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

2019

  1. Benjamin Goudey, Bowen J Fung, Christine Schieber, Noel G Faux, Alzheimer’s Disease Metabolomics Consortium (David Wishart), Alzheimer’s Disease Neuroimaging Initiative A blood-based signature of cerebrospinal fluid Aβ1-42 status Scientific Reports 10.1038/s41598-018-37149-7 (2019) PubMed ID: 30853713
  2. Marcia A LeVatte, Matthias Lipfert, Jiamin Zheng, David S Wishart A fast, sensitive, single-step colorimetric dipstick assay for quantifying ascorbic acid in urine Analytical biochemistry 10.1016/j.ab.2019.05.015 (2019) PubMed ID: 31153872
  3. Marco De Giorgi, Kelsey E Jarrett, Jason C Burton, Alexandria M Doerfler, Ayrea Hurley, Ang Li, Rachel H Hsu, Mia Furgurson, Jun Han, Christoph H Borchers, William R Lagor Acute Liver-Specific Deletion of HMG-CoA Reductase Results in Depletion of Essential Isoprenoids and ER Stress Arteriosclerosis, Thrombosis, and Vascular Biology (2019)
  4. Ray O Bahado‐Singh, Jiri Sonek, David McKenna, David Cool, Buket Aydas, Onur Turkoglu, Trent Bjorndahl, Rupasri Mandal, David Wishart, Perry Friedman, Stewart F Graham, Ali Yilmaz Artificial intelligence and amniotic fluid multiomics: the prediction of perinatal outcome in asymptomatic women with short cervix Ultrasound in Obstetrics & Gynecology 10.1002/uog.20168 (2019) PubMed ID: 30381856
  5. Jonas Patron, Arnau Serra Cayuela, Beomsoo Han, Carin Li, David Scott Wishart Assessing the performance of genome-wide association studies for predicting disease risk BioRxiv doi.org/10.1101/701086 (2019)
  6. Mohammad A Anwar, Darlene Liying Dai, Janet Wilson‐McManus, Derek Smith, Gordon A Francis, Christoph H Borchers, Bruce M McManus, John S Hill, Gabriela V Cohen Freue Back Cover: Multiplexed LC–ESI–MRM‐MS‐based Assay for Identification of Coronary Artery Disease Biomarkers in Human Plasma PROTEOMICS–Clinical Applications 10.1002/prca.201970044 (2019)
  7. Derrick Blackmore, Zaeem Siddiqi, Liang Li, Nan Wang, Walter Maksymowych Beyond the antibodies: serum metabolomic profiling of myasthenia gravis Metabolomics 10.1007/s11306-019-1571-9 (2019) PubMed ID: 31372762
  8. Yannick Djoumbou-Feunang, Jarlei Fiamoncini, Alberto Gil-de-la-Fuente, Russell Greiner, Claudine Manach, David S Wishart BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification Journal of cheminformatics 10.1186/s13321-018-0324-5 (2019) PubMed ID: 30612223
  9. Alberto Gil-de-la-Fuente, Joanna Godzien, Sergio Saugar, Rodrigo Garcia-Carmona, Hasan Badran, David S Wishart, Coral Barbas, Abraham Otero CEU Mass Mediator 3.0: A Metabolite Annotation Tool Journal of Proteome Research 10.1021/acs.jproteome.8b00720 (2019) PubMed ID: 30574788
  10. Yannick Djoumbou-Feunang, Allison Pon, Naama Karu, Jiamin Zheng, Carin Li, David Arndt, Maheswor Gautam, Felicity Allen, David S Wishart CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification Metabolites 10.3390/metabo9040072 (2019) PubMed ID: 31013937
  11. David Shultis, Pralay Mitra, Xiaoqiang Huang, Jarrett Johnson, Naureen Aslam Khattak, Felicia Gray, Clint Piper, Jeff Czajka, Logan Hansen, Bingbing Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, Jeanne Stuckey, Tomasz Cierpicki, Christoph H Borchers, Shaomeng Wang, Ming Lei, Yang Zhang Changing the Apoptosis Pathway through Evolutionary Protein Design Journal of molecular biology 10.1016/j.jmb.2018.12.016 (2019) PubMed ID: 30625288
  12. Filipa Teixeira, Eric Tse, Helena Castro, Karl AT Makepeace, Ben A Meinen, Christoph H Borchers, Leslie B Poole, James C Bardwell, Ana M Tomás, Daniel R Southworth, Ursula Jakob Chaperone activation and client binding of a 2-cysteine peroxiredoxin Nature communications 10.1038/s41467-019-08565-8 (2019) PubMed ID: 30737390
  13. Michelle Saoi, Michael Percival, Carine Nemr, Alice Li, Martin Gibala, Philip Britz-McKibbin Characterization of the Human Skeletal Muscle Metabolome for Elucidating the Mechanisms of Bicarbonate Ingestion on Strenuous Interval Exercise Analytical Chemistry 10.1021/acs.analchem.9b00149 (2019) PubMed ID: 30835436
  14. Foroutan A., Guo A.C., Vazquez- Fresno R., Lipfert M., Zhang L., Zheng J., Badran H., Budinski Z., Mandal R., Ametaj B.N., Wishart D.S. Chemical Composition of Commercial Cow's Milk Journal of agricultural and food chemistry 10.1021/acs.jafc.9b00204 (2019) PubMed ID: 30994344
  15. Dorothea Mung, Liang Li Chemical isotope labeling liquid chromatography mass spectrometry for investigating acute dietary effects of cow milk consumption on human urine metabolome Journal of Food and Drug Analysis 10.1016/j.jfda.2018.10.007 (2019) PubMed ID: 30987728
  16. Yoshimasa Oyama, Colleen M Bartman, Stephanie Bonney, J Scott Lee, Lori A Walker, Jun Han, Christoph H Borchers, Peter M Buttrick, Carol M Aherne, Nathan Clendenen, Sean P Colgan, Tobias Eckle Circadian light-mediated endothelial metabolic reprogramming bioRxiv 10.1016/j.celrep.2019.07.020 (2019)
  17. Ammar Hassanzadeh Keshteli, Karen L Madsen, Rupasri Mandal, Guy E Boeckxstaens, Premysl Bercik, Giada De Palma, David E Reed, David Wishart, Stephen Vanner, Levinus A Dieleman Comparison of the metabolomic profiles of irritable bowel syndrome patients with ulcerative colitis patients and healthy controls: new insights into pathophysiology and potential biomarkers Alimentary pharmacology & therapeutics 10.1111/apt.15141 (2019) PubMed ID: 30706502
  18. Nicholas I Brodie, Konstantin I Popov, Evgeniy V Petrotchenko, Nikolay V Dokholyan, Christoph H Borchers Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations PLoS computational biology 10.1371/journal.pcbi.1006859 (2019) PubMed ID: 30917118
  19. Deying Chen, Jiong Yu, Zhehua Zhang, Xiaoling Su, Liang Li, Lanjuan Li Controlling Preanalytical Process in High-Coverage Quantitative Metabolomics: Spot-Sample Collection for Mouse Urine and Fecal Metabolome Profiling Analytical Chemistry 10.1021/acs.analchem.9b00310 (2019) PubMed ID: 30900868
  20. V Boczonadi, MS King, AC Smith, M Olahova, B Bansagi, A Roos, F Eyassu, C Borchers, V Ramesh, H Lochmüller, T Polvikoski, RG Whittaker, A Pyle, H Griffin, RW Taylor, PF Chinnery, AJ Robinson, ERS Kunji, R Horvath Correction: Mitochondrial oxodicarboxylate carrier deficiency is associated with mitochondrial DNA depletion and spinal muscular atrophy–like disease Genetics in medicine: official journal of the American College of Medical Genetics 10.1038/s41436-019-0506-1 (2019) PubMed ID: 31028354
