Publications


Lab technician

Publication Policy

We request that any publications, posters, or oral presentations resulting from work performed by The Metabolomics Innovation Centre acknowledge TMIC. This allows the Centre to report information to our funding agencies, such as impact on Canadian researchers. Clients should also keep us apprised of any publications, posters, or oral presentations arising from work performed at TMIC.


Publication List

2017

  1. Ramirez-Gaona, M., Marcu, A., Grant, J., Wu, A., Wishart, D.S. A Web Tool for Generating High Quality Machine-readable Biological Pathways. J Vis Exp (120). doi: 10.3791/54869 (2017) PubMed ID: 28287524
  2. Chen, D., Su, X., Li, Y., Yin, H., Li, L., Li, L. Chemical Isotope Labeling LC-MS for Monitoring Disease Progression and Treatment in Animal Models: Plasma Metabolomics Study of Osteoarthritis Rat Model. Sci Rep 7:40543. doi: 10.1038/srep40543 (2017) PubMed ID: 28091618
  3. Deng, L., Chang, D., Foshaug, R.R., Eisner, R., Tso, V.K., Wishart, D.S., Fedorak, R.N. Development and Validation of a High-Throughput Mass Spectrometry Based Urine Metabolomic Test for the Detection of Colonic Adenomatous Polyps. Metabolites. 7(3). pii: E32. doi: 10.3390/metabo7030032 (2017) PubMed ID: 28640228
  4. Mung, D., Li, L. Development of Chemical Isotope Labeling LC-MS for Milk Metabolomics: Comprehensive and Quantitative Profiling of the Amine/Phenol Submetabolome. Anal Chem. 89(8):4435-4443. doi: 10.1021/acs.analchem.6b03737 (2017) PubMed ID: 28306241
  5. Zhang, G., Deng, Q., Mandal, R., Wishart, D.S., Ametaj, B.N. DI/LC-MS/MS-Based Metabolic Profiling for Identification of Early Predictive Serum Biomarkers of Metritis in Transition Dairy Cows. J Agric Food Chem 65(38):8510-8521 doi: 10.1021/acs.jafc.7b02000 (2017) PubMed ID: 28862839
  6. Dragsted, L.O., Gao, Q., Praticò, G., Manach, C., Wishart, D.S., Scalbert, A., Feskens, E.,J.,M. Dietary and health biomarkers-time for an update. Genes Nutr. 12:24 doi: 10.1186/s12263-017-0578-y (2017) PubMed ID: 28974991
  7. Keshteli, A.H., van den Brand, F.F., Madsen, K.L., Mandal, R., Valcheva, R., Kroeker, K.I., Han, B., Bell, R.C., Cole, J., Hoevers, T., Wishart, D.S., Fedorak, R.N., Dieleman, L.A. Dietary and metabolomic determinants of relapse in ulcerative colitis patients: A pilot prospective cohort study. World J Gastroenterol. 23(21):3890-3899. doi: 10.3748/wjg.v23.i21.3890. (2017) PubMed ID: 28638229
  8. Singh, R., Bezuidenhout, L.W., Jemere, A., Brett, M.J., Harrison, D.,J. Engineering matrix-free laser desorption ionization mass spectrometry using glancing angle deposition films. Rapid Commun Mass Spectrom. 31(7):631-638. doi: 10.1002/rcm.7826. (2017) PubMed ID: 28075041
  9. Reynolds, L.A., Redpath, S.A., Yurist-Doutsch S, Gill N, Brown EM, van der Heijden, J., Brosschot, T.P., Han, J., Marshall, N.C., Woodward, S.E., Valdez, Y., Borchers, C.H., Perona-Wright, G., Finlay, B.B. Enteric helminths promote Salmonella co-infection by altering the intestinal metabolome J. Infect. Dis. 215(8):1245-1254. doi: 10.1093/infdis/jix141 (2017) PubMed ID: 28368463
  10. Adutwum, L.A., de la Mata, A.P., Bean, H.D., Hill, J.E., Harynuk, J.J. Estimation of start and stop numbers for cluster resolution feature selection algorithm: an empirical approach using null distribution analysis of Fisher ratios. Anal Bioanal Chem. 409(28):6699-6708. doi: 10.1007/s00216-017-0628-8 (2017) PubMed ID: 28963623
  11. Neveu, V., Moussy, A., Rouaix, H., Wedekind, R., Pon, A., Knox, C., Wishart, D.S., Scalbert, A. Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors. Nucleic Acids Res. D1(D979-84) DOI: 10.1093/nar/gkw980 (2017) PubMed ID: 27924041
  12. Bridgman, S.L., Azad, M.B., Field, C.J., Haqq, A.M., Becker, A.B., Mandhane, P.J., Subbarao, P., Turvey, S.E., Sears, M.R., Scott, J.A., Wishart, D.S., Kozyrskyj, A.L.; CHILD Study Investigators. Fecal Short-Chain Fatty Acid Variations by Breastfeeding Status in Infants at 4 Months: Differences in Relative versus Absolute Concentrations. Front Nutr. 4:11 doi: 10.3389/fnut.2017.00011 (2017) PubMed ID: 28443284
  13. Dervishi, E., Zhang, G., Mandal, R., Wishart, D.S., Ametaj, B.N. GC-MS Metabolomics Identifies Metabolite Alterations That Precede Subclinical Mastitis in the Blood of Transition Dairy Cows. J Proteome Res 16(2):433-446. doi: 10.1021/acs.jproteome.6b00538 (2017) PubMed ID: 28152597
  14. Schultz, M.C., Zhang, J., Luo, X., Savchenko, O., Li, L., Deyholos, M., Chen, J. Impact of Low-Intensity Pulsed Ultrasound on Transcript and Metabolite Abundance in Saccharomyces cerevisiae. J Proteome Res. 16(8):2975-2982. doi: 10.1021/acs.jproteome.7b00273 (2017) PubMed ID: 28616987
  15. Sung, M.M., Kim, T.T., Soltys, C.M., Hamza, S.M., Byrne, N.J., Masson, G., Park, H., Wishart, D.S., Madsen, K.L., Schertzer, J.D., Dyck, J.R. Improved Glucose Homeostasis in Obese Mice Treated With Resveratrol Is Associated With Alterations in the Gut Microbiome. Diabetes 66(2):418-425. doi: 10.2337/db16-0680 (2017) PubMed ID: 27903747
  16. Goldansaz, S.A., Guo, A.C., Sajed, T., Steele, M.A., Plastow, G.S., Wishart, D.S. Livestock metabolomics and the livestock metabolome: A systematic review. PLoS One. 12(5):e0177675. doi: 10.1371/journal.pone.0177675 (2017) PubMed ID: 28531195
  17. Lopatka, M., Sampat, A.A., Jonkers, S., Adutwum, L.A., Mol, H.G., van der Weg, G., Harynuk, J.J., Schoenmakers, P.J., van Asten, A., Sjerps, M.J., Vivó-Truyols, G. Local Ion Signatures (LIS) for the examination of comprehensive two-dimensional gas chromatography applied to fire debris analysis. Forensic Chemistry 3. dx.doi.org/10.1016/j.forc.2016.10.003 (2017)
  18. Ryan, P.M., London, L.E., Bjorndahl, T.C., Mandal, R., Murphy, K., Fitzgerald, G.F., Shanahan, F., Ross, R.P., Wishart, D.S., Caplice, N.M., Stanton, C. Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E(-/-) mice. Microbiome 5(1):30. doi: 10.1186/s40168-017-0246-x (2017) PubMed ID: 28285599
  19. Arndt, D., Marcu, A., Liang, Y., Wishart, D.S. PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. Brief Bioinform doi: 10.1093/bib/bbx121 (2017) PubMed ID: 29028989
  20. Peixoto, R.J.M., Alves, E.S., Wang, M., Ferreira, R.B.R., Granato, A., Han, J., Gill, H., Jacobson, K., Lobo, L.A., Domingues, R.M.C.P, Borchers, C.H., Davies, J.E., Finlay, B.B., Antunes, L.C.M. Repression of Salmonella host cell invasion by aromatic small molecules from the human fecal metabolome. Appl Environ Microbiol. pii: AEM.01148-17. doi: 10.1128/AEM.01148-17 (2017) PubMed ID: 28754707
  21. Zhou, Ya., Peng, C., Harris, K.D., Harrison, J. Salt Segregation and Sample Cleanup on Perfluoro-Coated Nanostructured Surfaces for Laser Desorption Ionization Mass Spectrometry of Biofluid Samples Analytical Chemistry 89:3362-3369. doi: 10.1021/acs.analchem.6b03934 (2017)
  22. Graham, S.F., Turkoglu, O., Kumar, P., Yilmaz, A., Bjorndahl, T.C., Han, B., Mandal, R., Wishart, D.S., Bahado-Singh, R.O. Targeted Metabolic Profiling of Post-Mortem Brain from Infants Who Died from Sudden Infant Death Syndrome. J Proteome Res. 16(7):2587-2596 doi: 10.1021/acs.jproteome.7b00157 (2017) PubMed ID: 28608686
  23. Dervishi, E., Zhang, G., Mandal, R., Wishart, D.S., Ametaj, B.N. Targeted metabolomics: new insights into pathobiology of retained placenta in dairy cows and potential risk biomarkers. Animal. 2017 Oct 16:1-10. doi: 10.1017/S1751731117002506 (2017) PubMed ID: 29032783
  24. DiBattista, A., McIntosh, N., Lamoureux, M., Al-Dirbashi, O.Y., Chakraborty, P., Britz-McKibbin, P. Temporal Signal Pattern Recognition in Mass Spectrometry: A Method for Rapid Identification and Accurate Quantification of Biomarkers for Inborn Errors of Metabolism with Quality Assurance. Anal Chem. 89(15):8112-8121 doi: 10.1021/acs.analchem.7b01727 (2017) PubMed ID: 28648083
  25. Yang, J., Wang, N., Chen, D., Yu, J., Pan, Q., Wang, D., Liu, J., Shi, X., Dong, X., Cao, H., Li, L., Li, L. The Impact of GFP Reporter Gene Transduction and Expression on Metabolomics of Placental Mesenchymal Stem Cells Determined by UHPLC-Q/TOF-MS. Stem Cells Int. 2017;2017:3167985. doi: 10.1155/2017/3167985 (2017) PubMed ID: 29230249
  26. Macedo, A.N., Mathiaparanam, S., Brick, L., Keenan, K., Gonska, T., Pedder, L., Hill, S., Britz-McKibbin, P. The Sweat Metabolome of Screen-Positive Cystic Fibrosis Infants: Revealing Mechanisms beyond Impaired Chloride Transport. ACS Cent Sci. 3(8):904-913. doi: 10.1021/acscentsci.7b00299 (2017) PubMed ID: 28852705
  27. Gruber, M.Y., Xia, J., Steppuhn, H., Wall, K., Messer, D., Sharpe, A.G., Acharya, S.N., Wishart, D.S., Johnson, D., Miller, D.R., Taheri, A. Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population. Genome 60(2):104-127. doi: 10.1139/gen-2016-0111 (2017) PubMed ID: 28045337
  28. Blydt-Hansen, T.D., Sharma, A., Wishart, D.S., Mandal, R., Ho, J., Nickerson, P., Rush, D. Urinary metabolomics for noninvasive detection of antibody-mediated rejection in children after kidney transplantation. Transplantation. doi: 10.1097/TP.0000000000001662 (2017) PubMed ID: 28121909
  29. Ramirez-Gaona, M., Marcu, A., Guo, A.C., Sajed, T., Wishart, N.A., Karu, N., Djoumbou-Feunang, Y., Arndt, D., Wishart, D.S. YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res 45(D1):D440-D445. doi: 10.1093/nar/gkw1058 (2017) PubMed ID: 27899612

