plus – an integrative bioinformatics platform for precision medicine. BMC Bioinformatics.PMCID:PMC4851789
  3. Boca SM, Nishida M, Harris M, Rao S, Cheema AK, Gill K, Seol H, Morgenroth LP, Henricson E, McDonald C, Mah JK, Clemens PR, Hoffman EP, Hathout Y, Madhavan S.2016.Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study. PLoS One.PMCID:PMC4833348
  4. Boerma M, Sridharan V, Mao XW, Nelson GA, Cheema AK, Koturbash I, Singh SP, Tackett AJ, Hauer-Jensen M.2016.Effects of ionizing radiation on the heart.Mutat Res.PMCID:PMC5144922
  5. Cao L, Liu P, Gill K, Reece EA, Cheema AK, Zhao Z.2016.Identification of novel cell survival regulation in diabetic embryopathy via phospholipidomic profiling. Biochem Biophys Res Commun.PMCID:PMC4756589
  6. Cheema AK, Maier I, Dowdy T, Wang Y, Singh R, Ruegger PM, Borneman J, Fornace AJ Jr, Schiestl RH.2016.Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis.PLoS One.PMCID:PMC4830457
  7. Chen Z, Coy SL, Pannkuk EL, Laiakis EC, Hall AB, Fornace AJ Jr, Vouros P.2016.Rapid and High-Throughput Detection and Quantitation of Radiation Biomarkers in Human and Nonhuman Primates by Differential Mobility Spectrometry-Mass Spectrometry.J Am Soc Mass Spectrom.PMCID: PMC5018447
  8. Goudarzi M, Chauthe S, Strawn SJ, Weber WM, Brenner DJ, Fornace AJ.2016.Quantitative Metabolomic Analysis of Urinary Citrulline and Calcitroic Acid in Mice after Exposure to Various Types of Ionizing Radiation.Int J Mol Sci.PMCID:PMC4881599
  9. Laiakis EC, Strawn SJ, Brenner DJ, Fornace AJ Jr.2016.Assessment of Saliva as a Potential Biofluid for Biodosimetry: A Pilot Metabolomics Study in Mice.Radiat Res.PubMed:27332953
  10. Laiakis EC, Pannkuk EL, Diaz-Rubio ME, Wang YW, Mak TD, Simbulan-Rosenthal CM, Brenner DJ, Fornace AJ Jr.2016.Implications of genotypic differences in the generation of a urinary metabolomics radiation signature. Mutat Res. PMCID:PMC4887295
  11. Mapstone M, Cheema AK, Zhong X, Fiandaca MS, Federoff HJ.2016.Biomarker validation: Methods and matrix matter.Alzheimers Dement.PubMed:28010950
  12. Matos Do Canto L, Marian C, Varghese RS, Ahn J, Da Cunha PA, Willey S, Sidawy M, Rone JD, Cheema AK, Luta G, Nezami Ranjbar MR, Ressom HW, Haddad BR.2016.Metabolomic profiling of breast tumors using ductal fluid.Int J Oncol.PMCID:PMC5117995
  13. Menon SS, Uppal M, Randhawa S, Cheema MS, Aghdam N, Usala RL, Ghosh SP, Cheema AK, Dritschilo A.2016.Radiation Metabolomics: Current Status and Future Directions.Front Oncol.PMCID:PMC4736121
  14. Pannkuk EL, Laiakis EC, Mak TD, Astarita G, Authier S, Wong K, Fornace AJ Jr.2016.A Lipidomic and Metabolomic Serum Signature from Nonhuman Primates Exposed to Ionizing Radiation.Metabolomics.PMCID: PMC5314995

  15. Pannkuk EL, Laiakis EC, Authier S, Wong K, Fornace AJ Jr.2016.Targeted metabolomics of nonhuman primate serum after exposure to ionizing radiation: potential tools for high-throughput biodosimetry.PMCID:PMC5373493