  21. Evgeniy V Petrotchenko, Jason J Serpa, Christoph H Borchers Cross‐linking Applications in Structural Proteomics Proteomics for Biological Discovery 10.1002/9781119081661.ch7 (2019)
  22. Vijaya Kumar Hinge, Nikolay Blinov, Dipankar Roy, W Ted Allison, David S Wishart, Andriy Kovalenko Design and optimization of nucleic acid derivatives for inhibition of prion-like propagation at W32 site of SOD1 enzyme in Amyotrophic Lateral Sclerosis PRION (2019)
  23. Xiaohang Wang, Wei Han, Jing Yang, David Westaway, Liang Li Development of chemical isotope labeling LC-MS for tissue metabolomics and its application for brain and liver metabolome profiling in Alzheimer's disease mouse model Analytica Chimica Acta 10.1016/j.aca.2018.10.060 (2019) PubMed ID: 30661596
  24. Gabriele Rocchetti, Sudarshana Reddy Bhumireddy, Gianluca Giuberti, Rupasri Mandal, Luigi Lucini, David S Wishart Edible nuts deliver polyphenols and their transformation products to the large intestine: An in vitro fermentation model combining targeted/untargeted metabolomics Food research international 10.1016/j.foodres.2018.09.012 (2019) PubMed ID: 30717008
  25. Ammar Hassanzadeh Keshteli, Karen L Madsen, Rupasri Mandal, Guy E Boeckxstaens, Premysl Bercik, Giada De Palma, David E Reed, David Wishart, Stephen Vanner, Levinus A Dieleman Editorial: metabolomic biomarkers for colorectal adenocarcinoma and in the differentiation between irritable bowel syndrome and ulcerative colitis in clinical remission - confounded by the gut microbiome? Authors' reply Alimentary pharmacology & therapeutics 10.1111/apt.15200 (2019) PubMed ID: 30920043
  26. Yoshimasa Oyama, Colleen M Bartman, Stephanie Bonnie, J Scott Lee, Lori A Walker, Jun Han, Christoph H Borchers, Peter M Buttrick, Nathan Clendenen, Sean P Colgan, Tobias Eckle Endothelial specific PER2 at the crossroads of light elicited circadian amplitude enhancement as novel cardioprotective strategy and transcriptional regulation of HIF1A-dependent metabolic adaptation to myocardial ischemia bioRxiv 10.1101/561340 (2019)
  27. Claudio Iacobucci, Christine Piotrowski, Ruedi Aebersold, Bruno C Amaral, Philip Andrews, Katja Bernfur, Christoph Borchers, Nicolas I Brodie, James E Bruce, Yong Cao, Stephane Chaignepain, Juan D Chavez, Stéphane Claverol, Jurgen Cox, Trisha Davis, Gianluca Degliesposti, Meng-Qiu Dong, Nufar Edinger, Cecilia Emanuelsson, Marina Gay, Michael Götze, Francisco Gomes-Neto, Fabio C Gozzo, Craig Gutierrez, Caroline Haupt, Albert JR Heck, Franz Herzog, Lan Huang, Michael R Hoopmann, Nir Kalisman, Oleg Klykov, Zdenek Kukacka, Fan Liu, Michael J MacCoss, Karl Mechtler, Ravit Mesika, Robert L Moritz, Nagarjuna Nagaraj, Victor Nesati, Ana GC Neves-Ferreira, Robert Ninnis, Petr Novák, Francis J O’Reilly, Matthias Pelzing, Evgeniy Petrotchenko, Lolita Piersimoni, Manolo Plasencia, Tara Pukala, Kasper D Rand, Juri Rappsilber, Dana Reichmann, Carolin Sailer, Chris P Sarnowski, Richard A Scheltema, Carla Schmidt, David C Schriemer, Yi Shi, J Mark Skehel, Moriya Slavin, Frank Sobott, Victor Solis-Mezarino, Heike Stephanowitz, Florian Stengel, Christian E Stieger, Esben Trabjerg, Michael Trnka, Marta Vilaseca, Rosa Viner, Yufei Xiang, Sule Yilmaz, Alex Zelter, Daniel Ziemianowicz, Alexander Leitner, Andrea Sinz First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study Analytical chemistry 10.1021/acs.analchem.9b00658 (2019) PubMed ID: 31045356
  28. Ray O Bahado-Singh, Argyro Syngelaki, Rupsari Mandal, BeomSoo Han, Liang Li, Trent C Bjorndahl, Nan Wang, Dev Maulik, Edison Dong, Onur Turkoglu, Chiao-Li Tseng, Amna Zeb, Mark Redman, David S Wishart, Kypros H Nicolaides First-trimester metabolomic prediction of stillbirth The Journal of Maternal-Fetal & Neonatal Medicine 10.1080/14767058.2018.1465552 (2019) PubMed ID: 29712497
  29. Rosa Vázquez-Fresno, Albert Remus R Rosana, Tanvir Sajed, Tuviere Onookome-Okome, Noah A Wishart, David S Wishart Herbs and Spices-Biomarkers of Intake Based on Human Intervention Studies–A Systematic Review Genes & nutrition 10.1186/s12263-019-0636-8 (2019) PubMed ID: 31143299
  30. Meera Shanmuganathan, Sabrina Macklai, Clara Barrenas Cardenas, Zachary Kroezen, Marcus Kim, William Zizek, Howard Lee, Philip Britz-McKibbin High-throughput and Comprehensive Drug Surveillance Using Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry JoVE (Journal of Visualized Experiments) 10.3791/58986 (2019) PubMed ID: 31081805
  31. Wajiha Gohir, Katherine M Kennedy, Jessica G Wallace, Michelle Saoi, Christian J Bellissimo, Philip Britz‐McKibbin, Jim J Petrik, Michael G Surette, Deborah M Sloboda High‐fat diet intake modulates maternal intestinal adaptations to pregnancy and results in placental hypoxia, as well as altered fetal gut barrier proteins and immune markers The Journal of Physiology 10.1113/JP277353 (2019) PubMed ID: 31081119
  32. Renxue Wang, Jonathan A Sheps, Lin Liu, Jun Han, Patrick SK Chen, Jason Lamontagne, Peter D Wilson, Ian Welch, Christoph H Borchers, Victor Ling Hydrophilic bile acids prevent liver damage caused by lack of biliary phospholipid in Mdr2−/− mice Journal of lipid research 10.1194/jlr.M088070 (2019) PubMed ID: 30416103
  33. Simon Hayek, Nassima Bekaddour, Laurie Besson, Rodolphe Alves de Sousa, Nicolas Pietrancosta, Sébastien Viel, Nikaia Smith, Yves Jacob, Sébastien Nisole, Rupasri Mandal, David S Wishart, Thierry Walzer, Jean-Philippe Herbeuval, Pierre-Olivier Vidalain Identification of Primary Natural Killer Cell Modulators by Chemical Library Screening with a Luciferase-Based Functional Assay SLAS DISCOVERY: Advancing Life Sciences R&D 10.1177/2472555218797078 (2019) PubMed ID: 30184441
  34. Golam M Uddin, Liyan Zhang, Saumya Shah, Arata Fukushima, Cory S Wagg, Keshav Gopal, Rami Al Batran, Simran Pherwani, Kim L Ho, Jamie Boisvenue, Qutuba G Karwi, Tariq Altamimi, David S Wishart, Jason RB Dyck, John R Ussher, Gavin Y Oudit, Gary D Lopaschuk Impaired branched chain amino acid oxidation contributes to cardiac insulin resistance in heart failure Cardiovascular diabetology 31277657 (2019) PubMed ID: 10
  35. Fengfeng Mao, Teng Liu, Xinfeng Hou, Hanqing Zhao, Wenhui He, Cong Li, Zhiyi Jing, Jianhua Sui, Fengchao Wang, Xiaohui Liu, Jun Han, Christoph H Borchers, Jian-She Wang, Wenhui Li Increased sulfation of bile acids in mice and human subjects with sodium taurocholate cotransporting polypeptide deficiency Journal of Biological Chemistry 10.1074/jbc.RA118.007179 (2019) PubMed ID: 31201272