2016

  1. Li, X., Augustine, A., Sun, D., Li, L., Fliegel, L. Activation of the Na+/H+ exchanger in isolated cardiomyocytes through β-Raf dependent pathways. Role of Thr653 of the cytosolic tail. J Mol Cell Cardiol. 99:65-75. doi: 10.1016/j.yjmcc.2016.08.014. (2016) PubMed ID: 27555478
  2. Yu, X., Esanu, M., MacKay, S., Chen, J., Sawan, M., Wishart, D.S., Hiebert, W. An impedance detection circuit for applications in a portable biosensor system. In Circuits and Systems (ISCAS), 2016 IEEE International Symposium on 2016 May (pp. 1518-1521). IEEE. (2016)
  3. Wishart, D.S., Mandal, R., Stanislaus, A. & Ramirez-Gaona, M. Cancer Metabolomics and the Human Metabolome Database. Metabolites 6, 1; doi: 10.3390/metabo6010010 (2016) PubMed ID: 26950159
  4. Bround, M.J., Wambolt, R., Cen, H., Asghari, P., Albu, R.F., Han, J., McAfee, D., Pourrier, M., Scott, N.E., Bohunek, L., Kulpa, J.E., Chen, S.R., Fedida, D., Brownsey, R.W., Borchers, C.H., Foster, L.J., Mayor, T., Moore, E.D., Allard, M.F., Johnson, J.D. Cardiac Ryanodine Receptor (Ryr2)-mediated Calcium Signals Specifically Promote Glucose Oxidation via Pyruvate Dehydrogenase. J. Biol. Chem. 291(45):23490-23505. doi: doi.org/10.1074/jbc.M116.756973 (2016) PubMed ID: 27621312
  5. Huan, T., Xian, J.W., Leung, W.N., Li, L., Chan, C.W. Cerebrospinal Fluid Metabolomics After Natural Product Treatment in an Experimental Model of Cerebral Ischemia. OMICS: A Journal of Integrative Biology. 2016 Oct 12. (2016) PubMed ID: 27732148
  6. Allen, F., Greiner, R., Wishart, D.S. CFM-ID applied to CASMI 2014 Current Metabolomics, June 2016 (2016)
  7. Zhao, S., Luo, X., Li, L. Chemical Isotope Labeling LC-MS for High Coverage and Quantitative Profiling of the Hydroxyl Submetabolome in Metabolomics. Anal Chem. 88(21):10617-10623. doi: 10.1021/acs.analchem.6b02967 (2016) PubMed ID: 27690392
  8. Oliynyk, A.O., Adutwum, L.A., Harynuk, J.J., Mar, A. Classifying Crystal Structures of Binary Compounds AB through Cluster Resolution Feature Selection and Support Vector Machine Analysis. Chem. Mater. 28(18):6672-81. (2016) PubMed ID: 19152631
  9. Djoumbou, Y.F., Eisner, R., Chepelev, L., Hastings, J., Owen, G., Fahy, E., Steinbeck, C., Subramanian, S., Bolton, E., Greiner, R., Wishart, D.S. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J Cheminform 8:61. doi: 10.1186/s13321-016-0174-y (2016) PubMed ID: 27867422
  10. Vazquez-Fresno, R., Llorach, R., Perera, A., Mandal, R., Feliz, M., Tinahones, F.J., Wishart, D.S. & Andres-Lacueva, C. Clinical phenotype clustering in cardiovascular risk patients for the identification of responsive metabotypes after red wine polyphenol intake. J Nutr Biochem. 28, 114-120. doi.org/10.1016/j.jnutbio.2015.10.002 (2016) PubMed ID: 26878788
  11. Bolduc, F.V., Lau, A., Rosenfelt, C.S., Langer, S., Wang, N., Smithson, L., Lefebvre, D., Alexander, R.T., Dickson, C.T., Li, L., Becker, A.B., Subbarao, P., Turvey, S.E., Pei, J., Sears, M.R., Mandhane, P.J. Cognitive Enhancement in Infants Associated with Increased Maternal Fruit Intake During Pregnancy: Results from a Birth Cohort Study with Validation in an Animal Model. EBioMedicine. 8:331-40. doi: 10.1016/j.ebiom.2016.04.025. (2016) PubMed ID: 27428442
  12. Hooton, K., Han, W., Li, L. Comprehensive and Quantitative Profiling of the Human Sweat Submetabolome Using High-Performance Chemical Isotope Labeling LC-MS. Anal Chem. 88(14): 7378-86. doi: 10.1021/acs.analchem.6b01930 (2016) PubMed ID: 27351466
  13. de la Mata, A.P., McQueen, R.H., Harynuk, J.J. Comprehensive two-dimensional gas chromatographic profiling and chemometric interpretation of the volatile profiles of sweat in knit fabrics. Anal Bioanal Chem. doi: 10.1007/s00216-016-0137-1 (2016) PubMed ID: 28028595
  14. Allen, F., Pon, A., Greiner, R., Wishart, D.S. Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification. Anal Chem. 88(15):7689-97. (2016) PubMed ID: 27381172
  15. Dias, D.A., Jones, O.A., Boughton, B.A., Benheim, D., Kouremenos, K.A., Wolfender, J.L., Wishart, D.S. Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems. Metabolites 6(4). doi: 10.3390/metabo6040046 (2016) PubMed ID: 27983674
  16. Su, X., Wang, N., Chen, D., Li, Y., Lu, Y., Huan, T., Xu, W., Li, L., Li, L. Dansylation isotope labeling liquid chromatography mass spectrometry for parallel profiling of human urinary and fecal submetabolomes. Anal Chim Acta. 903:100-9. doi: 10.1016/j.aca.2015.11.027 (2016) PubMed ID: 26709303
  17. Qiu, Y.L., Gong, J.Y., Wang, R.X., Han, J., Liu, T., Lu, Y., Li, L.T., Zhang, M.H., Sheps, J.A., Wang, N.L., Yan, Y.Y., Li, J.Q., Chen, L., Borchers, C.H., Sipos, B., Knisely, A.S., Ling, V., Xing, Q.H., Wang, J.S. Defects in MYO5B are associated with a spectrum of previously undiagnosed low γ-glutamyltransferase cholestasis. Hepatology. doi: 10.1002/hep.29020 (2016) PubMed ID: 28027573
  18. Ho, J., Sharma, A., Mandal, R., Wishart, D.S., Wiebe, C., Storsely, L., Karpinski, M., Gibson, I.W., Nickerson, P.W., Rush, D.N. Detecting Renal Allograft Inflammation Using Quantitative Urine Metabolomics and CXCL10. Transplant Direct 2 (6) doi: 10.1097/TXD.0000000000000589 (2016) PubMed ID: 27500268
  19. Weber, B.M., Walsh, P., Harynuk, J.J. Determination of Hydrocarbon Group-Type of Diesel Fuels by Gas Chromatography with Vacuum Ultraviolet Detection. Anal Chem. 88(11):5809-17. doi: 10.1021/acs.analchem.6b00383. (2016) PubMed ID: 27125997
  20. Sobsey, C.A., Han, J., Lin, K., Swardfager, W., Levitt, A., Borchers, C.H. Development and evaluation of a liquid chromatography-mass spectrometry method for rapid, accurate quantitation of malondialdehyde in human plasma. J Chromatogr B Analyt Technol Biomed Life Sci. 1029-1030:205-12. doi: 10.1016/j.jchromb.2016.07.013 (2016) PubMed ID: 27437618
  21. Shen, W., Han, W., Li, Y., Meng, Z., Cai, L., Li, L. Development of Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry for Silkworm Hemolymph Metabolomics. Anal. Chim. Acta. June. dx.doi.org/10.1016/j.aca.2016.06.004 (2016)
  22. Achaintre, D., Buleté, A., Cren-Olivé, C., Li, L., Rinaldi, S., Scalbert, A. Differential Isotope Labeling of 38 Dietary Polyphenols and Their Quantification in Urine by Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry. Anal Chem. 88(5): 2637-44. doi: 10.1021/acs.analchem.5b03609 (2016) PubMed ID: 26814424
  23. Sajed, T., Marcu, A., Ramirez, M., Pon, A., Guo, A., Knox, C., Wilson, M., Grant, J., Djoumbou, Y. & Wishart, D.S. ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 44, D495-D501. doi.org/10.1093/nar/gkv1060 (2016) PubMed ID: 26481353
  24. Yao, L., Shen, H., Wang, N., Tatlay, J., Li, L., Tan, T.W., Lee, Y.K. Elevated acetyl-CoA by amino acid recycling fuels microalgal neutral lipid accumulation in exponential growth phase for biofuel production. Plant Biotechnol J. Oct 1. doi: 10.1111/pbi.12648. (2016) PubMed ID: 27734577
  25. Wishart, D.S. Emerging applications of metabolomics in drug discovery and precision medicine. Nat. Rev. Drug Discov. 2016 doi:10.1038/nrd.2016.32. (2016) PubMed ID: 26965202
  26. Tarailo-Graovac, M., Shyr, C., Ross, C.J., Horvath, G.A., Salvarinova, R., Ye, X.C., Zhang, L.H., Bhavsar, A.P., Lee, J.J., Drögemöller, B.I., Abdelsayed, M., Alfadhel, M., Armstrong, L., Baumgartner, M.R., Burda, P., Connolly, M.B., Cameron, J., Demos, M., Dewan, T., Dionne, J., Evans, A.M., Friedman, J.M., Garber, I., Lewis, S., Ling, J., Mandal, R., Mattman, A., McKinnon, M., Michoulas, A., Metzger, D., Ogunbayo, O.A., Rakic, B., Rozmus, J., Ruben, P., Sayson, B., Santra, S., Schultz, K.R., Selby, K., Shekel, P., Sirrs, S., Skrypnyk, C., Superti-Furga, A., Turvey, S.E., Van Allen, M.I., Wishart, D.S., Wu, J., Wu, J., Zafeiriou, D., Kluijtmans, L., Wevers, R.A., Eydoux, P., Lehman, A.M., Vallance, H., Stockler-Ipsiroglu, S., Sinclair, G., Wasserman, W.W., van Karnebeek, C.D. Exome Sequencing and the Management of Neurometabolic Disorders. N Engl J Med. 374(23): 2246-55. doi: 10.1056/NEJMoa1515792. (2016) PubMed ID: 27276562
  27. Bahado-Singh, R.O., Syngelaki, A., Mandal, R., Bjorndahl, T.C., Li, L., Maulik, D., Han, B., Dong, E., Turkoglu, O., Zeb, Z., Redman, M., Wishart, D.S., Nicolaides, K.H. First-trimester metabolomics prediction of subsequent stillbirth. Am J Obstet Gynecol. 214(1):S89 - S90 (2016)
  28. Bridgman, S., Koleva, P., Mandal, R., Azad, M., Field, C., Haqq, A., Becker, A., Turvey, S., Mandhane, P., Subbarao, P., Sears, M. Gut Microbiota Metabolites in Infancy: Associations with Breastfeeding and Childhood Overweight. The FASEB Journal. 30:146-3. (2016)
  29. Babicki, S., Arndt, D., Marcu, A., Liang, Y., Grant, J.R., Maciejewski, A., Wishart, D.S. Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res. 44(W1): W147-53. doi: 10.1093/nar/gkw 419 (2016) PubMed ID: 27190236
