Raftery Lab Publications

2016

2015

  • Targeted Serum Metabolite Profiling and Sequential Metabolite Ratio Analysis for Colorectal Cancer Progression Monitoring.
    Zhu, J., Djukovic, D., Deng, L., Gu, H., Himmati, F., Chiorean, E.G., Raftery, D.: Targeted Serum Metabolite Profiling and Sequential Metabolite Ratio Analysis for Colorectal Cancer Progression Monitoring. Anal. Bioanal. Chem., 2015, Oct;407(26):7857-63
  • Night-Time Serum Tryptophan Metabolite Levels During Sleep in Patients With and Without Irritable Bowel Syndrome (IBS).
    Heitkemper, M.M., Han, C.J., Jarrett, M.E., Gu, H., Djukovic, D., Shulman, R.J., Raftery, D., Cain, K.C.: Night-Time Serum Tryptophan Metabolite Levels During Sleep in Patients With and Without Irritable Bowel Syndrome (IBS). Biol. Res. Nurs., 2015, Jul 7. pii: 1099800415594251
  • Metabolic Signatures of Bacterial Vaginosis.
    Srinivasan, S., Morgan, M., Fiedler, T., Djukovic, D., Hoffman, N., Raftery, D., Marrazzo, J., Fredricks, D.: Metabolic Signatures of Bacterial Vaginosis. mBio., 6:e00204-15. PMID:25873373, 2015
  • Aggression is Associated With Aerobic Glycolysis in the Honey Bee Brain.
    Chandrasekaran, S., Rittschof, C.C., Djukovic, D., Gu, H., Raftery, D., Price, N.D., Robinson, G.E.: Aggression is Associated With Aerobic Glycolysis in the Honey Bee Brain. Genes, Brain and Behavior, 12:158-166, 2015.
  • Targeted Metabolic Profiling of Wounds in Diabetic and Nondiabetic Mice.
    Sood RF, Gu H, Djukovic D, Deng L, Ga M, Muffley LA, Raftery D, Hocking AM. Targeted metabolic profiling of wounds in diabetic and nondiabetic mice. Wound Repair Regen. 2015 May;23(3):423-34. doi: 10.1111/wrr.12299. PubMed PMID:25845676.
  • Quantitative Detection of Nitric Oxide in Exhaled Human Breath by Extractive Electrospray Ionization Mass Spectrometry.
    Pan S, Tian Y, Li M, Zhao J, Zhu L, Zhang W, Gu H, Wang H, Shi J, Fang X, Li P, Chen H. Quantitative detection of nitric oxide in exhaled human breath by extractive electrospray ionization mass spectrometry. Sci Rep. 2015 Mar 4;5:8725. doi: 10.1038/srep08725. PubMed PMID: 25735640; PubMed Central PMCID: PMC4348632.
  • Metabolomics Method to Comprehensively Analyze Amino Acids in Different Domains.
    Gu H, Du J, Carnevale Neto F, Carroll PA, Turner SJ, Chiorean EG, Eisenman RN,Raftery D. Metabolomics method to comprehensively analyze amino acids in different domains. Analyst. 2015 Apr 21;140(8):2726-34. doi: 10.1039/c4an02386b. Epub 2015 Feb 20. PubMed PMID: 25699545; PubMed Central PMCID: PMC4380628.
  • Deregulated Myc Requires MondoA/Mlx for Metabolic Reprogramming and Tumorigenesis.
    Carroll PA, Diolaiti D, McFerrin L, Gu H, Djukovic D, Du J, Cheng PF, Anderson S, Ulrich M, Hurley JB, Raftery D, Ayer DE, Eisenman RN. Deregulated Myc requires MondoA/Mlx for metabolic reprogramming and tumorigenesis. Cancer Cell. 2015 Feb 9;27(2):271-85. doi: 10.1016/j.ccell.2014.11.024. Epub 2015 Jan 29. PubMed PMID: 25640402; PubMed Central PMCID: PMC4326605.
  • Fnip1 Regulates Skeletal Muscle Fiber Type Specification, Fatigue Resistance, and Susceptibility to Muscular Dystrophy.
    Reyes NL, Banks GB, Tsang M, Margineantu D, Gu H, Djukovic D, Chan J, TorresM, Liggitt HD, Hirenallur-S DK, Hockenbery DM, Raftery D, Iritani BM. Fnip1 regulates skeletal muscle fiber type specification, fatigue resistance, and susceptibility to muscular dystrophy. Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):424-9. doi: 10.1073/pnas.1413021112. Epub 2014 Dec 29. PubMed PMID: 25548157; PubMed Central PMCID: PMC4299192.
  • Standardizing the Experimental Conditions for using Urine in NMR-based Metabolomic Studies with a Particular Focus on Diagnostic Studies: A Review.
    Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review. Metabolomics. 2015;11(4):872-894. Epub 2014 Nov 21. Review. PubMed PMID: 26109927; PubMed Central PMCID: PMC4475544.
  • Exploring Metabolic Profile Differences between Colorectal Polyp Patients and Controls Using Seemingly Unrelated Regression.
    Chen C, Deng L, Wei S, Nagana Gowda GA, Gu H, Chiorean EG, Abu Zaid M, Harrison ML, Pekny JF, Loehrer PJ, Zhang D, Zhang M, Raftery D. Exploring Metabolic Profile Differences between Colorectal Polyp Patients and Controls Using Seemingly Unrelated Regression. J Proteome Res. 2015 Jun 5;14(6):2492-9. doi: 10.1021/acs.jproteome.5b00059. Epub 2015 May 13. PubMed PMID: 25919433.
  • Massive Glutamine Cyclization to Pyroglutamic Acid in Human Serum Discovered using NMR Spectroscopy.
    Nagana Gowda GA, Gowda YN, Raftery D. Massive glutamine cyclization to pyroglutamic acid in human serum discovered using NMR spectroscopy. Anal Chem. 2015 Apr 7;87(7):3800-5. doi: 10.1021/ac504435b. Epub 2015 Mar 17. PubMed PMID: 25746059; PubMed Central PMCID: PMC4479397.
  • Expanding the Limits of Human Blood Metabolite Quantitation using NMR Spectroscopy.
    Nagana Gowda GA, Gowda YN, Raftery D. Expanding the limits of human blood metabolite quantitation using NMR spectroscopy. Anal Chem. 2015 Jan 6;87(1):706-15. doi: 10.1021/ac503651e. Epub 2014 Dec 8. PubMed PMID: 25485990; PubMed Central PMCID: PMC4287831.