  1. Cheema AK, Asara JM, Wang Y, Neubert TA, Tolstikov V, Turck CW.2015.The ABRF Metabolomics Research Group 2013 Study: Investigation of Spiked Compound Differences in a Human Plasma Matrix.J Biomol Tech.PMCID:PMC4540151
  2. Fiandaca MS, Zhong X, Cheema AK, Orquiza MH, Chidambaram S, Tan MT, Gresenz CR, FitzGerald KT, Nalls MA, Singleton AB, Mapstone M, Federoff HJ.2015.Plasma 24-metabolite Panel Predicts Preclinical Transition to Clinical Stages of Alzheimer’s Disease.Front Neurol.PMCID:PMC4642213
  3. Goudarzi M, Weber WM, Mak TD, Chung J, Doyle-Eisele M, Melo DR, Strawn SJ, Brenner DJ, Guilmette RA, Fornace AJ Jr.2015.A Comprehensive Metabolomic Investigation in Urine of Mice Exposed to Strontium-90.Radiat Res.PMCID:PMC5320572
  4. Goudarzi M, Weber WM, Mak TD, Chung J, Doyle-Eisele M, Melo DR, Brenner DJ, Guilmette RA, Fornace AJ Jr.2015.Metabolomic and lipidomic analysis of serum from mice exposed to an internal emitter, cesium-137, using a shotgun LC-MS(E) approach.J Proteome Res.PMCID:PMC4286155
  5. Goudarzi M, Weber WM, Chung J, Doyle-Eisele M, Melo DR, Mak TD, Strawn SJ, Brenner DJ, Guilmette R, Fornace AJ Jr.2015.Serum Dyslipidemia Is Induced by Internal Exposure to Strontium-90 in Mice, Lipidomic Profiling Using a Data-Independent Liquid Chromatography-Mass Spectrometry Approach.J Proteome Res.PMCID: PMC5327919
  6. LaConti JJ, Laiakis EC, Mays AD, Peran I, Kim SE, Shay JW, Riegel AT, Fornace AJ Jr., Wellstein A.2015.Distinct serum metabolomics profiles associated with malignant progression in the KrasG12D mouse model of pancreatic ductal adenocarcinoma.BMC Genomics.PMCID:PMC4315147
  7. Laiakis EC, Trani D, Moon BH, Strawn SJ, Fornace AJ Jr.2015.Metabolomic profiling of urine samples from mice exposed to protons reveals radiation quality and dose specific differences.Radiat Res.PMCID:PMC4524563
  8. Li HH, Wang YW, Chen R, Zhou B, Ashwell JD, Fornace AJ Jr.2015.Ionizing Radiation Impairs T Cell Activation by Affecting Metabolic Reprogramming.Int J Biol Sci.PMCID:PMC4466454
  9. Mak TD, Tyburski JB, Krausz KW, Kalinich JF, Gonzalez FJ, Fornace AJ Jr.2015.Exposure to ionizing radiation reveals global dose- and time-dependent changes in the urinary metabolome of rat.Metabolomics.PMCID:PMC4635442
  10. Mak TD, Laiakis EC, Goudarzi M, Fornace AJ Jr.2015.Selective paired ion contrast analysis: a novel algorithm for analyzing postprocessed LC-MS metabolomics data possessing high experimental noise.Anal Chem.PMCID:PMC4519008
  11. Pannkuk EL, Laiakis EC, Authier S, Wong K, Fornace AJ Jr.2015.Global Metabolomic Identification of Long-Term Dose-Dependent Urinary Biomarkers in Nonhuman Primates Exposed to Ionizing Radiation.Radiat Res.PMCID:PMC4539133
  12. Pathak R, Cheema AK, Boca SM, Krager KJ, Hauer-Jensen M, Aykin-Burns N.2015.Modulation of Radiation Response by the Tetrahydrobiopterin Pathway.Antioxidants (Basel).PMCID:PMC4665563
  13. Prasun P, Young S, Salomons G, Werneke A, Jiang YH, Struys E, Paige M, Avantaggiati ML, McDonald M.2015.Expanding the Clinical Spectrum of Mitochondrial Citrate Carrier (SLC25A1) Deficiency: Facial Dysmorphism in Siblings with Epileptic Encephalopathy and Combined D,L-2-Hydroxyglutaric Aciduria.JIMD Rep.PMCID:PMC4501236
  14. Shajahan-Haq AN, Cheema MS, Clarke R.2015.Application of metabolomics in drug resistant breast cancer research.Metabolites.PMCID:PMC4381292