  30. Luo, X., Zhao, S., Haun, T., Sun, D., Friis, R.M.N., Schultz, M.C., Li, L. High-Performance Chemical Isotope Labeling Liquid Chromatography−Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast. J Proteome Res. 15(5): 1602-12, doi: 10.1021/acs.jproteome.6b00070 (2016) PubMed ID: 26947805
  31. Bahado-Singh, R.O., Graham, S.F., Turkoglu, O., Beauchamp, K., Bjorndahl, T.C., Han, B., Mandal, R., Pantane, J., Kowalenko, T., Wishart, D.S., Stahel, P.F. Identification of candidate biomarkers of brain damage in a mouse model of closed head injury: a metabolomic pilot study. Metabolomics 12:42. doi: 10.1007/s11306-016-0957-1 (2016)
  32. Labeeuw, L., Khey, J., Bramucci, A.R., Atwal, H., de la Mata, A.P., Harynuk, J.J., Case, R.J. Indole-3-Acetic Acid Is Produced by Emiliania huxleyi Coccolith-Bearing Cells and Triggers a Physiological Response in Bald Cells. Front Microbiol. 7:828. doi: 10.3389/fmicb.2016.00828 (2016) PubMed ID: 27375567
  33. Manrai, A.K., Cui, Y., Bushel, P.R., Hall, M., Karakitsios, S., Mattingly, C., Ritchie, M., Schmitt, C., Sarigiannis, D.A., Thomas, D.C., Wishart, D.S. Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health Annu Rev Public Health. 38(1). Doi: 10.1146/annurev-publhealth-082516-012737 (2016) PubMed ID: 28068484
  34. Pham, H.T., Arnhard, K., Asad, Y.J., Deng, L., Felder, T.K., John-Williams, L.S., Kaever, V., Leadley, M., Mitro, N., Muccio, S., Prehn, C. Inter-Laboratory Robustness of Next-Generation Bile Acid Study in Mice and Humans: International Ring Trial Involving 12 Laboratories. The Journal of Applied Laboratory Medicine: An AACC Publication. 2016 Aug 23:jalm-2016. (2016)
  35. Wishart, D.S. Introduction to Cheminformatics. Curr Protoc Bioinformatics. 53:14.1.1-14.1.21. doi: 10.1002/0471250953.bi1401s18 (2016) PubMed ID: 27010335
  36. Hsin, M.K., Zamel, R., Cypel, M., Wishart, D.S., Han, B., Keshavjee, S., Liu, M.Y. Metabolic Profile of Ex Vivo Lung Perfusate Yields Biomarkers for Lung Transplant Outcomes. Annals of Surgery (2016)
  37. Graham, S.F., Kumar, P.K., Bjorndahl, T., Han, B., Yilmaz, A., Sherman, E., Bahado-Singh, R.O., Wishart, D.S., Mann, D., Green, B.D. Metabolic signatures of Huntingtons disease (HD): (1)H NMR analysis of the polar metabolome in post-mortem human brain. Biochim Biophys Acta. 2016 Sep; 1862(9): 1675-84. doi: 10.1016/j.bbadis.2016.06.007 (2016) PubMed ID: 27288730
  38. Huan, T., Troyer, D.A., Li, L. Metabolite Analysis and Histology on the Exact Same Tissue: Comprehensive Metabolomic Profiling and Metabolic Classification of Prostate Cancer. Sci Rep. 6:32272. doi: 10.1038/srep32272. (2016) PubMed ID: 27578275
  39. Bahado-Singh, R.O., Syngelaki, A., Mandal, R., Graham, S.F., Akolekar, R., Han, B., Bjondahl, T.C., Dong, E., Bauer, S., Alpay-Savasan, Z., Turkoglu, O., Ogunyemi, D., Poon, L.C., Wishart, D.S., Nicolaides, K.H. Metabolomic determination of pathogenesis of late-onset preeclampsia. J Matern Fetal Neonatal Med. 28:1-7. doi.org/10.1080/14767058.2016.1185411 (2016) PubMed ID: 27569705
  40. Wang, X., Han, J., Yang, J., Pan, J., Borchers, C.H. Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF). Biochim Biophys Acta. doi: 10.1016/j.bbapap.2016.12.012 (2016) PubMed ID: 28017863
  41. Beger, R.D., Dunn, W., Schmidt, M.A., Gross, S.S., Kirwan, J.A., Cascante, M., Brennan, L., Wishart, D.S., Oresic, M., Hankemeier, T., Broadhurst, D.I., Lane, A.N., Suhre, K., Kastenmüller, G., Sumner, S.J., Thiele, I., Fiehn, O., Kaddurah-Daouk, R. Metabolomics enables precision medicine: A White Paper, Community Perspective. Metabolomics. 12(10):149 (2016) PubMed ID: 27642271
  42. Han, J., Yi, Y., Lin, K., Birks, S.J., Gibson, J.J., Borchers, C.H. Molecular profiling of naphthenic acids in technical mixtures and oil sands process-affected water using polar reversed-phase liquid chromatography-mass spectrometry. Electrophoresis. 2016 Oct 1. doi: 10.1002/elps.201600250. (2016) PubMed ID: 27667503
  43. Venkatasubramanian, A., Sauer, V.T., Roy, S.K., Xia, M., Wishart, D.S., Hiebert, W.K. Nano-optomechanical systems for gas chromatography. Nano Lett. 16(11): 6975-81. doi: 10.1021/acs.nanolett.6b03066 (2016) PubMed ID: 27749074
  44. Wu, Y., Streijger, F., Lin G, Christie S, Mac-Thiong JM, Parent S, Bailey CS, Paquette S, Boyd MC, Ailon T, Street J, Fisher CG, Dvorak MF, Kwon BK, Li L Parallel Metabolomic Profiling of Cerebrospinal Fluid and Serum for Identifying Biomarkers of Injury Severity after Acute Human Spinal Cord Injury. Sci Rep 6:38718. doi: 10.1038/srep38718 (2016) PubMed ID: 27966539
  45. Arndt, D., Grant, J.R., Marcu, A., Sajed, T., Pon, A., Liang, Y., Wishart, D.S. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44 (W1): W16-21 (2016) PubMed ID: 27141966
  46. Berger, R.D., Dunn, W., Schmidt, M.A., Gross, S.S., Kirwan, J.A., Cascante, M., Brennan, L., Wishart, D.S., Oresic, M., Hankemeier, T., Broadhurst, D.I., Lane, A.N., Suhre, K., Kastenmaller, G., Sumner, S.J., Thiele, I., Fiehn, O., Kaddurah-Daouk, R. Precision Medicine and Pharmacometabolomics Task Group - Metabolomics Society Initiative. Metabolomics enables precision medicine: """"A White Paper, Community Perspective"""" Metabolomics 12(10):149. doi: dx.doi.org/10.1007/s11306-016-1094-6 (2016) PubMed ID: 27642271
  47. Webster, R.L., Rawson, P.M., Evans, D.J., Marriott, P.J. Quantification of trace fatty acid methyl esters in diesel fuel by using multidimensional gas chromatography with electron and chemical ionization mass spectrometry. J Sep Sci. 39(13):2537-43. doi: 10.1002/jssc.201600307. (2016) PubMed ID: 27159197
  48. Han, J., Lin, K., Sequria, C., Yang, J., Borchers, C.H. Quantitation of low molecular weight sugars by chemical derivatization-liquid chromatography/multiple reaction monitoring/mass spectrometry. Electrophoresis. 37(13): 1851-60. doi: 10.1002/elps.201600150 (2016) PubMed ID: 27120558
  49. Baker, T.C., Han, J., Borchers, C.H. Recent advancements in matrix-assisted laser desorption/ionization mass spectrometry imaging. Curr. Opin. Biotechnol. 43:62-69. doi: 10.1016/j.copbio.2016.09.003 (2016) PubMed ID: 27690313
  50. Emwas, A.H., Roy, R., McKay, R.T., Ryan, D., Brennan, L., Tenori, L., Luchinat, C., Gao, X., Zeri, A.C., Gowda, G.A., Raftery, D., Steinbeck, C., Salek, R.M. & Wishart, D.S. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J. Proteome Res. 15(2), 360-373. doi: 10.1021/acs.jproteome.5b00885 (2016) PubMed ID: 26745651
  51. Wu, Y., Li, L. Sample normalization methods in quantitative metabolomics. J Chromatogr A. 1430: 80-95. doi: 10.1016/j.chroma.2015.12.007 (2016) PubMed ID: 26763302
  52. Wu, Y., Li, L. Sample normalization methods in quatitative metabolomics Journal of Chromatography. A, A:80-95. doi: dx.doi.org/10.1016/j.chroma.2015.12.007 (2016)
  53. Janusson, E., McGarvey, G.B., Islam, F., Rowan, C., McIndoe, J.S. Selective mass spectrometric analysis of thiols using charge-tagged disulfides. Analyst. 141(19):5520-6. doi: 10.1039/c6an01210h. (2016) PubMed ID: 27390787
  54. Bahado-Singh, R.O., Graham, S.F., Han, B., Turkoglu, O., Ziadeh, J., Mandal, R., Er, A., Wishart, D.S., Stahel, P.L. Serum metabolomic markers for traumatic brain injury: a mouse model. Metabolomics. 12(6):1-2 (2016)
  55. Hermansen, P., MacKay, S., Wishart, D.S., Chen, J. Simulations and design of microfabricated interdigitated electrodes for use in a gold nanoparticle enhanced biosensor. Engineering in Medicine and Biology Society (EMBC), 2016 IEEE 38th Annual International Conference of the 2016 Oct 18 (pp. 299-302). IEEE. (2016)
  56. Wohlgemuth, G., Mehta, S.S., Neumann, S., Pedrosa, D., Pluskal, T., Schymanski, E.L., Willighagen, E.L., Wilson, M., Wishart, D.S., Arita, M., Dorrestein, P.C., Bandeira, N., Wang, M., Schulze, T., Salek, R.M., Steinbeck, C., Nainala, V.C., Mistrik, R., Nishioka, T., Fiehn, O. SPLASH, a hashed identifier for mass spectra. Nat Biotechnol 34(11):1099-1101. doi: 10.1038/nbt.3689 (2016) PubMed ID: 27824832
  57. Ametaj, B.N., G. Zhang, E. Dervishi, S. M. Dunn, R. Mandal and D. S. Wishart Targeted Metabolomics Reveals multiple metabolite alterations in the urine of transition dairy cows preceding the incidence of lameness Journal of Animal Science 94(5):72-73. doi: 10.2527/jam2016-0150 (2016)
  58. Markley, J.L., Brüschweiler, R., Edison, A.S., Eghbalnia, H.R., Powers, R., Raftery, D., Wishart, D.S. The future of NMR-based metabolomics. Curr Opin Biotechnol. 43:34-40. doi: 10.1016/j.copbio.2016.08.001. (2016) PubMed ID: 27580257
  59. Lee, X.Q., Sandercock, P.M.L. & Harynuk, J.J. The influence of temperature on the pyrolysis of household materials. Anal. Appl. Pyrolysis. 118, 75-85 (2016)
  60. Wishart, D.S., Wu, A. Using DrugBank for In Silico Drug Exploration and Discovery. Curr Protoc Bioinformatics. 54:14.4.1-14.4.31. doi: 10.1002/cpbi.1. (2016) PubMed ID: 27322405
  61. Xia, J., Wishart, D.S. Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis. Curr Protoc Bioinformatics. 55:14.10.1-14.10.91. doi: 10.1002/cpbi.11. (2016) PubMed ID: 27603023