2014

  • Dai, D.F., Karunadharma, P.P., Chiao, Y.A., Basisty, N., Crispin D., Hsieh, E.J., Chen, T., Gu, H., Djukovic, D., Raftery, D., Beyer, R.P., MacCoss, M.J., Rabinovitch, P.S.: Altered Proteome Turnover and Remodeling by Subacute Caloric Restriction and Rapamycin Rejuvenate the Aging Heart, Aging Cell, 13:529-539, 2014.
  • Bowers, J., Hughes, E., Skill, M., Maluccio, M., Raftery, D.: Detection of Hepatocellular Carcinoma in Hepatitis C Patients: Biomarker Discovery by LC-MS, J. Chromatogr. B 966:154-162, 2014.
  • Nagana Gowda, G.A., Raftery, D.: Quantitative Metabolites in Protein Precipitated Serum Using NMR Spectroscopy. Anal. Chem. 86:5433-5440, 2014
  • Zhu, J., Djukovic, D., Deng, L., Gu, H., Himmati, F., Chiorean, E.G., Raftery, D.: Colorectal Cancer Detection using Targeted Serum Metabolic Profiling. J. Proteome Res. 13:4120-4130, 2014.
  • Abdul-Hamid Emwas, A.-H., Luchinat, C., Turano, P., Tenori, L., Roy, R., Salek, R.M., Ryan, D., Merzaban, J.S., Kaddurah-Daouk, R., Zeri, A.C., Nagana Gowda, G.A., Raftery, D., Wang, Y., Brennan, L., Wishart, D.S., “Standardizing the Experimental Conditions for using Urine in NMR-Based Metabolomic Studies with a Particular Focus on Diagnostic Studies: a Review,” Metabolomics, in press.
  • Carroll, P. Diolaiti, D., McFerrin, L., Gu, H., Djukovic, D., Du, D., Cheng, P.F., Anderson, S., Ulrich, M., Hurley, J.B., Raftery, D., Ayer, D.E., Eisenman, R.N.: Deregulated Myc Requires MondoA/Mlx for Metabolic Reprogramming and Tumorigenesis. Cancer Cell, in press.
  • Reyes, N.L., Banks, G.B., Tsang, M., Margineantu, D., Gu, H., Chan, J., Torres, M., Liggitt, H.D., Hockenbery, D.M., Raftery, D., Iritani, B.: Fnip1 Regulates Skeletal Muscle Fiber Type Specification, Fatigue Resistance, and Susceptibility to Muscular Dystrophy. PNAS, accepted.
  • Nagana Gowda, G.A., Gowda, Y.N., Raftery, D.: Expanding the Limits of Human Blood Metabolite Quantitation using NMR Spectroscopy. Anal. Chem. in press.
  • Raftery, D., ed., Mass Spectrometry in Metabolomics: Methods and Protocols, Methods in Molecular Biology, Vol. 1198. Humana Press/Springer Science. (2014). ISBN 978-1-4939-1257-5.
  • Nagana Gowda, G.A., Raftery, D.: Advances in NMR-Based Metabolomics. In Simo, C., Cifuentes, A., Garcia-Canas, V. (eds.): Fundamentals of Advanced Omics Technologies: From Genes to Metabolites. Elsevier, Amsterdam. 2014 pp 187-211.
  • Xi, B., Baniasadi, H., Raftery, D.: Statistical Analysis and Modeling of Mass Spectrometry-Based Metabolomics Data. In Raftery, D. (eds.): Methods in Molecular Biology. 2014; 1198: 333-53.
  • Zhang, S. Raftery, D.: Headspace SPME-GC-MS Metabolomics Analysis of Urinary Organic Compounds (VOCs). In Raftery, D. (eds.): Methods in Molecular Biology. 2014; 1198: 265-72.