  1. Cheema AK, Pathak R, Zandkarimi F, Kaur P, Alkhalil L, Singh R, Zhong X, Ghosh S, Aykin-Burns N, Hauer-Jensen M.2014.Liver metabolomics reveals increased oxidative stress and fibrogenic potential in gfrp transgenic mice in response to ionizing radiation.J Proteome Res.PMCID:PMC4053308
  2. Cheema AK, Suman S, Kaur P, Singh R, Fornace AJ Jr., Datta K.2014.Long-term differential changes in mouse intestinal metabolomics after gamma and heavy ion radiation exposure.PLoS One.PMCID:PMC3903607
  3. Fiandaca MS, Mapstone ME, Cheema AK, Federoff HJ.2014.The critical need for defining preclinical biomarkers in Alzheimer’s disease.Alzheimers Dement.PubMed:24924671
  4. Goudarzi M, Weber W, Mak TD, Chung J, Doyle-Eisele M, Melo D, Brenner DJ, Guilmette RA, Fornace AJ.2014.Development of urinary biomarkers for internal exposure by cesium-137 using a metabolomics approach in mice.Radiat Res.PMCID:PMC4029349
  5. Goudarzi M, Mak TD, Chen C, Smilenov LB, Brenner DJ, Fornace AJ.2014.The effect of low dose rate on metabolomic response to radiation in mice.Radiat Environ Biophys.PMCID:PMC4206600
  6. Infantino V, Iacobazzi V, Menga A, Avantaggiati ML, Palmieri F.2014.A key role of the mitochondrial citrate carrier (SLC25A1) in TNFalpha- and IFNgamma-triggered inflammation.Biochim Biophys Acta.PMCID:PMC4346166
  7. Kolukula VK, Sahu G, Wellstein A, Rodriguez OC, Preet A, Lacobazzi V, D’Orazi G, Albanese C, Palmieri F, Avantaggiati ML.2014.SLC25A1, or CIC, is a novel transcriptional target of mutant p53 and a negative tumor prognostic marker.Oncotarget.PMCID:PMC4012738
  8. Laiakis EC, Mak TD, Anizan S, Amundson SA, Barker CA, Wolden SL, Brenner DJ, Fornace AJ Jr.2014.Development of a Metabolomic Radiation Signature in Urine from Patients Undergoing Total Body Irradiation.Radiat Res.PMCID:PMC4071158
  9. Laiakis EC, Strassburg K, Bogumil R, Lai S, Vreeken RJ, Hankemeier T, Langridge J, Plumb RS, Fornace AJ Jr., Astarita G.2014.Metabolic phenotyping reveals a lipid mediator response to ionizing radiation.J Proteome Res.PMCID:PMC4156265
  10. Li HH, Tyburski JB, Wang YW, Strawn S, Moon BH, Kallakury BV, Gonzalez FJ, Fornace AJ Jr.2014.Modulation of fatty acid and bile acid metabolism by peroxisome proliferator-activated receptor alpha protects against alcoholic liver disease.Alcohol Clin Exp Res.PMCID:PMC4047177
  11. Mak TD, Laiakis EC, Goudarzi M, Fornace AJ Jr.2014.MetaboLyzer: a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data.Anal Chem.PMCID:PMC3973431
  12. Mapstone M, Cheema AK, Fiandaca MS, Zhong X, Mhyre TR, MacArthur LH, Hall WJ, Fisher SG, Peterson DR, Haley JM, Nazar MD0, Rich SA, Berlau DJ, Peltz CB, Tan MT, Kawas CH, Federoff HJ.2014.Plasma phospholipids identify antecedent memory impairment in older adults.Nat Med.PubMed:24608097
  13. 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.2014.Noninvasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer.Cancer Res.PMCID:PMC4100625
  14. Sengupta M, Cheema A, Kaminski HJ, Kusner LL; Muscle Study Group.2014.Serum metabolomic response of myasthenia gravis patients to chronic prednisone treatment.PLoS One.PMCID:PMC4102553
  15. Shajahan-Haq AN, Cook KL, Schwartz-Roberts JL, Eltayeb AE, Demas DM, Warri AM, Facey CO, Hilakivi-Clarke LA, Clarke R.2014.MYC regulates the unfolded protein response and glucose and glutamine uptake in endocrine resistant breast cancer.Mol Cancer.PMCID:PMC4216870