2015

  1. Han, J., Lin, K., Sequeira, C. & Borchers, C.H. An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography-tandem mass spectrometry. Anal Chim Acta. 854, 86-94 (2015) PubMed ID: 25479871
  2. Han, J., Parker, C., Borchers, C.H. Chemical derivatization to enhance metabolomic analysis by LC/ESI-MS. """"Advanced LC-MS Applications in Metabolomics"""", May 2015 Future Science. doi: org/10.4155/fseb2013.13.80 (2015)
  3. Allen, F., Greiner, R., Wishart, D.S. Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics 11, 98-110 (2015)
  4. Ravanbakhsh, S., Liu, P., Bjordahl, T.C., Mandal, R., Grant, J.R., Wilson, M., Eisner, R., Sinelnikov, I., Hu, X., Luchinat, C., Greiner, R. & Wishart, D.S. Correction: Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics. PloS One. 10, e0132873 (2015) PubMed ID: 26222058
  5. Huan, T. & Li, L. Counting Missing Values in a Metabolite-Intensity Data Set for Measuring the Analytical Performance of a Metabolomics Platform. Anal. Chem. 87, 1306-1313 (2015) PubMed ID: 25496403
  6. Sirrs, S., Peng, X., Shyr, C., Tarailo-Graovac, M., Mandal, R., Testa, D., Dubin, D., Carbonetti, G., Glynn, S.E., Sayson, B., Robinson, W.P., Han, B., Wishart, D.S., Ross, C.J., Wasserman, W.W., Hurwitz, T.A., Sinclair, G., Kaczocha, M., van Karnebeek C.D. Defects in fatty acid amide hydrolase 2 associated with developmental and psychiatric disorders. Mol. Genet. Metabolism. 114:355-356. (2015)
  7. Sirrs, S., van Karnebeek C.D., Peng, X., Shyr, C., Tarailo-Graovac, M., Mandal, R., Testa, D., Dubin, D., Carbonetti, G., Glynn, S.E., Sayson, B., Robinson, W.P., Han, B., Wishart, D.S., Ross, C.J., Wasserman, W.W., Hurwitz, T.A., Sinclair, G., Kaczocha, M. Defects in fatty acid amide hydrolase 2 in a male with neurologic and psychiatric symptoms. Orphanet J. Rare Dis. 10:38. (2015) PubMed ID: 25885783
  8. Xu, W., Chen, D., Wang, N., Zhang, T., Zhou, R., Huan, T., Lu, Y., Su, X., Xie, Q., Li, L. & Li, L. Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Human Fecal Metabolome. Anal. Chem. 87, 829-836 (2015) PubMed ID: 25486321
  9. Zhou, R., Huan, T. & Li, L. Development of versatile isotopic labeling reagents for profiling the amine submetabolome by liquid chromatography mass spectrometry. Anal. Chim. Acta. 881, 107-116 (2015) PubMed ID: 26041526
  10. Brown, E.M., Wlodarska, M., Willing, B.P., Vonaesch, P., Han, J., Reynolds, L.A., Arrieta, M.C., Uhrig, M., Scholz, R., Partida, O., Borchers, C.H., Sansonetti, P.J., Finlay, B.B. Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model. Nat. Commun. 6, 7806 (2015) PubMed ID: 26241678
  11. Huan, T., Wu, Y., Tang, C., Lin, G. & Li, L. DnsID in MyCompoundID for Rapid Identification of Dansylated Amine- and Phenol-Containing Metabolites in LC-MS-Based Metabolomics. Anal. Chem. 87, 9838-9845. doi: 10.1021/acs.analchem.5b02282 (2015) PubMed ID: 26327437
  12. Zhou, R. & Li, L. Effects of sample injection amount and time-of-flight mass spectrometric detection dynamic range on metabolome analysis by high-performance chemical isotope labeling LC-MS. J. Proteomics 118, 130-139 (2015) PubMed ID: 25134441
  13. Yang, K., Hashemi, Z., Han, W., Jin, A., Yang, H., Ozga, J., Li, L. & Chan, C. Hydrolysis enhances bioavailability of proanthocyanidin-derived metabolites and improves β-cell function in glucose intolerant rats. J Nutr Biochem. 26, 850-859 (2015) PubMed ID: 25987165
  14. Wishart, D.S. Identifying putative drug targets and potential drug leads: starting points for virtual screening and docking. Methods Mol. Biol. 1215:425-444 (2015) PubMed ID: 25330974
  15. Wishart, D.S. Is Cancer a Genetic Disease or a Metabolic Disease? EBioMedicine 2, 478-479 (2015) PubMed ID: 26288805
  16. Abou El-Magd, R.M., Vozza, N.F., Tuszynski, J.A. & Wishart, D.S. Isolation of soluble scFv antibody fragments specific for small biomarker molecule, L-Carnitine, using phage display. J. of Immunol. Methods. 428, 9-19. doi: 10.1016/j.jim.2015.11.006 (2015) PubMed ID: 26608419
  17. Han, W. & Li, L. Matrix effect on chemical isotope labeling and its implication in metabolomic sample preparation for quantitative metabolomics. Metabolomics 11(6), 1733-1742. doi: 10.1007/s11306-015-0826-3 (2015)
  18. Xia, J., Sinelnikov, I.V., Han, B. & Wishart, D.S. MetaboAnalyst 3.0--making metabolomics more meaningful. Nucleic Acids Res. 43, W251-W257 (2015) PubMed ID: 25897128
  19. Han, J., Liu, Y., Wang, R., Yang, J., Ling, V. & Borchers, C.H. Metabolic Profiling of Bile Acids in Human and Mouse Blood by LC-MS/MS in Combination with Phospholipid-Depletion Solid-Phase Extraction. Anal Chem. 87, 1127-1136 (2015) PubMed ID: 25496250
  20. Fatima, T., Kesari, V., Watt, I., Wishart, D.S., Todd, J.F., Schroeder, W.R., Paliyath, G., Krishna, P. Metabolite profiling and expression analysis of flavonoid, vitamin C and tocopherol biosynthesis genes in the antioxidant-rich sea buckthorn (Hippophae rhamnoides L.) Phytochemistry. 118:181-91 (2015) PubMed ID: 26318327
  21. Hagel, J.M., Mandal, R., Han, B., Han, J., Dinsmore, D.R., Borchers, C.H., Wishart, D.S. & Facchini, P.J. Metabolome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants. BMC Plant Biol. 15:220 (2015) PubMed ID: 26369413
  22. Zordoky, B.N., Sung, M.M., Ezekowitz, J., Mandal, R., Han, B., Bjorndahl, T.C., Bouatra, S., Anderson, T., Oudit, G.Y., Wishart, D.S. & Dyck, J.R. Metabolomic Fingerprint of Heart Failure with Preserved Ejection Fraction. PLoS One. 10, e0124844. doi: 10.1371/journal.pone.0124844 (2015) PubMed ID: 26010610
  23. Huan, T., Tang, C., Li, R., Shi, Y., Lin, G., Li, L. MyCompoundID MS/MS Search: Metabolite Identification Using a Library of Predicted Fragment-Ion-Spectra of 383,830 Possible Human Metabolites. Anal Chem. 87(20): 10619-26. doi: 10.1021/acs.analchem.5b03126 (2015) PubMed ID: 26415007
  24. Li, Z., Tatlay, J., Li, L. Nanoflow LC-MS for High-Performance Chemical Isotope Labeling Quantitative Metabolomics. Anal Chem. 2015 87(22): 11468-74. doi: 10.1021/acs.analchem.5b03209 (2015) PubMed ID: 26482335
  25. Gutmanas, A., Adams, P.D., Bardiaux, B., Berman, H.M., Case, D.A., Fogh, R.H., Gantert, P.,Hendrickx, P.M., Herrmann, T., Kleywegt, G.J., Kobayashi, N., Lange, O.F., Markley, J.L., Montelione, G.T., Nilges, M., Ragan, T.J., Schwieters, C.D., Tejero, R., Ulrich, E.L., Velankar, S., Vranken, W.F., Wedell, J.R., Westbrook, J., Wishart, D.S., Vuister, G.W. NMR Exchange Format: a unified and open standard for representation of NMR restraint data Nat Struct Mol Biol 22(6). doi: 10.1038/nsmb.3041 (2015) PubMed ID: 26036565
  26. Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M. & Wishart, D.S. Pathways with PathWhiz. Nucleic Acids Res. 43, W552-W559 (2015) PubMed ID: 25934797
  27. Liu, Y., Liang, Y. & Wishart, D.S. PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. Nucleic Acids Res. 43, W535-W542 (2015) PubMed ID: 25925572
  28. Huan, T. & Li, L. Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry. Anal. Chem. 87, 7011-7016 (2015) PubMed ID: 26086729
  29. Szabat, M., Page, M.M., Panzhinskiy, E., Skovsø, S., Mojibian, M., Fernandez-Tajes, J., Bruin, J.E., Bround, M.J., Lee, J.T., Xu, E.E., Taghizadeh, F., ODwyer, S., van de Bunt, M., Moon, K.M., Sinha, S., Han, J., Fan, Y., Lynn, F.C., Trucco, M., Borchers, C.H., Foster, L.J., Nislow, C., Kieffer, T.J., Johnson, J.D. Reduced Insulin Production Relieves Endoplasmic Reticulum Stress and Induces β Cell Proliferation. Cell Metab. 23(1): 179-93. doi: 10.1016/j.cmet.2015.10.016 (2015) PubMed ID: 26626461
  30. Huang, W., Blinov, N., Wishart, D.S., Kovalenko, A. Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation. J. Chem. Inf. Model. 55(2):317-328 (2015) PubMed ID: 25545470
  31. Stanley, J.L., Sulek, K., Andersson, I.J., Davidge, S.T., Kenny, L.C., Sibley, C.P., Mandal, R., Wishart, D.S., Broadhurst, D.I. & Baker, P.N. Sildenafil Therapy Normalizes the Aberrant Metabolomic Profile in the Comt(-/-) Mouse Model of Preeclampsia/Fetal Growth Restriction. Sci. Rep. 5, 18241. doi.org/10.1038/srep18241 (2015) PubMed ID: 26667607
  32. MacKay, S., Hermansen, P., Wishart, D.S., Chen, J. Simulations of Interdigitated Electrode Interactions with Gold Nanoparticles for Impedance-Based Biosensing Applications. Sensors (Basel). 15(9):22192-208 (2015) PubMed ID: 26364638
  33. 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 11, 872-894. doi.org/10.1007/s11306-014-0746-7 (2015) PubMed ID: 26109927
  34. Wishart, D.S., Arndt, D., Pon, A., Sajed, T., Guo, A.C., Djoumbou, Y., Knox, C., Wilson, M., Liang, Y., Grant, J., Liu, Y., Goldansaz, S.A. & Rappaport, S.M. T3DB: the toxic exposome database. Nucleic Acids Res. 43, D928-D934 (2015) PubMed ID: 25378312
  35. Denihan, N.M., Walsh, B.H., Reinke, S.N., Sykes, B.D., Mandal, R., Wishart, D.S., Broadhurst, D.I., Boylan, G.B., Murray, D.M. The effect of haemolysis on the metabolomic profile of umbilical cord blood. Clin Biochem. 48(7-8):534-7. doi: 10.1016/j.clinbiochem.2015.02.004 (2015) PubMed ID: 25697106
  36. Dame, Z.T., Aziat, F., Mandal, R., Krishnamurthy, R., Bouatra, S., Borzouie, S., Guo, A.C., Sajed, T., Deng, L., Lin, H., Liu, P., Dong, E., Wishart, D.S. The Human Saliva Metabolome Metabolomics 11:1864-1883 (2015)
  37. Silva, A.C., Ebrahimi-Najafadabi, H., McGinitie, T.M., Casilli, A., Pereira, H.M., Aquino Neto, F.R. & Harynuk, J.J. Thermodynamic-based retention time predictions of endogenous steroids in comprehensive two-dimensional gas chromatography. Anal Bioanal Chem. 407, 4091-4099 (2015) PubMed ID: 25845527
  38. Bahado-Singh, R.O., Syngelaki, A., Akolekar, R., Mandal, R., Bjondahl, T.C., Han, B., Dong, E., Bauer, S., Alpay-Savasan, Z., Graham, S., Turkoglu, O., Wishart, D.S., Nicolaides, K.H. Validation of metabolomic models for prediction of early-onset preeclampsia. Am J Obstet Gynecol. 213, 530.e1-530.e10 (2015) PubMed ID: 26116099