2013

  • Wei, S., Liu, L., Zhang, J., Bowers, J., Nagana Gowda, G.A., Seeger, H., Fehm, T., Neubauer, H.J., Vogel, U., Clare, S.E., Raftery, D.: Metabolomics Approach for Predicting Response to Neoadjuvant Chemotherapy for Breast Cancer. Mol. Oncol. 7:297-307, 2013.
  • Thornton, J.M., Raftery, D.: Hydrogen Evolution by Templated Cadmium Indate Nanoparticles under Natural Sunlight Illumination. Int. J. Hydrogen Energy 38:7741–7749, 2013.
  • Zheng, W., Tayyari, F., Nagana Gowda, G.A., Raftery, D., McLamore, E.S., Shi, J., Porterfield, D.M., Donkin, S., Bequette, B., Teegarden, D.: 1, 25 Dihydroxyvitamin D Regulation of Glucose Metabolism in Harvey-ras Transformed MCF10A Human Breast Epithelial Cells. J. Steroid Biol. Molec. Biol. 138:81-89, 2013.
  • Appiah-Amponsah, E., Owusu-Sarfo, K., Nagana Gowda, G.A., Ye, T., Raftery, D.: Combining Hydrophilic Interaction Chromatography (HILIC) and Isotope Tagging for Off-Line LC-NMR Applications in Metabolite Analysis. Metabolites 3:575-591, 2013.
  • Baniasadi, H., Nagana Gowda, G.A., Gu, H., Zeng, A., Zhuang, S., Skill, N., Maluccio, M., Raftery, D.: Targeted Metabolic Profiling of Hepatocellular Carcinoma and Hepatitis C using LC-MS/MS. Electrophoresis, 34:2910-2917, 2013.
  • Zheng, W., Tayyari, F., Nagana Gowda, G.A., Raftery, D., McLamore , E.S., Shi, J., Porterfield, D.M., Bequette, B., Donkin, S., Teegarden, D.: Altered Glucose Metabolism in Harvey-ras Transformed MCF10A Cells. Mol Carcinogenesis. Published online Sept 2, 2013. DOI 10.1002/mc.22079.
  • Zhang, S., Myracle, A., Xiao, K., Yan, P., Ye, T., Janle, E., Raftery, D. Metabolic Profiling of Green Tea Treatments in Zucker Diabetic Rats Using 1H NMR. J. Nutr. Food. Sci. 3:1000239, 2013.
  • Nagana Gowda, G.A., Raftery, D.: Biomarker Discovery and Translation in Metabolomics, Current Metabolomics, 1:227-240, 2013.
  • Thornton, J.M., Raftery, D.: Photocatalysts for Solar Hydrogen Conversion. In Suib, S. (ed.): Photocatalysts for Solar Hydrogen Conversion, New and Future Developments in Catalysis. Solar Photocatalysis, 1st Ed. Elsevier. Amsterdam. 2013 ISBN: 9780444538727
  • Tayyari, F., Nagana Gowda, G.A., Gu, H., Raftery, D.: 15N-Cholamine – A Smart Isotope Tag for Combining NMR- and MS-Based Metabolite Profiling. Anal. Chem. 85:8715-8721, 2013.
  • Gu, H., Nagana Gowda, G.A., Carnevale Neto, F., Opp, M.R., Raftery, D.: RAMSY: Ratio Analysis of Mass Spectrometry to Improve Compound Identification, Anal. Chem. 85:10771-10779, 2013.
  • Kalyuzhnaya, M., Yang, S., Rozova, O., Smalley, N., Clubb, J., Lamb, A., Ajjappa, N.-G., Raftery, D., Fu, Y., Bringel, F., Vuilleumier, S., Beck, D.A.C., Trotsenko, Y.A., Khmelenina V.N., Lidstrom, M.E. Highly Efficient Methane Biocatalysis Revealed in a Methanotrophic Bacterium. Nature Comm. 4:2795, 2013.