  1. Avantaggiati ML.2013.Cancer metabolism as a therapeutic target: finding the right target(s) in the context of tumor heterogeneity, evolution, and metabolic plasticity.Oncology (Williston Park).PMCID:PMC4172372
  2. Cheema AK, Varghese RS, Timofeeva O, Zhang L, Kirilyuk A, Zandkarimi F, Kaur P, Ressom HW, Jung M, Dritschilo A.2013.Functional proteomics analysis to study ATM dependent signaling in response to ionizing radiation.Radiat Res.PMCID:PMC4301981
  3. Choudhury S, Kolukula VK, Preet A, Albanese C, Avantaggiati ML .2013.Dissecting the pathways that destabilize mutant p53: the proteasome or autophagy?.Cell Cycle.PMCID:PMC3646859
  4. Ghosh SP, Singh R, Chakraborty K, Kulkarni S, Uppal A, Luo Y, Kaur P, Pathak R, Kumar KS, Hauer-Jensen M, Cheema AK.2013.Metabolomic changes in gastrointestinal tissues after whole body radiation in a murine model.Mol Biosyst.PMCID:PMC3601576
  5. Goudarzi M, Koga T, Khozoie C, Mak TD, Kang BH, Fornace AJ Jr., Peters JM.2013.PPARbeta/delta modulates ethanol-induced hepatic effects by decreasing pyridoxal kinase activity.Toxicology.PMCID:PMC3811069
  6. Hsu PC, Zhou B, Zhao Y, Ressom HW, Cheema AK, Pickworth W, Shields PG.2013.Feasibility of identifying the tobacco-related global metabolome in blood by UPLC-QTOF-MS.J Proteome Res.PMCID:PMC3579455
  7. Kaur P, Rizk N, Ibrahim S, Luo Y, Younes N, Perry B, Dennis K, Zirie M, Luta G, Cheema AK.2013.Quantitative metabolomic and lipidomic profiling reveals aberrant amino acid metabolism in type 2 diabetes.Mol Biosyst.PubMed:23247761
  8. Laiakis EC, Hyduke DR, Fornace AJ.2013.Comparison of mouse urinary metabolic profiles after exposure to the inflammatory stressors gamma radiation and lipopolysaccharide.Radiat Res.PMCID:PMC3286010
  9. McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, McGovern DP, Fornace AJ Jr., Borneman J, Braun J.2013.Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships.Microbiome.PMCID:PMC3971612
  10. Yuan H, Lu J, Xiao J, Upadhyay G, Umans R, Kallakury B, Yin Y, Fant ME, Kopelovich L, Glazer RI.2013.PPARdelta induces estrogen receptor-positive mammary neoplasia through an inflammatory and metabolic phenotype linked to mTOR activation.Cancer Res.PMCID:PMC3723355