  36. Chia-Wei Hsu, Yi-Ting Chen, Ya-Ju Hsieh, Kai-Ping Chang, Pei-Chun Hsueh, Ting-Wen Chen, Jau-Song Yu, Yu-Sun Chang, Liang Li, Chih-Ching Wu Integrated analyses utilizing metabolomics and transcriptomics reveal perturbation of the polyamine pathway in oral cavity squamous cell carcinoma Analytica Chimica Acta 10.1016/j.aca.2018.10.070 (2019) PubMed ID: 30661578
  37. Yoshimasa Oyama, Colleen M Bartman, Stephanie Bonney, J Scott Lee, Lori A Walker, Jun Han, Christoph H Borchers, Peter M Buttrick, Carol M Aherne, Nathan Clendenen, Sean P Colgan, Tobias Eckle Intense light-mediated circadian cardioprotection via transcriptional reprogramming of the endothelium Cell Reports 10.1016/j.celrep.2019.07.020 (2019) PubMed ID: 31390562
  38. Alastair Barr, Michael Overduin JoVE Methods Collection Highlights: Protein-Protein Interactions JoVE (Journal of Visualized Experiments) 10.3791/59816 (2019) PubMed ID: 31219457
  39. Lei Chen, Nan Li, Shunnan Ge, Andres M Lozano, Darrin J Lee, Chen Yang, Liang Li, Qianrong Bai, Hongbing Lu, Jing Wang, Xin Wang, Jiaming Li, Jiangpeng Jing, Mingming Su, Longxiao Wei, Xuelian Wang, Guodong Gao Long-term results after deep brain stimulation of nucleus accumbens and the anterior limb of the internal capsule for preventing heroin relapse: An open-label pilot study Brain Stimulation 10.1016/j.brs.2018.09.006 (2019) PubMed ID: 30245163
  40. Yunong Li, Liang Li Mass Accuracy Check Using Common Background Peaks for Improving Metabolome Data Quality in Chemical Isotope Labeling LC-MS Journal of The American Society for Mass Spectrometry 10.1007/s13361-019-02248-w (2019) PubMed ID: 31140076
  41. Carol E Parker, Maria RE Warren Hines, Viorel Mocanu, Susanna F Greer, Christoph H Borchers Mass Spectrometric Determination of Protein Ubiquitination Post-Translational Modification of Proteins 10.1007/978-1-4939-9055-9_13 (2019)
  42. Michelle Saoi, Alice Li, Chris McGlory, Tanner Stokes, Mark T von Allmen, Stuart M Phillips, Philip Britz-McKibbin Metabolic Perturbations from Step Reduction in Older Persons at Risk for Sarcopenia: Plasma Biomarkers of Abrupt Changes in Physical Activity Metabolites 10.3390/metabo9070134 (2019) PubMed ID: 31288431
  43. Alicia DiBattista, Nathan McIntosh, Monica Lamoureux, Osama Y Al-Dirbashi, Pranesh Chakraborty, Philip Britz-McKibbin Metabolic Signatures of Cystic Fibrosis Identified in Dried Blood Spots for Newborn Screening Without Carrier Identification Journal of Proteome Research 10.1021/acs.jproteome.8b00351 (2019) PubMed ID: 30507207
  44. Nadine Wellington, Meera Shanmuganathan, Russell J de Souza, Michael A Zulyniak, Sandi Azab, Jonathon Bloomfield, Alicia Mell, Ritchie Ly, Dipika Desai, Sonia S Anand, Philip Britz-McKibbin Metabolic Trajectories Following Contrasting Prudent and Western Diets from Food Provisions: Robust Biomarkers of Short-Term Changes in Habitual Diet Preprints 10.20944/preprints201908.0149.v1 (2019)
  45. Indranil Sarkar, Adriana Zardini Buzatto, Ravendra Garg, Liang Li, Sylvia van Drunen Littel-van den Hurk Metabolomic and immunological profiling of respiratory syncytial virus infection after intranasal immunization with a subunit vaccine candidate Journal of Proteome Research 10.1021/acs.jproteome.8b00806 (2019) PubMed ID: 30706717
  46. Perry Friedman, Ali Yilmaz, Amna Zeb, Aydas Buket, Amy Whitten, Ali Alhousseini, Dotun Ogunyemi, BeomSoo Han, Rupasri Mandal, David Wishart, Stewart Graham, Ray Bahado-Singh Metabolomic prediction of prematurity in asymptomatic short cervix American Journal of Obstetrics and Gynecology (2019)
  47. Phurpa Wangchuk, Konstantinos Kouremenos, Ramon M Eichenberger, Mark Pearson, Atik Susianto, David S Wishart, Malcolm J McConville, Alex Loukas Metabolomic profiling of the excretory–secretory products of hookworm and whipworm Metabolomics 10.1007/s11306-019-1561-y (2019) PubMed ID: 31254203
  48. Paiboon Tunsagool, Xiaohang Wang, Wichitra Leelasuphakul, Warangkana Jutidamrongphan, Narumon Phaonakrop, Janthima Jaresitthikunchai, Sittiruk Roytrakul, Guanqun Chen, Liang Li Metabolomic study of stress responses leading to plant resistance in mandarin fruit mediated by preventive applications of Bacillus subtilis cyclic lipopeptides Postharvest Biology and Technology 10.1016/j.postharvbio.2019.110946 (2019)
  49. David S Wishart Metabolomics for Investigating Physiological and Pathophysiological Processes Physiological reviews 10.1152/physrev.00035.2018 (2019) PubMed ID: 31434538
  50. Mai Yamamoto, Maria Ines Pinto-Sanchez, Premysl Bercik, Philip Britz-McKibbin Metabolomics reveals elevated urinary excretion of collagen degradation and epithelial cell turnover products in irritable bowel syndrome patients Metabolomics 10.1007/s11306-019-1543-0 (2019) PubMed ID: 31111238
  51. Paul M Ryan, Elaine Patterson, Ilaria Carafa, Rupasri Mandal, David S Wishart, Timothy G Dinan, John F Cryan, Kieran M Tuohy, Catherine Stanton, R Paul Ross Metformin and DPP-4 Inhibitor Differentially Modulate the Intestinal Microbiota and Plasma Metabolome of Metabolically Dysfunctional Mice Canadian Journal of Diabetes 10.1016/j.jcjd.2019.05.008 (2019)
  52. Ammar H Keshteli, Richa Chibbar, Rupasri Mandal, David S Wishart, Levinus A Dieleman Mo1846 – Ulcerative Colitis (UC) Patients with Primary Sclerosing Cholangitis (PSC) Have Distinctive Serum Metabolomic Fingerprints Versus Uc Patients Without Psc Gastroenterology 10.1016/S0016-5085(19)39113-9 (2019)
  53. Xiaowei Shi, Jingqi Liu, Deying Chen, Minglei Zhu, Jiong Yu, Haiyang Xie, Lin Zhou, Liang Li, Shusen Zheng MSC-triggered metabolomic alterations within liver-resident immune cells isolated from CCl4-induced mouse ALI model detected by CIL LC-MS Experimental Cell Research 10.1016/j.yexcr.2019.111511 (2019) PubMed ID: 31362001
  54. Mohammad A Anwar, Darlene Liying Dai, Janet Wilson‐McManus, Derek Smith, Gordon A Francis, Christoph H Borchers, Bruce M McManus, John S Hill, Gabriela V Cohen Freue Multiplexed LC–ESI–MRM‐MS‐based Assay for Identification of Coronary Artery Disease Biomarkers in Human Plasma PROTEOMICS–Clinical Applications 10.1002/prca.201700111 (2019) PubMed ID: 30632678
  55. Michael Overduin, Mansoore Esmaili Native Nanodiscs and the Convergence of Lipidomics, Metabolomics, Interactomics and Proteomics Applied Sciences 10.3390/app9061230 (2019)