2014

  1. McGinitie, T.M., Ebrahimi-Najafabadi, H., Harynuk, J.J. A standardized method for the calibration of thermodynamic data for use in the prediction of gas chromatographic retention times. J. Chromatogr. A. 1330 69-76 (2014) PubMed ID: 24484693
  2. McQueen, R.H., Harynuk, J.J., Wismer, W.V., Keelan, M., Xu, Y., de la Mata, A.P. Axillary odour build-up in knit fabrics following multiple use cycles. Int J Cloth Sci Tech. 26, 274-290 (2014)
  3. Nayidu, N.K., Tan, Y., Taheri, A., Li, X., Bjorndahl, T.C., Nowak, J., Wishart, D.S., Hegedus, D., Gruber, M.Y. Brassica villosa, a system for studying non-glandular trichomes and genes in the Brassicas. Plant Mol Biol. 85(4-5):519-39 (2014) PubMed ID: 24831512
  4. Allen, F., Pon, A., Wilson, M., Greiner R., Wishart, D.S. CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res. 42(Web Server issue):W94-9 (2014) PubMed ID: 24895432
  5. Li, Z and Li, L. Chemical-vapor-assisted Electrospray Ionization for Increasing Analyte Signals in ESI Mass Spectrometry. Anal. Chem. 86, 331-335 (2014) PubMed ID: 24364716
  6. Sinkov, N.A., Sandercock, P.M.L., Harynuk, J.J. Chemometric classification of casework arson samples based on gasoline content. Forensic Sci Int. 235 24-31. (2014) PubMed ID: 24447448
  7. Wang, X., Han, J., Pan, J., Borchers, C.H. Comprehensive imaging of porcine adrenal gland lipids by MALDI-FTMS using quercetin as a matrix. Anal Chem. 86, 638-46 (2014) PubMed ID: 24341451
  8. Wu, Y. & Li, L. Dansylation Metabolite Assay: A Simple and Rapid Method for Sample Amount Normalization in Metabolomics. Anal. Chem. 86, 9428-9433 (2014) PubMed ID: 25215550
  9. MacKay, S., Wishart, D.S., Xing, J.Z., Chen, J. Developing trends in aptamer-based biosensor devices and their applications. IEEE Trans Biomed Circuits Syst. 8(1):4-14 (2014) PubMed ID: 24681915
  10. Peng, J., Chen, Y., Chen, C. & Li, L. Development of a Universal Metabolome-Standard Method for Long-Term LC-MS Metabolome Profiling and Its Application for Bladder Cancer Urine-Metabolite-Biomarker Discovery. Anal. Chem. 86, 6540-7 (2014) PubMed ID: 24877652
  11. Peng, J., Guo, K., Xia, J., Zhou, J., Yang, J., Westaway, D., Wishart, D.S. & Li, L. Development of Isotope Labeling Liquid Chromatography Mass Spectrometry for Mouse Urine Metabolomics: Quantitative Metabolomic Study of Transgenic Mice Related to Alzheimer’s Disease. J. Proteome Res. 13, 4457-4469 (2014) PubMed ID: 25164377
  12. Law, V., Knox, C., Djoumbou, Y., Jewison, T., Guo, A.C., Liu, Y., Maciejewski, A., Arndt, D., Wilson, M., Neveu, V., Tang, A., Gabriel, G., Ly, C., Adamjee, S., Dame, Z.T., Han, B., Zhou, Y., Wishart, D.S. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 42, D1091-7 (2014) PubMed ID: 24203711
  13. Chen, J., Subramaniam, S., Wishart, D.S., Wong, S. Guest Editorial- special issue on ‘-omics’ based companion diagnostics for personalized medicine. IEEE Trans. Biomed. Circuits Syst. 8(1):1-3. (2014) PubMed ID: 24809069
  14. Sulek, K., Han, T.L., Villas-Boas, S.G., Wishart, D.S., Soh, S.E., Kwek, K., Gluckman, P.D., Chong, Y.S., Kenny, L.C. Baker, P.N. Hair Metabolomics: Identification of Fetal Compromise Provides Proof of Concept for Biomarker Discovery. Theranostics 4, 953-959 (2014) PubMed ID: 25057319
  15. Tseng, C., and Li, L. High-Performance Isotope-Labeling Liquid Chromatography Mass Spectrometry for Investigating the Effect of Drinking Goji Tea on Urine Metabolome Profiling. Science China Chemistry 57, 678-685 (2014)
  16. Hailemariam, D., Mandal, R., Saleem, F., Dunn, S.M., Wishart, D.S., Ametaj, B.N. Identification of predictive biomarkers of disease state in transition dairy cows. J Dairy Sci. 97, 2680-93 (2014) PubMed ID: 24630653
  17. Zhou, R., Tseng, C., Huan, T., Li, L. IsoMS: Automated Processing of LC-MS Data Generated by a Chemical Isotope Labeling Metabolomics Platform. Anal. Chem. 86, 4675-4679 (2014) PubMed ID: 24766305
  18. Ichu, T.A., Han, J., Borchers, C.H., Lesperance, M., Helbing, C.C. Metabolomic insights into system-wide coordination of vertebrate metamorphosis. BMC Dev Biol. 14, 5. (2014) PubMed ID: 24495308
  19. Bahado-Singh, R.O., Ertl, R., Mandal, R., Bjorndahl, T.C., Syngelaki, A., Han, B., Dong, E., Liu, P.B., Alpay-Savasan, Z., Wishart, D.S., Nicolaides, K.H. Metabolomic Prediction of Fetal Congenital Heart Defect in the First Trimester. Am J Obstet Gynecol. 211, 240.e1-240.e14 (2014) PubMed ID: 24704061
  20. Peng, J., St. Laurent, C.D., Befus, A.D., Zhou, R., Li, L. Metabolomic Profiling of Bronchoalveolar Lavage Fluids by Isotope Labeling Liquid Chromatography Mass Spectrometry: a Promising Approach to Studying Experimental Asthma. Metabolomics 10:1305- 1317 (2014)
  21. Mattos, K.A., Oliveira, V.C., Berrêdo-Pinho, M., Amaral, J.J., Antunes, L.C., Melo, R.C., Acosta, C.C., Moura, D.F., Olmo, R., Han, J., Rosa, P.S., Almeida, P.E., Finlay, B.B., Borchers, C.H., Sarno, E.N., Bozza, P.T., Atella, G.C., Pessolani, M.C. Mycobacterium leprae intracellular survival relies on cholesterol accumulation in infected macrophages: a potential target for new drugs for leprosy treatment. Cell Microbiol. 16, 797-815 (2014) PubMed ID: 24552180
  22. Tang, Y., Li, R., Lin, G., Li, L. PEP Search in MyCompoundID: Detection and Identification of Dipeptides and Tripeptides Using Dimethyl Labeling and Hydrophilic Interaction Liquid Chromatography Tandem Mass Spectrometry. Anal. Chem. 86, 3568-3574 (2014) PubMed ID: 24635831
  23. Zhou, R and Li, L. Quantitative Metabolome Profiling Using Dansylation Isotope Labeling and LC-MS Methods Mol Biol. 1198:127-36 (2014) PubMed ID: 25270927
  24. McGinitie, T.M., Ebrahimi-Najafabadi, H., Harynuk, J.J. Rapid determination of thermodynamic parameters from one-dimensional programmed-temperature gas chromatography for use in retention time prediction in comprehensive multidimensional chromatography. J. Chromatogr. A. 1325 201-212. (2014) PubMed ID: 24377740
  25. Friis, R.M.N., Glaves, J.P., Huan, T., Li, L., Sykes, B.D., Schultz, M.C. Rewiring AMPK and mitochondrial retrograde signaling for metabolic control of aging and histone acetylation in respiratory-defective cells. Cell Rep. 7, 565-574 (2014) PubMed ID: 24726357
  26. Jewison, T., Su, Y., Disfany, F.M., Liang, Y., Knox, C., Maciejewski, A., Poelzer, J., Huynh, J., Zhou, Y., Arndt, D., Djoumbou, Y., Liu, Y., Deng, L., Guo, A.C., Han, B., Pon, A., Wilson, M., Rafatnia, S., Liu, P., Wishart, D.S. SMPDB 2.0: big improvements to the Small Molecule Pathway Database. Nucleic Acids Res. 42, D478-D484 (2014) PubMed ID: 24203708
  27. Rappaport, S.M., Barupal, D.K., Wishart, D.S., Vineis, P. & Scalbert, A. The Blood Exposome and Its Role in Discovering Causes of Disease. Environ Health Perspect. 122(8):769-74 (2014) PubMed ID: 24659601
  28. Scalbert, A., Brennan, L., Manach, C., Andres-Lacueva, C., Dragsted, L.O., Draper, J., Rappaport, S.M., van der Hooft, J.J., Wishart, D.S. The food metabolome: a window over dietary exposure. Am J Clin Nutr. 99, 1286-1308 (2014) PubMed ID: 24760973
  29. Su, L.J., Fiehn, O., Maruvada, P., Moore, S.C., O Keefe, S.J., Wishart, D.S. & Zanetti, K.A. The Use of Metabolomics in Population-Based Research. Adv Nutr. 5, 785-788 (2014) PubMed ID: 25398741
  30. Adutwum, L.A., Harynuk, J.J. Unique Ion Filter: A Data Reduction Tool for GC/MS Data Preprocessing Prior to Chemometric Analysis. Anal. Chem. 86, 7726-7733 (2014) PubMed ID: 25002039
  31. Blydt-Hansen, T.D., Sharma, A., Gibson, I.W., Mandal, R., Wishart, D.S. Urinary Metabolomics for Noninvasive Detection of Borderline and Acute T Cell-Mediated Rejection in Children After Kidney Transplantation. Am J Transplant. 14, 2339-2349 (2014) PubMed ID: 25138024