  1. Catalina-Rodriguez O, Kolukula VK, Tomita Y, Preet A, Palmieri F, Wellstein A, Byers S, Giaccia AJ, Glasgow E, Albanese C, Avantaggiati ML.2012.The mitochondrial citrate transporter, CIC, is essential for mitochondrial homeostasis.Oncotarget.PMCID:PMC3717962
  2. Girlanda R, Cheema AK, Kaur P, Kwon Y, Li A, Guerra J, Matsumoto CS, Zasloff M, Fishbein TM.2012.Metabolomics of human intestinal transplant rejection.Am J Transplant.PubMed:22759354
  3. Kaur P, Sheikh K, Kirilyuk A, Kirilyuk K, Kallakury B, Ressom HW, Cheema A .2012.Metabolomic profiling for biomarker discovery in pancreatic cancer.International Journal of Mass Spectrometry.International Journal of Mass Spectrometry.DOI: 10.1111/j.1600-6143.2012.04183.x
  4. Ressom HW, Xiao JF, Tuli L, Varghese RS, Zhou B, Tsai TH, Ranjbar MR, Zhao Y, Wang J, Di Poto C, Cheema AK, Tadesse MG, Goldman R, Shetty K.2012.Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis.Anal Chim Acta.Anal Chim Acta.PMCID:PMC3419576
  5. Xiao JF, Varghese RS, Zhou B, Nezami Ranjbar MR, Zhao Y, Tsai TH, Di Poto C, Wang J, Goerlitz D, Luo Y, Cheema AK, Sarhan N, Soliman H, Tadesse MG, Ziada DH, Ressom HW.2012.LC-MS based serum metabolomics for identification of hepatocellular carcinoma biomarkers in Egyptian cohort.J Proteome Res.PMCID:PMC3719870


  1. Cheema AK, Timofeeva O, Varghese R, Dimtchev A, Shiekh K, Shulaev V, Suy S, Collins S, Ressom H, Jung M, Dritschilo A.2011.Integrated analysis of ATM mediated gene and protein expression impacting cellular metabolism.J Proteome Res.PubMed:21322649
  2. Coy SL, Cheema AK, Tyburski JB, Laiakis EC, Collins SP, Fornace A Jr.2011.Radiation metabolomics and its potential in biodosimetry.Int J Radiat Biol.PMCID:PMC3572797
  3. Jung M, Timofeeva O, Cheema AK, Varghese R, Ressom H, Dritschilo A.2011.Human fibroblasts for large-scale “omics” investigations of ATM gene function.Adv Exp Med Biol.PMCID:PMC3744187
  4. Manna SK, Patterson AD, Yang Q, Krausz KW, Idle JR, Fornace AJ, Gonzalez FJ.2011.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.J Proteome Res.PMCID:PMC3170755
  5. Pollock CB, Yin Y, Yuan H, Zeng X, King S, Li X, Kopelovich L, Albanese C, Glazer RI.2011.PPARdelta activation acts cooperatively with 3-phosphoinositide-dependent protein kinase-1 to enhance mammary tumorigenesis.PLoS One.PMCID:PMC3020974
  6. Sheikh KD, Khanna S, Byers SW, Fornace A Jr, Cheema AK.2011.Small molecule metabolite extraction strategy for improving LC/MS detection of cancer cell metabolome.J Biomol Tech.PMCID:PMC3059537


  1. Laiakis EC, Morris GA, Fornace AJ, Howie SR.2010.Metabolomic analysis in severe childhood pneumonia in the Gambia, West Africa: findings from a pilot study.PLoS One.PMCID:PMC2936566
  2. Manna SK, Patterson AD, Yang Q, Krausz KW, Li H, Idle JR, Fornace AJ Jr., Gonzalez FJ.2010.Identification of noninvasive biomarkers for alcohol-induced liver disease using urinary metabolomics and the Ppara-null mouse.J Proteome Res.PMCID:PMC2917755
  3. Varghese RS, Cheema A, Cheema P, Bourbeau M, Tuli L, Zhou B, Jung M, Dritschilo A, Ressom HW.2010.Analysis of LC-MS data for characterizing the metabolic changes in response to radiation.J Proteome Res.PubMed:20329776


  1. Tyburski JB, Patterson AD, Krausz KW, Slavík J, Fornace AJ Jr., Gonzalez FJ, Idle JR.2009.Radiation metabolomics.2.Dose- and time-dependent urinary excretion of deaminated purines and pyrimidines after sublethal gamma-radiation exposure in mice.Radiat Res.PMCID: PMC2794378


  1. Glazer RI, Yuan H, Xie Z, Yin Y.2008.PPAR-gamma and PPAR-delta as modulators of neoplasia and cell fate.PPAR Res.PMCID:PMC2430014