  56. Meera Shanmuganathan, Philip Britz-McKibbin New Advances for Newborn Screening of Inborn Errors of Metabolism by Capillary Electrophoresis-Mass Spectrometry (CE-MS) Clinical Applications of Capillary Electrophoresis 10.1007/978-1-4939-9213-3_10 (2019) PubMed ID: 30847789
  57. Meera Shanmuganathan, Philip Britz-McKibbin New Advances in Amino Acid Profiling in Biological Samples by Capillary Electrophoresis-Mass Spectrometry Amino Acid Analysis 10.1007/978-1-4939-9639-1_25 (2019) PubMed ID: 31347129
  58. David S Wishart NMR metabolomics: A look ahead Journal of Magnetic Resonance 10.1016/j.jmr.2019.07.013 (2019) PubMed ID: 31377153
  59. Abdul-Hamid Emwas, Raja Roy, Ryan T McKay, Leonardo Tenori, Edoardo Saccenti, GA Gowda, Daniel Raftery, Fatimah Alahmari, Lukasz Jaremko, Mariusz Jaremko, David S Wishart Nmr spectroscopy for metabolomics research Metabolites 10.3390/metabo9070123 (2019)
  60. Ben Archdekin, Atul Sharma, Ian W Gibson, David Rush, David S Wishart, Tom D Blydt‐Hansen Non‐invasive differentiation of non‐rejection kidney injury from acute rejection in pediatric renal transplant recipients Pediatric transplantation 10.1111/petr.13364 (2019) PubMed ID: 30719822
  61. Marynka M Ulaszewska, Christoph H Weinert, Alessia Trimigno, Reto Portmann, Cristina Andres Lacueva, René Badertscher, Lorraine Brennan, Carl Brunius, Achim Bub, Francesco Capozzi, Marta Cialiè Rosso, Chiara E Cordero, Hannelore Daniel, Stéphanie Durand, Bjoern Egert, Paola G Ferrario, Edith JM Feskens, Pietro Franceschi, Mar Garcia‐Aloy, Franck Giacomoni, Pieter Giesbertz, Raúl González‐Domínguez, Kati Hanhineva, Lieselot Y Hemeryck, Joachim Kopka, Sabine E Kulling, Rafael Llorach, Claudine Manach, Fulvio Mattivi, Carole Migné, Linda H Münger, Beate Ott, Gianfranco Picone, Grégory Pimentel, Estelle Pujos‐Guillot, Samantha Riccadonna, Manuela J Rist, Caroline Rombouts, Josep Rubert, Thomas Skurk, Pedapati SC Sri Harsha, Lieven Van Meulebroek, Lynn Vanhaecke, Rosa Vázquez‐Fresno, David Wishart, Guy Vergères Nutrimetabolomics: an integrative action for metabolomic analyses in human nutritional studies Molecular nutrition & food research 10.1002/mnfr.201800384 (2019) PubMed ID: 30176196
  62. Padma Maruvada, Johanna W Lampe, David S Wishart, Dinesh Barupal, Deirdra N Chester, Dylan Dodd, Yannick Djoumbou-Feunang, Pieter C Dorrestein, Lars O Dragsted, John Draper, Linda C Duffy, Johanna T Dwyer, Nancy J Emenaker, Oliver Fiehn, Robert E Gerszten, Frank B Hu, Robert W Karp, David M Klurfeld, Maren R Laughlin, A Roger Little, Christopher J Lynch, Steven C Moore, Holly L Nicastro, Diane M O'Brien, José M Ordovás, Stavroula K Osganian, Mary Playdon, Ross Prentice, Daniel Raftery, Nichole Reisdorph, Helen M Roche, Sharon A Ross, Shengmin Sang, Augustin Scalbert, Pothur R Srinivas, Steven H Zeisel Perspective: Dietaryiomarkers of Intake and Exposure—Exploration with Omics Approaches Advances in Nutrition 10.1093/advances/nmz075 (2019) PubMed ID: 31386148
  63. Anandram Venkatasubramanian, Vincent TK Sauer, Jocelyn N Westwood-Bachman, Kai Cui, Mike Xia, David S Wishart, Wayne K Hiebert Porous Nanophotonic Optomechanical Beams for Enhanced Mass Adsorption ACS sensors 10.1021/acssensors.8b01366 (2019) PubMed ID: 30942578
  64. Marcia A LeVatte, Matthias Lipfert, Carol Ladner-Keay, David S Wishart Preparation and characterization of a highly soluble Aβ1-42 peptide variant Protein expression and purification 10.1016/j.pep.2019.105480 (2019) PubMed ID: 31425755
  65. Irina M Larina, Andrew J Percy, Juncong Yang, Christoph H Borchers, Andrei M Nosovsky, Anatoli I Grigoriev, Evgeny N Nikolaev Protein expression changes caused by spaceflight as measured for 18 Russian cosmonauts (vol 7, 8142, 2017) SCIENTIFIC REPORTS (2019)
  66. Aidin Foroutan, Seyed Ali Goldansaz, Matthias Lipfert, David S Wishart Protocols for NMR Analysis in Livestock Metabolomics Metabolomics 10.1007/978-1-4939-9488-5_23 (2019) PubMed ID: 31127564
  67. Irina M Larina, Andrew J Percy, Juncong Yang, Christoph H Borchers, Andrei M Nosovsky, Anatoli I Grigoriev, Evgeny N Nikolaev Publisher Correction: Protein expression changes caused by spaceflight as measured for 18 Russian cosmonauts Scientific reports 10.1038/s41598-019-43121-w (2019) PubMed ID: 31171809
  68. Glenn R Masson, John E Burke, Natalie G Ahn, Ganesh S Anand, Christoph Borchers, Sébastien Brier, George M Bou-Assaf, John R Engen, S Walter Englander, Johan Faber, Rachel Garlish, Patrick R Griffin, Michael L Gross, Miklos Guttman, Yoshitomo Hamuro, Albert JR Heck, Damian Houde, Roxana E Iacob, Thomas JD Jørgensen, Igor A Kaltashov, Judith P Klinman, Lars Konermann, Petr Man, Leland Mayne, Bruce D Pascal, Dana Reichmann, Mark Skehel, Joost Snijder, Timothy S Strutzenberg, Eric S Underbakke, Cornelia Wagner, Thomas E Wales, Benjamin T Walters, David D Weis, Derek J Wilson, Patrick L Wintrode, Zhongqi Zhang, Jie Zheng, David C Schriemer, Kasper D Rand Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments Nature methods 10.1038/s41592-019-0459-y (2019) PubMed ID: 31249422
  69. Sandi Azab, Ritchie Ly, Philip Britz-McKibbin Robust Method for High-Throughput Screening of Fatty Acids by Multisegment Injection-Nonaqueous Capillary Electrophoresis–Mass Spectrometry with Stringent Quality Control Analytical Chemistry 10.1021/acs.analchem.8b05054 (2019) PubMed ID: 30570251
  70. Nikolay Blinov, David S Wishart, Andriy Kovalenko Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation The Journal of Physical Chemistry B 10.1021/acs.jpcb.9b00480 (2019) PubMed ID: 30811210
  71. Nikolay Blinov, David S Wishart, Neil R Cashman, Andriy Kovalenko Structural characterization of amyloidogenic proteins implicated in neurodegeneration under conditions of intracellular crowding and in nonpolar environments PRION (2019)
  72. Zabed Mahmud, Somaya Zahran, Philip B Liu, Bela Reiz, Brandon YH Chan, Andrej Roczkowsky, Christian-Scott E McCartney, Peter L Davies, Liang Li, Richard Schulz, Peter M Hwang Structure and proteolytic susceptibility of the inhibitory C-terminal tail of cardiac troponin I Biochimica et Biophysica Acta (BBA) - General Subjects 10.1016/j.bbagen.2019.01.008 (2019) PubMed ID: 30659884
  73. Michael Overduin, Mansoore Esmaili Structures and Interactions of Transmembrane Targets in Native Nanodiscs SLAS DISCOVERY: Advancing Life Sciences R&D 10.1177/2472555219857691 (2019) PubMed ID: 31242812