2013

  1. Han, J., Tschernutter, V., Yang, J., Eckle, T., Borchers, C.H. Analysis of selected sugars and sugar phosphates in mouse heart tissue by reductive amination and liquid chromatography-electrospray ionization mass spectrometry. Anal Chem. 85(12), 5965-73 (2013) PubMed ID: 23682691
  2. Headley, J.V., Peru, K.M., Mohamed, M.H., Frank, R.A., Martin, J.W., Hazewinkel, R.R., Humphries, D., Gurprasad, N.P., Hewitt, L.M., Muir, D.C., Lindeman, D., Strub, R., Young, R.F., Grewer, D.M., Whittal, R.M., Fedorak, P.M., Birkholz, D.A., Hindle, R., Reisdorph, R., Wang, X., Kasperski, K.L., Hamilton, C., Woudneh, M., Wang, G., Loescher, B., Farwell, A., Dixon, D.G., Ross, M., Pereira Ados, S., King, E., Barrow, M.P., Fahlman, B., Bailey, J., McMartin, D.W., Borchers, C.H., Ryan, C.H., Toor, N.S., Gillis, H.M., Zuin, L., Bickerton, G., McMaster, M., Sverko, E., Shang, D., Wilson, L.D., Wrona, F.J. Chemical fingerprinting of naphthenic acids and oil sands process waters-A review of analytical methods for environmental samples. J Environ Sci Health A Tox Hazard Subst Environ Eng. 48(10), 1145-63. (2013) PubMed ID: 23647107
  3. Wu, G., Zhang, L., Li, T., Zuniga, A., Lopaschuk, G.D., Li, L., Jacobs, R.L. & Vance, D.E. Choline supplementation promotes hepatic insulin resistance in phosphatidylethanolamine N-methyltransferase-deficient mice via increased glucagon action. J Biol Chem 288, 837-847 (2013) PubMed ID: 23179947
  4. Nyakas, A., Han, J., Peru, K.M., Headley, J.V., Borchers, C.H. Comprehensive analysis of oil sands processed water by direct-infusion Fourier-transform ion cyclotron resonance mass spectrometry with and without offline UHPLC sample prefractionation. Environ Sci Technol. 47(9):4471-9. (2013) PubMed ID: 23566025
  5. Murray, K.K., Boyd, R.K., Eberlin, M.N., Langley, G.H., Li, L., and Naito, Y. Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013). Pure Appl. Chem. 85 (2013)
  6. Wu, Y., and Li, L. Development of Isotope Labeling LC-MS for Metabolic Profiling of Bacterial Cells and Its Application for Bacterial Differentiation. Anal. Chem. 85, 5755-5763 (2013) PubMed ID: 23495969
  7. Canam, T., Li, X., Holowachuk, J., Yu, M., Xia, J., Mandal, R., Krishnamurthy, R., Bouatra, S., Sinelnikov, I., Yu, B., Grenkow, L., Wishart, D. S., Steppuhn, H., Falk, K.C., Dumonceaux, T.J. & Gruber, M.Y. Differential metabolite profiles and salinity tolerance between two genetically related brown-seeded and yellow-seeded Brassica carinata lines. Plant Sci 198, 17-26 (2013) PubMed ID: 23199683
  8. Le, C.H., Han, J., Borchers, C.H. Dithranol as a matrix for matrix assisted laser desorption/ionization imaging on a fourier transform ion cyclotron resonance mass spectrometer. J Vis Exp. 81, e50733. (2013) PubMed ID: 24300588
  9. Guo, A.C., Jewison, T., Wilson, M., Liu, Y., Knox, C., Djoumbou, Y., Lo, P., Mandal, R., Krishnamurthy, R. & Wishart, D.S. ECMDB: the E. coli Metabolome Database. Nucleic Acids Res 41, D625-D630 (2013) PubMed ID: 23109553
  10. Mane, J.Y., Semenchenko, V., Perez-Pineiro, R., Winter, P., Wishart, D.S., Tuszynski, J.A. Experimental and Computational Study of the Interaction of Novel Colchicinoids with a Recombinant Human αI/βI-Tubulin Heterodimer. Chem. Biol. Drug Des. 82(1):60-70 (2013) PubMed ID: 23480279
  11. Wishart, D.S. Exploring the Human Metabolome by NMR Spectroscopy & Mass Spectroscopy. Methodologies for Metabolomics: Experimental Strategies and Techniques; Cambridge University; ISBN: 9780521765909 (2013)
  12. Bahado-Singh, R.O., Akolekar, R., Mandal, R., Dong, E., Xia, J., Kruger, M., Wishart, D.S. & Nicolaides, K. First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol 208, 58.e1-7 (2013) PubMed ID: 23159745
  13. Weber, B.M., Harynuk, J.J. Gas chromatographic retention of alkyl phosphates on ionic liquid stationary phases. J Chromatogr A. 1271(1), 170-5 (2013) PubMed ID: 23237714
  14. Eckle, T., Brodsky, K., Bonney, M., Packard, T., Han, J., Borchers, C.H., Mariani, T.J., Kominsky, D.J., Mittelbronn, M., Eltzschig, H.K. HIF1A reduces acute lung injury by optimizing carbohydrate metabolism in the alveolar epithelium. PLoS Biol. (9):e1001665 (2013) PubMed ID: 24086109
  15. Wishart, D.S., Jewison, T., Guo, A.C., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E., Bouatra, S., Sinelnikov, I., Arndt, D., Xia, J., Liu, P., Yallou, F., Bjorndahl, T., Perez-Pineiro, R., Eisner, R., Allen, F., Neveu, V., Greiner, R. & Scalbert, A. HMDB 3.0--The Human Metabolome Database in 2013. Nucleic Acids Res 41, D801-D807 (2013) PubMed ID: 23161693
  16. Wang, X., Han, J., Chou, A., Yang, J., Pan, J., Borchers, C.H. Hydroxyflavones as a new family of matrices for MALDI tissue imaging. Anal Chem. 85(15):7566-73. (2013) PubMed ID: 23895229
  17. Xia, J., Fjell, C.D., Mayer, M.L., Pena, O.M., Wishart, D.S., Hancock, R.E. INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res. 41(W1), W63-W70 (2013) PubMed ID: 23766290
  18. Li, L. MALDI Mass Spectrometry for Polymer Characterization """"A Practical Guide to MALDI MS, 2nd Edition"""", F. Hillenkam, Ed., Wiley-VCH, Germany (2013)
  19. Antunes, L.C., Han, J., Pan, J., Moreira, C.J., Azambuja, P., Borchers, C.H., Carels, N. Metabolic signatures of triatomine vectors of Trypanosoma cruzi unveiled by metabolomics. PLoS One. 8(10):e77283. (2013) PubMed ID: 24204787
  20. Bahado-Singh, R.O., Akolekar, R., Mandal, R., Dong, E., Xia, J., Kruger, M., Wishart, D.S. & Nicolaides, K. Metabolomic analysis for first-trimester Down syndrome prediction. Am J Obstet Gynecol. 208(5):371.e1-8 (2013) PubMed ID: 23313728
  21. Bahado-Singh, R.O., Akolekar, R., Chelliah, A., Mandal, R., Dong, E., Kruger, M., Wishart, D.S., Nicolaides, K. Metabolomic analysis for first-trimester trisomy 18 detection. Am J Obstet Gynecol. 209(1):65.e1-9 (2013) PubMed ID: 23535240
  22. Ghobakhlou, A., Laberge, S., Antoun, H., Wishart, D.S., Xia, J., Krishnamurthy, R., Mandal, R. Metabolomic analysis of cold acclimation of Arctic Mesorhizobium sp. strain N33. PLoS One. 8, e84801 (2013) PubMed ID: 24386418
  23. Han, J., Gagnon, S., Eckle, T., Borchers, C.H. Metabolomic analysis of key central carbon metabolism carboxylic acids as their 3-nitrophenylhydrazones by UPLC/ESI-MS. Electrophoresis. 34(19):2891-900. (2013) PubMed ID: 23580203
  24. Amaral, J.J., Antunes, L.C., de Macedo, C.S., Mattos, K.A., Han, J., Pan, J., Candéa, A.L., Henriques, Md., Ribeiro-Alves, M., Borchers, C.H., Sarno, E.N., Bozza, P.T., Finlay, B.B., Pessolani, M.C. Metabonomics reveals drastic changes in anti-inflammatory/pro-resolving polyunsaturated fatty acids-derived lipid mediators in leprosy disease. PLoS Negl Trop Dis. 7(8):e2381. (2013) PubMed ID: 23967366
  25. Pagadala, N.S., Bjorndahl, T.C., Blinov, N., Kovalenko, A., Wishart, D.S. Molecular docking of thiamine reveals similarity in binding properties between the prion protein and other thiamine-binding proteins. J. Mol. Model. 19(12):5225-5235 (2013) PubMed ID: 24126825
  26. Li, L., Li, R., Zhou, J., Zuniga, A., Stanislaus, A.E., Wu, Y., Huan, T., Zheng, J., Shi, Y., Wishart, D.S. & Lin, G. MyCompoundID: Using an Evidence-based Metabolome Library for Metabolite Identification. Anal Chem. 85(6):3401-8 (2013) PubMed ID: 23373753
  27. Rothwell, J.A., Perez-Jimenez, J., Neveu, V., Medina-Remón, A., M hiri, N., García-Lobato, P., Manach, C., Knox, C., Eisner, R., Wishart, D.S., Scalbert, A. Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content. Database (Oxford) 2013, bat070-bat070 (2013) PubMed ID: 24103452
  28. Jordheim, L.P., Barakat, K.H., Heinrich-Balard, L., Matera, E.L., Cros-Perrial, E., Bouledrak, K., El Sabeh, R., Perez-Pineiro, R., Wishart, D.S., Cohen, R., Tuszynski, J., Dumontet, C. Small Molecule Inhibitors of ERCC1-XPF Protein-Protein Interaction Synergize Alkylating Agents in Cancer Cells. Mol Pharmacol. 84(1), 12-24 (2013) PubMed ID: 23580445
  29. Saleem, F., Bouatra, S., Guo, A.C., Psychogios, N, Mandal, R., Dunn, S.M., Ametaj, B.N. and Wishart, D.S. The Bovine Ruminal Fluid Metabolome. Metabolomics 9, 360-378 (2013)
  30. Bouatra, S., Aziat, F., Mandal, R., Guo, A.C., Wilson, M.R., Knox, C., Bjorndahl, T.C., Krishnamurthy, R., Saleem, F., Liu, P., Dame, Z.T., Poelzer, J., Huynh, J., Yallou, F.S., Psychogios, N., Dong, E., Bogumil, R., Roehring, C., Wishart, D.S. The human urine metabolome. PLoS One. 8(9):e73076 (2013) PubMed ID: 24023812
  31. Sinkov, N.A., Harynuk, J.J. Three-dimensional cluster resolution for guiding automatic chemometric model optimization. Talanta. 103:252-9 (2013) PubMed ID: 23200385
  32. Xia, J., Broadhurst, D.I., Wilson, M., Wishart, D.S. Translational biomarker discovery in clinical metabolomics: an introductory tutorial. Metabolomics. 9(2), 280-299 (2013) PubMed ID: 23543913

