Publications


Tmic10

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

2016

  1. 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 (2016). 26608419.
  2. 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). 26814424.
  3. Allen, F., Greiner, R., Wishart, D.S. CFM-ID applied to CASMI 2014 Current Metabolomics, June 2016 (2016).
  4. 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). 27381172.
  5. 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). 27141966.
  6. 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 (2016). 27190236.
  7. 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).
  8. 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 (2016).
  9. 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).
  10. 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. (2016). 27569705.
  11. 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). 27642271.
  12. 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). 27428442.
  13. 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).
  14. 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 (2016). 26745651.
  15. 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 Huntington's disease (HD): (1)H NMR analysis of the polar metabolome in post-mortem human brain. Biochim Biophys Acta. 2016 Sep; 1862(9): 1675-84 (2016). 27288730.
  16. 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). 27120558.
  17. 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). 27667503.
  18. 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).
  19. 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). 27500268.
  20. 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). 27351466.
  21. 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).
  22. 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). 27578275.
  23. 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). 27732148.
  24. 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). 27390787.
  25. 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). 27375567.
  26. 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).
  27. 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). 27555478.
  28. 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 dx.doi.org/10.1016/j.forc.2016.10.003 (2016).
  29. 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). 26947805.
  30. 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 Annual Review of Public Health. 38(1). (2016).
  31. 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). 27580257.
  32. 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 Research. gkw980. (2016).
  33. 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 Chemistry of Materials. 28(18):6672-81. (2016).
  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. 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 (2016). 26481353.
  36. 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 Cover Article (2016).
  37. 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). 27437618.
  38. 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). 26709303.
  39. 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). 27276562.
  40. 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 (2016). 26878788.
  41. Venkatasubramanian, A., Sauer, V.T., Roy, S.K., Xia, M., Wishart, D.S., Hiebert, W.K. Nano-optomechanical systems for gas chromatography. Nano Lett. 2016 Oct 17. (2016). 27749074.
  42. 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). 27125997.
  43. 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). 27159197.
  44. 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). 26965202.
  45. Wishart, D.S. Introduction to Cheminformatics. Curr Protoc Bioinformatics. 53:14.1.1-14.1.21 (2016). 27010335.
  46. Wishart, D.S., Mandal, R., Stanislaus, A. & Ramirez-Gaona, M. Cancer Metabolomics and the Human Metabolome Database. Metabolites 6, 10; doi: 10.3390/metabo6010010 (2016). 26950159.
  47. 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). 27322405.
  48. 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). 26763302.
  49. 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). 27603023.
  50. 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). 27734577.
  51. 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).
  52. 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. (2016). 27690392.

2015

  1. Allen, F., Greiner, R., Wishart, D.S. Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics 11, 98-110 (2015).
  2. 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). 26116099.
  3. 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). 26241678.
  4. 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).
  5. 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 (2015). 25697106.
  6. 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 (2015). 26109927.
  7. 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). 26318327.
  8. 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). 26369413.
  9. 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). 25479871.
  10. 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). 25496250.
  11. Han, J., Parker, C., Borchers, C.H. Chapter one. Chemical derivatization to enhance metabolomic analysis by LC/ESI-MS. """"Advanced LC-MS Applications in Metabolomics"""", May 2015 Future Science. eisbn: 978-1-910419-44-1 (2015).
  12. 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 (2015).
  13. 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). 25496403.
  14. 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). 26086729.
  15. 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). 26415007.
  16. 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 (2015). 26327437.
  17. 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). 25545470.
  18. 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). 26482335.
  19. 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). 25925572.
  20. 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). 26364638.
  21. 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). 25934797.
  22. 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). 26222058.
  23. 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). 25845527.
  24. 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).
  25. 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). 25885783.
  26. 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 (2015). 26667607.
  27. 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., O'Dwyer, 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). 26626461.
  28. 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). 25330974.
  29. Wishart, D.S. Is Cancer a Genetic Disease or a Metabolic Disease? EBioMedicine 2, 478-479 (2015). 26288805.
  30. 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). 25378312.
  31. Xia, J., Sinelnikov, I.V., Han, B. & Wishart, D.S. MetaboAnalyst 3.0--making metabolomics more meaningful. Nucleic Acids Res. 43, W251-W257 (2015). 25897128.
  32. 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). 25486321.
  33. 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). 25987165.
  34. 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). 25134441.
  35. 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). 26041526.
  36. 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 (2015). 26010610.

2014

  1. 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). 25002039.
  2. 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). 24895432.
  3. 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). 24704061.
  4. 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). 25138024.
  5. 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). 24809069.
  6. 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). 24726357.
  7. 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). 24630653.
  8. 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). 24495308.
  9. 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). 24203708.
  10. 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). 24203711.
  11. Li, Z and Li, L. Chemical-vapor-assisted Electrospray Ionization for Increasing Analyte Signals in ESI Mass Spectrometry. Anal. Chem. 86, 331-335 (2014). 24364716.
  12. 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). 24681915.
  13. 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). 24552180.
  14. 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). 24484693.
  15. 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). 24377740.
  16. 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).
  17. 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). 24831512.
  18. 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). 24877652.
  19. 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). 25164377.
  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. 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). 24659601.
  22. 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). 24760973.
  23. 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). 24447448.
  24. 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). 25398741.
  25. 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). 25057319.
  26. 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). 24635831.
  27. 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).
  28. 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). 24341451.
  29. Wu, Y. & Li, L. Dansylation Metabolite Assay: A Simple and Rapid Method for Sample Amount Normalization in Metabolomics. Anal. Chem. 86, 9428-9433 (2014). 25215550.
  30. Zhou, R and Li, L. Quantitative Metabolome Profiling Using Dansylation Isotope Labeling and LC-MS Methods Mol Biol. 1198:127-36 (2014). 25270927.
  31. 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). 24766305.