  74. Farhana R Pinu, David J Beale, Amy M Paten, Konstantinos Kouremenos, Sanjay Swarup, Horst J Schirra, David Wishart Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community Metabolites 10.3390/metabo9040076 (2019) PubMed ID: 31003499
  75. Chen, Y.T., Huang, H.C., Hsieh, Y.J., Fu, S.H., Li, L., Chen, C.L.., Chu, L.J., Yu, J.S. Targeting amine-and phenol-containing metabolites in urine by dansylation isotope labeling and liquid chromatography mass spectrometry for evaluation of bladder cancer biomarkers Journal of Food and Drug Analysis 10.1016/j.jfda.2018.11.008 (2019) PubMed ID: 30987717
  76. Éder Soares Pires, Cristiane Cassiolato Pires Hardoim, Karla Rodrigues Miranda, Danielle Angst Secco, Leandro Araujo Lobo, Denise P Carvalho, Jun Han, Christoph Borchers, Rosana Barreto Rocha Ferreira, Joana Falcão Salles, Regina Maria Cavalcanti Pilotto Domingues, Luis Caetano Martha Antunes The gut microbiome and metabolome of two riparian communities in the Amazon Frontiers in Microbiology 10.3389/fmicb.2019.02003 (2019)
  77. Daria N Kashirina, Andrew J Percy, Liudmila Kh Pastushkova, Christoph H Borchers, Kirill S Kireev, Vladimir A Ivanisenko, Alexey S Kononikhin, Eugene N Nikolaev, Irina M Larina The molecular mechanisms driving physiological changes after long duration space flights revealed by quantitative analysis of human blood proteins BMC medical genomics 10.1186/s12920-019-0490-y (2019) PubMed ID: 30871558
  78. Keisean AJM Stevenson, Leonid M Blumberg, James J Harynuk Thermodynamics-based Retention Maps to Guide Column Choices for Comprehensive Multi-Dimensional Gas Chromatography Analytica Chimica Acta 10.1016/j.aca.2019.08.011 (2019)
  79. Keisean AJM Stevenson, James J Harynuk Thermodynamics‐based modelling of gas chromatography separations across column geometries and systems, including the prediction of peak widths Journal of Separation Science 10.1002/jssc.201801294 (2019) PubMed ID: 30964226
  80. Brittney A Klein, Ian M Robertson, Béla Reiz, Thomas Kampourakis, Liang Li, Brian D Sykes Thioimidate Bond Formation between Cardiac Troponin C and Nitrile-containing Compounds ACS Medicinal Chemistry Letters 10.1021/acsmedchemlett.9b00168 (2019)
  81. Gabriele Rocchetti, Luigi Lucini, Gianluca Giuberti, Sudarshana Reddy Bhumireddy, Rupasri Mandal, Marco Trevisan, David S Wishart Transformation of polyphenols found in pigmented gluten-free flours during in vitro large intestinal fermentation Food Chemistry 10.1016/j.foodchem.2019.125068 (2019) PubMed ID: 31260977
  82. Nicola Cherry, Yayne-abeba Aklilu, Jeremy Beach, Philip Britz-McKibbin, Rebecca Elbourne, Jean-Michel Galarneau, Biban Gill, David Kinniburgh, Xu Zhang Urinary 1-hydroxypyrene and skin contamination in firefighters deployed to the Fort McMurray fire Annals of Work Exposures and Health 10.1093/annweh/wxz006 (2019) PubMed ID: 30753267
  83. Biban Gill, Alicia Mell, Meera Shanmuganathan, Karl Jobst, Xu Zhang, David Kinniburgh, Nicola Cherry, Philip Britz-McKibbin Urinary hydroxypyrene determination for biomonitoring of firefighters deployed at the Fort McMurray wildfire: an inter-laboratory method comparison Analytical and Bioanalytical Chemistry 10.1007/s00216-018-01569-1 (2019) PubMed ID: 30683964
  84. Allison I Daniel, Matilda E Arvidsson Kvissberg, Edward Senga, Christian J Versloot, Philliness Prisca Harawa, Wieger Voskuijl, David Wishart, Rupasri Mandal, Robert Bandsma, Céline Bourdon Urinary Organic Acids Increase After Clinical Stabilization of Hospitalized Children With Severe Acute Malnutrition Food and nutrition bulletin 10.1177/0379572119853930 (2019) PubMed ID: 31303023

2018

  1. Keshteli, A.H., Tso, R., Dieleman, L.A., Park, H., Kroeker, K.I., Jovel, J., Gillevet, P.M., Sikaroodi, M., Mandal, R., Fedorak, R.N., Madsen, K.L. A Distinctive Urinary Metabolomic Fingerprint Is Linked With Endoscopic Postoperative Disease Recurrence in Crohn's Disease Patients. Inflamm Bowel Dis. 2018 Mar 19;24(4):861-870 10.1093/ibd/izx070 (2018) PubMed ID: 29562272
  2. Naama Karu, Lu Deng, Mordechai Slae, An Chi Guo, Tanvir Sajed, Hien Huynh, Eytan Wine, David S Wishart A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database Analytica Chimica Acta 10.1016/j.aca.2018.05.031 (2018) PubMed ID: 30032758
  3. Zheng, J., Mandal, R., Wishart, D.S. A sensitive, high-throughput LC-MS/MS method for measuring catecholamines in low volume serum. Analytica Chimica Acta. 10.1016/j.aca.2018.01.021 (2018)
  4. Yeganeh Khaniani, Matthias Lipfert, Dipanjan Bhattacharyya, Rolando Perez Pineiro, Jiamin Zheng, David Wishart A Simple and Convenient Synthesis of Unlabeled and 13C-Labeled 3-(3-Hydroxyphenyl)-3-Hydroxypropionic Acid and Its Quantification in Human Urine Samples Metabolites 10.3390/metabo8040080 (2018) PubMed ID: 30469313
  5. Hou, S., Stevenson, K.A.J.M., Harynuk, J.J. A simple, fast, and accurate thermodynamic-based approach for transfer and prediction of gas chromatography retention times between columns and instruments Part I: Estimation of reference column geometry and thermodynamic parameters. J Sep Sci. 2018 Mar 26 10.1002/jssc.201701343 (2018) PubMed ID: 29579350
  6. Keshteli, A.H., Madsen, K., Nickurak, C., Kroeker, K.I., Mandal, R., Valcheva, R.S., Wishart, D.S., Veldhuyzen van Zanten, S., Halloran, B.P., Fedorak, R., Dieleman, L.A. A16 FOLLOWING AN ANTI-INFLAMMATORY DIET PREVENTS INCREASES OF FECAL CALPROTECTIN AND ALTERS METABOLOMIC PROFILE OF ULCERATIVE COLITIS PATIENTS, A RANDOMIZED CONTROLLED TRIAL. Journal of the Canadian Association of Gastroenterology, Volume 1, Issue suppl_2, 1 March 2018, Pg 25–26 10.1093/jcag/gwy009.016 (2018)
  7. Shraddha Sapkota, Tao Huan, Tran Tran, Jiamin Zheng, Richard Camicioli, Liang Li, Roger A Dixon Alzheimer's Biomarkers from Multiple Modalities Selectively Discriminate Clinical Status: Relative Importance of Salivary Metabolomics Panels, Genetic, Lifestyle, Cognitive, Functional Health, and Demographic Risk Markers Frontiers in Aging Neuroscience 10.3389/fnagi.2018.00296 (2018) PubMed ID: 30333744
  8. Sonek, J., Bahado-Singh, R., McKenna, D., Cool, D., Bjorndahl, T., Han, B., Mandal, R., Wishart, D.S., Cayuela, A., Kumar, P., Yilmex, A., Graham, S., Friedman, P. Amniotic fluid metabolomics and targeted proteomics in prediction of preterm birth. American Journal of Obstetrics and Gynecology, January 2018, Volume 218, Issue 1, pg S432 10.1016/j.ajog.2017.11.249 (2018)