2012

  1. Nikolic, D., Blinov, N., Wishart, D.S., Kovalenko, A. 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol. J. Chem. Theory and Comput. 8: 3356-3372 (2012) PubMed ID: 26605742
  2. Saleem, F., Ametaj, B.N., Bouatra, S., Mandal, R., Zebeli, Q., Dunn, S.M. & Wishart, D.S. A metabolomics approach to uncover the effects of grain diets on rumen health in dairy cows. J Dairy Sci 95, 6606-6623 (2012) PubMed ID: 22959937
  3. Eckle, T., Hartmann, K., Bonney, S., Reithel, S., Mittelbronn, M., Walker, L.A., Lowes, B.D., Han, J., Borchers, C.H., Buttrick, P.M., Kominsky, D.J., Colgan, S.P. & Eltzschig, H.K. Adora2b-elicited Per2 stabilization promotes a HIF-dependent metabolic switch crucial for myocardial adaptation to ischemia. Nat Med 18, 774-782 (2012) PubMed ID: 22504483
  4. Wu, Y. & Li, L. Determination of total concentration of chemically labeled metabolites as a means of metabolome sample normalization and sample loading optimization in mass spectrometry-based metabolomics. Anal Chem 84, 10723-10731 (2012) PubMed ID: 23190334
  5. Chen, Y.T., Wang, F.S., Li, Z., Li, L. & Ling, Y.C. Development of a matrix-assisted laser desorption ionization mass spectrometric method for rapid process-monitoring of phthalocyanine compounds. Anal Chim Acta 736, 69-77 (2012) PubMed ID: 22769007
  6. Stanislaus, A., Guo, K. & Li, L. Development of an isotope labeling ultra-high performance liquid chromatography mass spectrometric method for quantification of acylglycines in human urine. Anal Chim Acta 750, 161-172 (2012) PubMed ID: 23062437
  7. Hall, L.M., Hall, L.H., Kertesz, T.M., Hill, D.W., Sharp, T.R., Oblak, E.Z., Dong, Y.W., Wishart, D.S., Chen, M.H. & Grant, D.F. Development of Ecom(5)(0) and retention index models for nontargeted metabolomics: identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry. J Chem Inf Model 52, 1222-1237 (2012) PubMed ID: 22489687
  8. Zheng, J., Dixon, R.A. & Li, L. Development of isotope labeling LC-MS for human salivary metabolomics and application to profiling metabolome changes associated with mild cognitive impairment. Anal Chem 84, 10802-10811 (2012) PubMed ID: 23150892
  9. Friesen, D.E., Barakat, K.H., Semenchenko, V., Perez-Pineiro, R., Fenske, B.W., Mane, J., Wishart, D.S. and Tuszynski, J.A. Discovery of Small Molecule Inhibitors that Interact with γ-Tubulin. Chem. Biol. Drug Des. 79:639-652 (2012) PubMed ID: 22268380
  10. Le, C.H., Han, J. & Borchers, C.H. Dithranol as a MALDI matrix for tissue imaging of lipids by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 84, 8391-8398 (2012) PubMed ID: 22931516
  11. Fatima, T., Snyder, C.L., Schroeder, W.R., Cram, D., Datla, R., Wishart, D.S., Weselake, R.J. & Krishna, P. Fatty acid composition of developing sea buckthorn (Hippophae rhamnoides L.) berry and the transcriptome of the mature seed. PLoS One 7, e34099 (2012) PubMed ID: 22558083
  12. Zheng, J.M. & Li, L. Fragmentation of Protonated Dansyl-labeled Amines for Structural Analysis of Amine-containing Metabolites. Int J Mass Spectrom. 316–318, 292–299 (2012)
  13. Xia, J., Mandal, R., Sinelnikov, I.V., Broadhurst, D. & Wishart, D.S. MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis. Nucleic Acids Res 40, W127-W133 (2012) PubMed ID: 22553367
  14. Bahado-Singh, R. O., Akolekar, R., Mandal, R., Dong, E., Xia, J., Kruger, M., Wishart, D. S. & Nicolaides, K. Metabolomics and first-trimester prediction of early-onset preeclampsia. J Matern Fetal Neonatal Med 25, 1840-1847 (2012) PubMed ID: 22494326
  15. Arndt, D., Xia, J., Liu, Y., Zhou, Y., Guo, A.C., Cruz, J.A., Sinelnikov, I., Budwill, K., Nesbø, C.L. and Wishart, D.S. METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. 40:W88-W95 (2012) PubMed ID: 22645318
  16. Mandal, R., Guo, A.C., Chaudhary, K.K., Liu, P., Yallou, F.S., Dong, E., Aziat, F. & Wishart, D.S. Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update. Genome Med 4, 38 (2012) PubMed ID: 22546835
  17. Rush, D., Mandal, R., Wishart, D., Wiebe, C., Ho, J., Storsely, L., Karpinski, M, Gibson, I., Nickerson, P. Non‐Invasive Diagnosis of Renal Allograft Inflammation Using Quantitative Urine Metabolomics. Transplantation 94, 1186 (2012)
  18. Rothwell, J.A., Urpi-Sarda, M., Boto-Ordonez, M., Knox, C., Llorach, R., Eisner, R., Cruz, J., Neveu, V., Wishart, D.S., Manach, C., Andres-Lacueva, C. & Scalbert, A. Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals. Database (Oxford) 2012, bas031 (2012) PubMed ID: 22879444
  19. Stretch, C., Eastman, T., Mandal, R., Eisner, R., Wishart, D.S., Mourtzakis, M., Prado, C.M., Damaraju, S., Ball, R.O., Greiner, R. & Baracos, V.E. Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach. J Nutr 142, 14-21 (2012) PubMed ID: 22157537
  20. Mandal, R., Kathiria, P., Psychogios, N., Bouatra, S. Krishnamurthy, R. Wishart, D.S. and Kovalchuk, I. Progeny of tobacco mosaic virus-infected Nicotiana tabacum plants exhibit trans-generational changes in metabolic profiles. Biocatalysis and Agricultural Biotechnology 1, 115-123 (2012)
  21. Han, J., Kalyan, S., Prior, JC., Borchers, C. H. Quantitation of Urinary 6 β-Hydroxycortisol and Free Cortisol by Ultra-Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry. Clinical and Experimental Pharmacology 01 (2012)
  22. Antunes, L.C., Wang, M., Andersen, S.K., Ferreira, R.B., Kappelhoff, R., Han, J., Borchers, C.H. & Finlay, B.B. Repression of Salmonella enterica phoP expression by small molecules from physiological bile. J Bacteriol 194, 2286-2296 (2012) PubMed ID: 22366421
  23. Orchard, S., Al-Lazikani, B., Bryant, S., Clark, D., Calder, E., Dix, I., Engkvist, O., Forster, M., Gaulton, A., Gilson, M., Glen, R., Grigorov, M., Hammond-Kosack, K., Harland, L., Hopkins, A., Larminie, C., Lynch, N., Mann, R.K., Murray-Rust, P., Piparo, E.L., Southan, C., Steinbeck, C., Wishart, D.S., Hermjakob, H., Overington, J. and Thornton, J. Shouldnt enantiomeric purity be included in the minimum information about a bioactive entity? Response from the MIABE group. Nat. Rev. Drug Discov. 11(9):730 (2012) PubMed ID: 22935805