2013

  1. 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). 23967366.
  2. 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). 24204787.
  3. 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). 23535240.
  4. 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). 23159745.
  5. 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). 23313728.
  6. 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). 24023812.
  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). 23199683.
  8. 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). 24086109.
  9. 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). 24386418.
  10. 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). 23109553.
  11. 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). 23580203.
  12. 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). 23682691.
  13. 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). 23647107.
  14. 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). 23580445.
  15. 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). 24300588.
  16. Li, L. MALDI Mass Spectrometry for Polymer Characterization """"A Practical Guide to MALDI MS, 2nd Edition"""", F. Hillenkam, Ed., Wiley-VCH, Germany (2013).
  17. 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). 23373753.
  18. 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). 23480279.
  19. 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).
  20. 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). 23566025.
  21. 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). 24126825.
  22. 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). 24103452.
  23. 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).
  24. Sinkov, N.A., Harynuk, J.J. Three-dimensional cluster resolution for guiding automatic chemometric model optimization. Talanta. 103:252-9 (2013). 23200385.
  25. 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). 23895229.
  26. 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). 23237714.
  27. Wishart, D.S. Exploring the Human Metabolome by NMR Spectroscopy & Mass Spectroscopy. Methodologies for Metabolomics: Experimental Strategies and Techniques; Cambridge University; ISBN: 9780521765909 (2013).
  28. 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). 23161693.
  29. 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). 23179947.
  30. 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). 23495969.
  31. 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). 23543913.
  32. 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). 23766290.

2012

  1. 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). 22366421.
  2. 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). 22645318.
  3. 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). 22494326.
  4. 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). 23272099.
  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). 22769007.
  6. 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). 22504483.
  7. 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). 22558083.
  8. 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). 22268380.
  9. 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). 22489687.
  10. 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).
  11. 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). 22064855.
  12. 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). 22931516.
  13. 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). 22546835.
  14. 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).
  15. 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). 26605742.
  16. 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., Thornton, J. Shouldn't 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). 22935805.
  17. 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). 22879444.
  18. 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).
  19. 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). 22959937.
  20. 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). 23062437.
  21. 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). 22157537.
  22. 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). 23227182.
  23. Wishart, D.S. Chapter 3: Small molecules and disease. PLoS Comput Biol. 8(12):e1002805 (2012). 23300405.
  24. 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).
  25. 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).
  26. 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). 23190334.
  27. 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). 22553367.
  28. 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). 23150892.
  29. 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).

2011

  1. 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). 21764918.
  2. 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). 21321075.
  3. 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). 21875964.
  4. 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). 22132112.
  5. Blydt-Hansen, T.D., Mandal, R. & Wishart, D.S. Urine Metabolite Profiles Distinguish Acute Rejection from Acute Allograft Injury and Normal Functioning Allografts in Pediatric Renal Tranpslant Recipients. Pediatric Transplantation 15, SI98-99 (2011).
  6. 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). 21168549.
  7. 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).
  8. 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). 21472593.
  9. 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). 21543078.
  10. Hall, R.D., Wishart, D.S. and Roessner, U. Metabolomics and the move towards biology. Metabolomics 7, 454-456 (2011).
  11. 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). 21059682.
  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). 21962426.
  13. Mercier, P., Lewis, M.J., Chang, D., Baker, D. & Wishart, D.S. Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra. J Biomol NMR 49, 307-323 (2011). 21360156.
  14. 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). 21878981.
  15. Perez-Pineiro, R., Bjorndahl, T.C., Berjanskii, M.V., Hau, D., Li, L., Huang, A., Lee, R., Gibbs, E., Ladner, C., Dong, Y.W., Abera, A., Cashman, N.R. & Wishart, D.S. The prion protein binds thiamine. FEBS J. 278, 4002-4014 (2011). 21848803.
  16. 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). 21359215.
  17. 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). 21438636.
  18. Wishart, D.S. Advances in metabolite identification. Bioanalysis 3, 1769-1782 (2011). 21827274.
  19. Xia, J. & Wishart, D.S. Metabolomic data processing, analysis, and interpretation using MetaboAnalyst. Curr Protoc Bioinformatics Chapter 14, Unit 14.10 (2011). 21633943.
  20. Xia, J. & Wishart, D.S. Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst. Nat Protoc 6, 743-760 (2011). 21637195.
  21. 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). 21712247.
  22. Zuniga, A. & Li, L. Ultra-high performance liquid chromatography tandem mass spectrometry for comprehensive analysis of urinary acylcarnitines. Anal Chim Acta 689, 77-84 (2011). 21338760.


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.