  9. Mung, D., Li, L. Applying quantitative metabolomics based on chemical isotope labeling LC-MS for detecting potential milk adulterant in human milk. Anal Chim Acta. 2018 Feb 25; 1001:78-85 10.1016/j.aca.2017.11.019 (2018) PubMed ID: 29291809
  10. Linda H Münger, Mar Garcia-Aloy, Rosa Vázquez-Fresno, Doreen Gille, Albert Remus R Rosana, Anna Passerini, María-Trinidad Soria-Florido, Grégory Pimentel, Tanvir Sajed, David S Wishart, Cristina Andres Lacueva, Guy Vergères, Giulia Praticò Biomarker of food intake for assessing the consumption of dairy and egg products Genes & Nutrition 10.1186/s12263-018-0615-5 (2018) PubMed ID: 30279743
  11. Cheng-Chia Lee, Ya-Ju Hsieh, Shao-Wei Chen, Shu-Hsuan Fu, Chia-Wei Hsu, Chih-Ching Wu, Wei Han, Yunong Li, Tao Huan, Yu-Sun Chang, Jau-Song Yu, Liang Li, Chih-Hsiang Chang, Yi-Ting Chen Bretschneider solution-induced alterations in the urine metabolome in cardiac surgery patients Scientific Reports 10.1038/s41598-018-35631-w (2018) PubMed ID: 30538262
  12. Han, W., Li, L. Chemical Isotope Labeling LC-MS for Human Blood Metabolome Analysis. Methods Mol Biol. 2018; 1730:213-225 10.1007/978-1-4939-7592-1_14 (2018) PubMed ID: 29363075
  13. Cassiède, M., Mercier, P., Shipley, P.R., Dueck, M., Kamravaei, S., Nair, S., Mino, J., Pei, L., Broadhurst, D., Lacya, P., Quémeraisa, B. Comparison of computational approaches for identification and quantification of urinary metabolites in 1H NMR spectra. Anal. Methods (2018); 10:2129-37 10.1039/C8AY00830B (2018)
  14. Liu, T., Wang, R.X., Han, J., Hao, C.Z., Qiu, Y.L., Yan, Y.Y., Li, L.T., Wang, N.L., Gong, J.Y., Lu, Y., Zhang, M.H., Xie, X.B., Yang, J.C., You, Y.J., Li, J.Q., Knisely, A.S., Borchers, C.H., Ling, V., Wang, J.S. Comprehensive bile acid profiling in hereditary intrahepatic cholestasis: Genetic and clinical correlations. Liver Int. 10.1111/liv.13714 (2018) PubMed ID: 29412511
  15. Siyang Tian, Yannick Djoumbou-Feunang, Russell Greiner, David S Wishart CypReact: a software tool for in silico reactant prediction for human cytochrome P450 enzymes Journal of chemical information and modeling 10.1021/acs.jcim.8b00035 (2018) PubMed ID: 29738669
  16. Shuang Zhao, Liang Li Dansylhydrazine Isotope Labeling LC-MS for Comprehensive Carboxylic Acid Submetabolome Profiling Analytical Chemistry 10.1021/acs.analchem.8b03435 (2018) PubMed ID: 30339755
  17. Wishart, D.S. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018 Jan 4; 46(D1):D1074-D1082 10.1093/nar/gkx1037 (2018) PubMed ID: 29126136
  18. Christine M Mincham, Ian W Gibson, Atul Sharma, Chris Wiebe, Rupasri Mandal, David Rush, Peter Nickerson, Julie Ho, David S Wishart, Tom D Blydt‐Hansen Evolution of renal function and urinary biomarker indicators of inflammation on serial kidney biopsies in pediatric kidney transplant recipients with and without rejection Pediatric Transplantation 10.1111/petr.13202 (2018) PubMed ID: 29696778
  19. Ty T Kim, Nirmal Parajuli, Miranda M Sung, Suresh C Bairwa, Jody Levasseur, Carrie-Lynn M Soltys, David S Wishart, Karen Madsen, Jonathan D Schertzer, Jason RB Dyck Fecal transplant from resveratrol-fed donors improves glycaemia and cardiovascular features of the metabolic syndrome in mice American Journal of Physiology-Endocrinology and Metabolism 10.1152/ajpendo.00471.2017 (2018) PubMed ID: 29870676
  20. Kovalchuk, A., Nersisyan, L., Mandal, R., Wishart, D.S., Mancini, M., Sidransky, D., Kolb, B., Kovalchuk, O. Growth of Malignant Non-CNS Tumors Alters Brain Metabolome. Front Genet. 2018 Feb 20; 9:41 10.3389/fgene.2018.00041 (2018) PubMed ID: 29515623
  21. Giulia Praticò, Qian Gao, Augustin Scalbert, Guy Vergères, Marjukka Kolehmainen, Claudine Manach, Lorraine Brennan, Sri Harsha Pedapati, Lydia A Afman, David S Wishart, Rosa Vázquez-Fresno, Cristina Andres-Lacueva, Mar Garcia-Aloy, Hans Verhagen, Edith JM Feskens, Lars O Dragsted Guidelines for Biomarker of Food Intake Reviews (BFIRev): how to conduct an extensive literature search for biomarker of food intake discovery Genes & Nutrition 10.1186/s12263-018-0592-8 (2018) PubMed ID: 29484030
  22. Xian Luo, Mingrui An, Kyle C Cuneo, David M Lubman, Liang Li High-performance chemical isotope labeling liquid chromatography mass spectrometry for exosome metabolomics Analytical Chemistry 10.1021/acs.analchem.8b01726 (2018) PubMed ID: 29920066
  23. Wishart, D.S., Feunang, Y.D., Marcu, A., Guo, A.C., Liang, K., Vázquez-Fresno, R., Sajed, T., Johnson, D., Li, C., Karu, N., Sayeeda, Z., Lo, E., Assempour, N., Berjanskii, M., Singhal, S., Arndt, D., Liang, Y., Badran, H., Grant, J., Serra-Cayuela, A., Liu, Y., Mandal, R., Neveu, V., Pon, A., Knox, C., Wilson, M., Manach, C., Scalbert, A. HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res. 2018 Jan 4; 46(D1):D608-D617 10.1093/nar/gkx1089 (2018) PubMed ID: 29140435
  24. Hailemariam, D., Zhang, G., Mandal, R., Wishart, D.S., Ametaj, B. Identification of serum metabolites associated with the risk of metritis in transition dairy cows. Canadian Journal of Animal Science 10.1139/CJAS-2017-0069 (2018)
  25. Yunong Li, Liang Li Improving accuracy of peak-pair intensity ratio measurement in differential chemical isotope labeling LC–MS for quantitative metabolomics International Journal of Mass Spectrometry 10.1016/j.ijms.2018.09.027 (2018)
  26. Han, J., Higgins, R., Lim, M.D., Atkinsona, K., Yang, J., Lin, K., Borchers, C.H. Isotope-labeling derivatization with 3-nitrophenylhydrazine for LC/multiple-reaction monitoring-mass-spectrometry-based quantitation of carnitines in dried blood spots Analytica Chimica Acta 10.1016/j.aca.2018.01.045 (2018)
  27. Jasmine Chong, Othman Soufan, Carin Li, Iurie Caraus, Shuzhao Li, Guillaume Bourque, David S Wishart, Jianguo Xia MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis Nucleic Acids Research 10.1093/nar/gky310 (2018) PubMed ID: 29762782
  28. Yanni Sun, Deying Chen, Jingqi Liu, Yanping Xu, Xiaowei Shi, Xian Luo, Qiaoling Pan, Jiong Yu, Jinfeng Yang, Hongcui Cao, Liang Li, Lanjuan Li Metabolic profiling associated with autophagy of human placenta-derived mesenchymal stem cells by chemical isotope labeling LC-MS Experimental Cell Research 10.1016/j.yexcr.2018.09.009 (2018) PubMed ID: 30227120
  29. AWL Bayci, DA Baker, AE Somerset, O Turkoglu, Z Hothem, RE Callahan, R Mandal, B Han, T Bjorndahl, D Wishart, R Bahado-Singh, SF Graham, R Keidan Metabolomic identification of diagnostic serum-based biomarkers for advanced stage melanoma Metabolomics 10.1007/s11306-018-1398-9 (2018) PubMed ID: 30830422