  24. Wishart, D.S. Small molecules and disease. PLoS Comput Biol. 8(12):e1002805 (2012) PubMed ID: 23300405
  25. Wishart, D.S. Systems Biology Resource Arising from the Human Metabolome Project. Genetics Meets Metabolomics (ed. K. Suhre). Springer New York, NY. 157-175 (2012)
  26. Walsh, B.H., Broadhurst, D.I., Mandal, R., Wishart, D.S., Boylan, G.B., Kenny, L.C. & Murray, D.M. The metabolomic profile of umbilical cord blood in neonatal hypoxic ischaemic encephalopathy. PLoS One 7, e50520 (2012) PubMed ID: 23227182
  27. Barakat, K.H., Jordheim, L.P., Perez-Pineiro, R., Wishart, D.S., Dumontet, C. and Tuszynski, J.A. Virtual Screening and Biological Evaluation of Inhibitors Targeting the XPA-ERCC1 Interaction. PLoS One. 7(12):e51329 (2012) PubMed ID: 23272099
  28. Jewison, T., Knox, C., Neveu, V., Djoumbou, Y., Guo, A.C., Lee, J., Liu, P., Mandal, R., Krishnamurthy, R., Sinelnikov, I., Wilson, M. & Wishart, D.S. YMDB: the Yeast Metabolome Database. Nucleic Acids Res 40, D815-D820 (2012) PubMed ID: 22064855
  29. Wishart, D.S. “DrugBank” in Principles of Pharmacogenetics and Pharmacogenomics. (eds. R.B. Altman, D. Flockhart, D.B. Goldstein), Cambridge University Press, Cambridge UK, pp. 55-66 (2012)

2011

  1. Wishart, D.S. Advances in metabolite identification. Bioanalysis 3, 1769-1782 (2011) PubMed ID: 21827274
  2. Scalbert, A., Andres-Lacueva, C., Arita, M., Kroon, P., Manach, C., Urpi-Sarda, M. & Wishart, D. Databases on food phytochemicals and their health-promoting effects. J Agric Food Chem 59, 4331-4348 (2011) PubMed ID: 21438636
  3. Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V., Djoumbou, Y., Eisner, R., Guo, A.C. & Wishart, D.S. DrugBank 3.0: a comprehensive resource for """"omics"""" research on drugs. Nucleic Acids Res 39, D1035-D1041 (2011) PubMed ID: 21059682
  4. Antunes, L.C., Arena, E.T., Menendez, A., Han, J., Ferreira, R.B., Buckner, M.M., Lolic, P., Madilao, L.L., Bohlmann, J., Borchers, C.H. & Finlay, B.B. Impact of Salmonella infection on host hormone metabolism revealed by metabolomics. Infect Immun 79, 1759-1769 (2011) PubMed ID: 21321075
  5. Guo, K., Peng, J., Zhou, R. & Li, L. Ion-pairing reversed-phase liquid chromatography fractionation in combination with isotope labeling reversed-phase liquid chromatography-mass spectrometry for comprehensive metabolome profiling. J Chromatogr A 1218, 3689-3694 (2011) PubMed ID: 21543078
  6. Eisner, R., Stretch, C., Eastman, T., Xia, J. Hau, D., Damaraju, S., Greiner, R., Wishart, D., Baracos, V. Learning to predict cancer-associated skeletal muscle wasting from 1H-NMR profiles of urinary metabolites. Metabolomics 7, 25–34 (2011)
  7. Xia, J. & Wishart, D.S. Metabolomic data processing, analysis, and interpretation using MetaboAnalyst. Curr Protoc Bioinformatics Chapter 14, Unit 14.10 (2011) PubMed ID: 21633943
  8. Hall, R.D., Wishart, D.S. and Roessner, U. Metabolomics and the move towards biology. Metabolomics 7, 454-456 (2011)
  9. Antunes, L.C., Andersen, S.K., Menendez, A., Arena, E.T., Han, J., Ferreira, R.B., Borchers, C.H. & Finlay, B.B. Metabolomics reveals phospholipids as important nutrient sources during Salmonella growth in bile in vitro and in vivo. J Bacteriol 193, 4719-4725 (2011) PubMed ID: 21764918
  10. Xia, J., Sinelnikov, I.V. & Wishart, D.S. MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets. Bioinformatics 27, 2455-2456 (2011) PubMed ID: 21712247
  11. Orchard, S., Al-Lazikani, B., Bryant, S., Clark, D., Calder, E., Dix, I., Engkvist, O., Forster, M., Gaulton, A., Gilson, M., Glen, R., Grigorov, M., Hammond-Kosack, K., Harland, L., Hopkins, A., Larminie, C., Lynch, N., Mann, R. K., Murray-Rust, P., Lo Piparo, E., Southan, C., Steinbeck, C., Wishart, D., Hermjakob, H., Overington, J. & Thornton, J. Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov 10, 661-669 (2011) PubMed ID: 21878981
  12. Lin, D., Hollander, Z., Meredith, A., Stadnick, E., Sasaki, M., Cohen Freue, G., Qasimi, P., Mui, A., Ng, R.T., Balshaw, R., Wilson-McManus, J.E., Wishart, D., Hau, D., Keown, P.A., McMaster, R. & McManus, B.M. Molecular signatures of end-stage heart failure. J Card Fail. 17, 867-874 (2011) PubMed ID: 21962426
  13. Guo, K., Bamforth, F. & Li, L. Qualitative metabolome analysis of human cerebrospinal fluid by 13C-/12C-isotope dansylation labeling combined with liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 22, 339-347 (2011) PubMed ID: 21472593
  14. Clements, M. & Li, L. Strategy of using microsome-based metabolite production to facilitate the identification of endogenous metabolites by liquid chromatography mass spectrometry. Anal Chim Acta 685, 36-44 (2011) PubMed ID: 21168549
  15. Bhomkar, P., Materi, W. and Wishart, D.S. The bacterial nanorecorder: engineering E. coli to function as a chemical recording device. PLoS One. 6(11):e27559 (2011) PubMed ID: 22132112
  16. Arena, E.T., Auweter, S.D., Antunes, L.C., Vogl, A.W., Han, J., Guttman, J.A., Croxen, M.A., Menendez, A., Covey, S.D., Borchers, C.H. & Finlay, B.B. The deubiquitinase activity of the Salmonella pathogenicity island 2 effector, SseL, prevents accumulation of cellular lipid droplets. Infect Immun 79, 4392-4400 (2011) PubMed ID: 21875964
  17. Psychogios, N., Hau, D.D., Peng, J., Guo, A.C., Mandal, R., Bouatra, S., Sinelnikov, I., Krishnamurthy, R., Eisner, R., Gautam, B., Young, N., Xia, J., Knox, C., Dong, E., Huang, P., Hollander, Z., Pedersen, T.L., Smith, S.R., Bamforth, F., Greiner, R., McManus, B., Newman, J.W., Goodfriend, T. & Wishart, D.S. The human serum metabolome. PLoS One 6, e16957 (2011) PubMed ID: 21359215
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