2012

  • Gu, H., Nagana Gowda, G.A., Raftery, D.: Metabolic profiling: Are we en route to better diagnostic tests for cancer?  Future Oncology. In press.
  • Liu, L., Mo, H., Wei, S., Raftery, D.: Quantitative Analysis of Urea in Human Urine and Serum by 1H Nuclear Magnetic Resonance. Analyst 137:595-600, 2012.
  • Zhang, J., Bowers, J., Liu, L., Wei, S., Nagana Gowda, G.A., Hammoud, Z., Raftery, D.: Esophageal Cancer Metabolite Biomarkers Detected by LC-MS and NMR Methods. PlosOne. 7:e30181, 2012.
  • Ye, T., Zheng, C., Zhang, S., Nagana Gowda, G.A., Vitek, O., Raftery, D.: “Add to Subtract”: A Simple Method to Remove Complex Background Signals from the 1H Nuclear Magnetic Resonance Spectra of Mixtures, Analytical Chemistry 84:994-1002, 2012. PMCID: PMC3282557
  • Thornton, J.M., Raftery, D.: Efficient Photocatalytic Hydrogen Production by Platinum-Loaded Carbon-Doped Cadmium Indate Nanoparticles. ACS Appl. Mater. Interfaces 4:2426-2431,2012.
  • Blount, J.W., Ferruzzi, M., Raftery D., Pasinetti, G.M., Dixon, R.A.: Enzymatic Synthesis of Substituted Epicatechins for Bioactivity Studies in Neurological Disorders. Biochem. Biophys. Res. Comm. 417:457-461, 2012.
  • Wang, J., Ferruzzi, M.G., Ho, L., Blount, J., Janle, E.M., Gong, B., Pan, Y., Nagana Gowda, G.A., Raftery, D., Arrieta-Cruz, I., Sharma, V., Cooper, B., Lobo, J., Simon, J., Zhang, C., Cheng, A., Qian, X., Ono, K., Teplow, D., Pavlides, C., Dixon, R., and Pasinetti G.: Brain-Targeted Proanthocyanidin Metabolites for Alzheimer’s Disease Treatment. J. Neuroscience 32:5144-5150, 2012.  PMCID: PMC3348654
  • Wei, S., Suryani, Y., Nagana Gowda, G.A., Skill, N., Maluccio, M., Raftery, D.: Differentiating Hepatocellular Carcinoma from Hepatitis C Using Metabolite Profiling. Metabolites 2:701-716, 2012.
  • Wei, S., Liu, L., Zhang, J., Bowers, J., Nagana Gowda, G.A., Seeger, H., Fehm, T., Neubauer, H.J., Vogel, U., Clare, S.E., Raftery, D.: Metabolomics Approach for Predicting Response to Neoadjuvant Chemotherapy for Breast Cancer. Mol. Oncol. In press.
  • Gowda, G.A.N., Shanaiah, N., Raftery D.: Isotope enhanced approaches in metabolomics. Adv. Exp. Med. Biol. 992:147-64, 2012.