  30. Luehr, T.C., Koide, E.M., Wang, X., Han, J., Borchers, C.H., Helbing, C.C. Metabolomic insights into the effects of thyroid hormone on Rana [Lithobates] catesbeiana metamorphosis using whole-body Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI). Gen Comp Endocrinol. 2018 Feb 19. pii: S0016-6480(17)30797-9 10.1016/j.ygcen.2018.02.012 (2018) PubMed ID: 29470956
  31. Bahado-Singh, R.O., Lugade, A., Field, J., Al-Wahab, Z., Han, B., Mandal, R., Bjorndahl, T., Türkoğlu, O., Graham, S., Wishart, D.S., Odunsi, K. Metabolomic prediction of endometrial cancer. Metabolomics (2018) 14: 6 10.1007/s11306-017-1290-z (2018)
  32. Tao Huan, Tran Tran, Jiamin Zheng, Shraddha Sapkota, Stuart W MacDonald, Richard Camicioli, Roger A Dixon, Liang Li Metabolomics analyses of saliva detect novel biomarkers of Alzheimer's disease Journal of Alzheimer's Disease 10.3233/JAD-180711 (2018) PubMed ID: 30175979
  33. Veronika Boczonadi, Martin S King, Anthony C Smith, Monika Olahova, Boglarka Bansagi, Andreas Roos, Filmon Eyassu, Christoph Borchers, Venkateswaran Ramesh, Hanns Lochmüller, Tuomo Polvikoski, Roger G Whittaker, Angela Pyle, Helen Griffin, Robert W Taylor, Patrick F Chinnery, Alan J Robinson, Edmund RS Kunji, Rita Horvath Mitochondrial oxodicarboxylate carrier deficiency is associated with mitochondrial DNA depletion and spinal muscular atrophy-like disease Genetics in Medicine 10.1038/gim.2017.251 (2018) PubMed ID: 29517768
  34. Schober, D., Jacob, D., Wilson, M., Cruz, J.A., Marcu, A., Grant, J.R., Moing, A., Deborde, C., de Figueiredo, L.F., Haug, K., Rocca-Serra, P., Easton, J., Ebbels, T.M.D., Hao, J., Ludwig, C., Günther, U.L., Rosato, A., Klein, M.S., Lewis, I.A., Luchinat, C., Jones, A.R., Grauslys, A., Larralde, M., Yokochi, M., Kobayashi, N., Porzel, A., Griffin, J.L., Viant, M.R., Wishart, D.S., Steinbeck, C., Salek, R.M., Neumann, S. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. Anal Chem. 2018 Jan 2; 90(1):649-656 10.1021/acs.analchem.7b02795 (2018) PubMed ID: 29035042
  35. Gaser N Abdelrasoul, Scott MacKay, Saad Y Salim, Kathleen P Ismond, Marcus Tamura, Charfeddine Khalifa, Emma Mannan, Donghai Lin, Tanushree Mandal, Ruth R Montgomery, David S Wishart, Jie Chen, Rachel G Khadaroo Non-invasive point-of-care device to diagnose acute mesenteric ischemia ACS Sensors 10.1021/acssensors.8b00558 (2018) PubMed ID: 30335977
  36. Adina Landsberg, Atul Sharma, Ian W Gibson, David Rush, David S Wishart, Tom D Blydt‐Hansen Non-invasive staging of chronic kidney allograft damage using urine metabolomic profiling Pediatric Transplantation 10.1111/petr.13226 (2018) PubMed ID: 29855144
  37. Huang, W., Brewer, L.K., Jones, J.W., Nguyen, A.T., Marcu, A., Wishart, D.S., Oglesby-Sherrouse, A.G., Kane, M.A., Wilks, A. PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. Nucleic Acids Res. 2018 Jan 4; 46(D1):D575-D580 10.1093/nar/gkx1061 (2018) PubMed ID: 29106626
  38. Tom O’Callaghan, Rosa Vázquez-Fresno, Arnau Serra-Cayuela, Edison Dong, Rupasri Mandal, Deirdre Hennessy, Stephen McAuliffe, Pat Dillon, David Wishart, Catherine Stanton, R Ross Pasture feeding changes the bovine rumen and milk metabolome Metabolites 10.3390/metabo8020027 (2018) PubMed ID: 29642378
  39. David Wishart, Guowang Xu Preface Analytica Chimica Acta 10.1016/j.aca.2018.09.046 (2018) PubMed ID: 30292283
  40. K Roveran Genga, H Kong, D Wishart, C Borchers, L Brunham, P Cullis, KR Walley, JH Boyd, JA Russell Proteomic, Metabolomic and Lipidomic Deficiencies in Human Sepsis Compared to Health-Preliminary Study ATS Journal 10.1164/ajrccm-conference.2018.197.1_MeetingAbstracts.A1813 (2018)
  41. David Achaintre, Audrey Gicquiau, Liang Li, Sabina Rinaldi, Augustin Scalbert Quantification of 38 dietary polyphenols in plasma by differential isotope labelling and liquid chromatography electrospray ionization tandem mass spectrometry Journal of Chromatography A 10.1016/j.chroma.2018.05.017 (2018) PubMed ID: 29759646
  42. Abdul-Hamid Emwas, Edoardo Saccenti, Xin Gao, Ryan T McKay, Vitor AP Martins dos Santos, Raja Roy, David S Wishart Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine Metabolomics 10.1007/s11306-018-1321-4 (2018) PubMed ID: 29479299
  43. John Paul Glaves, Carol L Ladner-Keay, Trent C Bjorndahl, David S Wishart, Brian D Sykes Residue-specific mobility changes in soluble oligomers of the prion protein define regions involved in aggregation Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 10.1016/j.bbapap.2018.06.005 (2018) PubMed ID: 29935976
  44. Klein, B.A., Reiz, B., Robertson, I.M., Irving, M., Li, L., Sun, Y.B., Sykes, B.D. Reversible Covalent Reaction of Levosimendan with Cardiac Troponin C in Vitro and in Situ. Biochemistry. 2018 Apr 17; 57(15):2256-2265 10.1021/acs.biochem.8b00109 (2018) PubMed ID: 29558109
  45. Ammar H Keshteli, Karen Madsen, Cheryl Nickurak, Karen I Kroeker, HeeKuk Park, Rosica Valcheva, Rupasri Mandal, David S Wishart, Sander Veldhuyzen van Zanten, Brendan P Halloran, Richard N Fedorak, Levinus A Dieleman Sa1747-An Anti-Inflammatory Diet Prevents Subclinical Inflammation and Associated Changes in Gut Microbiota and Metabolomic Profiles in Ulcerative Colitis Patients Gastroenterology 10.1016/S0016-5085(18)31571-3 (2018)
  46. Han, J., Higgins, R., Lim, M.D., Lin, K., Yang, J., Borchers, C.H. Short-Term Stabilities of 21 Amino Acids in Dried Blood Spots Clin Chem. 2018 Feb; 64(2):400-402 10.1373/clinchem.2017.278457 (2018) PubMed ID: 29097508
  47. Mohammed M Abdul-Bari, Rachel H McQueen, Ha Nguyen, Wendy V Wismer, A Paulina de la Mata, James J Harynuk Synthetic Clothing and the Problem With Odor: Comparison of Nylon and Polyester Fabrics Clothing and Textiles Research Journal 10.1177/0887302X18772099 (2018)
  48. 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 (2018); 12(5), 1050-1059 10.1017/S1751731117002506 (2018) PubMed ID: 29032783
  49. Rupasri Mandal, Danuta Chamot, David S Wishart The role of the Human Metabolome Database in inborn errors of metabolism Journal of inherited metabolic disease 10.1007/s10545-018-0137-8 (2018) PubMed ID: 29663269
  50. Mitchell J Geer, Johanna P van Geffen, Piraveen Gopalasingam, Timo Vögtle, Christopher W Smith, Silke Heising, Marijke JE Kuijpers, Bibian ME Tullemans, Gavin E Jarvis, Johannes A Eble, Mark Jeeves, Michael Overduin, Johan WM Heemskerk, Alexandra Mazharian, Yotis A Senis Uncoupling ITIM receptor G6b-B from tyrosine phosphatases Shp1 and Shp2 disrupts murine platelet homeostasis Blood 10.1182/blood-2017-10-802975 (2018) PubMed ID: 29891536
  51. Jonathan Martens, Giel Berden, Herman Bentlage, Karlien LM Coene, Udo F Engelke, David Wishart, Monique van Scherpenzeel, Leo AJ Kluijtmans, Ron A Wevers, Jos Oomens Unraveling the unknown areas of the human metabolome: the role of infrared ion spectroscopy Journal of inherited metabolic disease 10.1007/s10545-018-0161-8 (2018) PubMed ID: 29556837
  52. E Dervishi, G Zhang, D Hailemariam, R Mandal, DS Wishart, BN Ametaj Urine metabolic fingerprinting can be used to predict the risk of metritis and highlight the pathobiology of the disease in dairy cows Metabolomics 10.1007/s11306-018-1379-z (2018) PubMed ID: 30830348
  53. Lars O Dragsted, Qian Gao, Augustin Scalbert, Guy Vergères, Marjukka Kolehmainen, Claudine Manach, Lorraine Brennan, Lydia A Afman, David S Wishart, C Andres Lacueva, Mar Garcia-Aloy, H Verhagen, EJM Feskens, Giulia Praticò Validation of biomarkers of food intake-critical assessment of candidate biomarkers Genes & Nutrition 10.1186/s12263-018-0603-9 (2018) PubMed ID: 29861790

2017

  1. Dervishi, Elda & Zhang, Guanshi & Mandal, R & S. Wishart, D & Ametaj, Burim 043 Metabolomics uncovers serum biomarkers that can predict the risk of retained placenta in transition dairy cows. Journal of Animal Science 95:21 10.2527/asasann.2017.043 (2017)
  2. Zhang, G., Mandal, R., Wishart, D.S., Ametaj, B. 046 Serum and urine metallotyping of preketotic and ketotic dairy cows reveals major alterations in multiple mineral elements. Journal of Animal Science. 95:23 10.2527/asasann.2017.046 (2017)
  3. B. N. Ametaj E. Dervishi R. Mandal D. S. Wishart G. Zhang 1H-NMR–based metabolomics identifies new predictive urinary biomarkers and highlights the pathobiology of ketosis in periparturient dairy cows. Journal of Animal Science, Volume 95, Suppliment 4, pg 167-8, 1 August 2017, 10.2527/asasann.2017.339 (2017)
  4. Zhang, Guanshi & Deng, Qilan & Mandal, R & S. Wishart, D & Ametaj, Burim 340 Metabolomics-based profiling identifies serum signatures that predict the risk of metritis in transition dairy cows. Journal of Animal Science. 95:168 10.2527/asasann.2017.340 (2017)
  5. Alicia DiBattista, Dianne Rampersaud, Howard Lee‡Marcus Kim, Philip Britz-McKibbin A High Throughput Screening Method for Systematic Surveillance of Drugs of Abuse by Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry Analytical Chemistry 10.1021/acs.analchem.7b03590 (2017)
  6. Gao, Q., Praticò, G., Scalbert, A., Vergères, G., Kolehmainen, M., Manach, C., Brennan, L., Afman, L.A., Wishart, D.S., Andres-Lacueva, C., Garcia-Aloy, M., Verhagen, H., Feskens, E.J.M., Dragsted, L.O. A scheme for a flexible classification of dietary and health biomarkers Genes Nutr. 2017 Dec 12;12:34 (2017) PubMed ID: 29255495
  7. 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) 10.3791/54869 (2017) PubMed ID: 28287524
  8. Keshteli, A.H., Madsen, K., Nickurak, C., Kroeker, K., Mandal, R., Wishart, D.S., Veldhuyzen van Zanten, S., Halloran, B., Fedorak, R., Valcheva, R., Dieleman, L. Adherence to an Anti-Inflammatory Diet Prevents Increases in Colonic Inflammation in Ulcerative Colitis Patients in Remission. Gastroenterology. 152. S599 10.1016/S0016-5085(17)32142-X (2017)
  9. Wishart, D.S. Bioinformatics Computing and Software Bioinformatics Computing and Software isbn 978-7-03-0426390 (2017)
  10. 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 10.1038/srep40543 (2017) PubMed ID: 28091618
  11. Brouwer-Brolsma, E.M., Brennan, L., Drevon, C.A., van Kranen, H., Manach, C., Dragsted, L.O., Roche, H.M., Andres-Lacueva, C., Bakker, S.J.L., Bouwman, J., Capozzi, F., De Saeger, S., Gundersen, T.E., Kolehmainen, M., Kulling, S.E., Landberg, R., Linseisen, J., Mattivi, F., Mensink, R.P., Scaccini, C., Skurk, T., Tetens, I., Vergeres, G., Wishart, D.S., Scalbert, A., Feskens, E.J.M. Combining traditional dietary assessment methods with novel metabolomics techniques: present efforts by the Food Biomarker Alliance. Proc Nutr Soc. 2017 Nov; 76(4):619-627 10.1017/S0029665117003949 (2017) PubMed ID: 29137687
  12. Qiu YL, Gong JY, Feng JY, Wang RX, Han J, Liu T, Lu Y, Li LT, Zhang MH, Sheps JA, Wang NL, Yan YY, Li JQ, Chen L, Borchers CH, Sipos B, Knisely AS, Ling V, Xing QH, Wang JS. Defects in myosin VB are associated with a spectrum of previously undiagnosed low γ-glutamyltransferase cholestasis. Hepatology 10.1002/hep.29020 (2017) PubMed ID: 28027573
  13. 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 10.3390/metabo7030032 (2017) PubMed ID: 28640228
  14. Luo, X., Gu, X., Li, L. Development of a simple and efficient method of harvesting and lysing adherent mammalian cells for chemical isotope labeling LC-MS-based cellular metabolomics. Analytica Chimica Acta 10.1016/j.aca.2017.11.054 (2017)
  15. 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
  16. Zhao, S., Dawe, M., Guo, K., Li, L. Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Carbonyl Submetabolome. Anal Chem. 2017 Jun 20; 89(12):6758-6765 10.1021/acs.analchem.7b01098 (2017) PubMed ID: 28505421
  17. 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. 2017 Sep 27; 65(38):8510-8521 10.1021/acs.jafc.7b02000 (2017) PubMed ID: 28862839
  18. 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 10.1186/s12263-017-0578-y (2017) PubMed ID: 28974991
  19. 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. 2017 Jun 7; 23(21):3890-3899 10.3748/wjg.v23.i21.3890 (2017) PubMed ID: 28638229
  20. Oliynyk, A.O., Adutwum, L.A., Rudyk, B.W., Pisavadia, H., Lotfi, S., Hlukhyy, V., Harynuk, J.J., Mar, A., Brgoch, J. Disentangling Structural Confusion through Machine Learning: Structure Prediction and Polymorphism of Equiatomic Ternary Phases ABC. J Am Chem Soc. 2017 Dec 13; 139(49):17870-17881 10.1021/jacs.7b08460 (2017) PubMed ID: 29129069
  21. 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. 2017 Apr; 15(4):497-509 10.1111/pbi.12648 (2017) PubMed ID: 27734577
  22. 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
  23. 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 Coinfection by Altering the Intestinal Metabolome. J Infect Dis. 2017 Apr 15; 215(8):1245-1254 10.1093/infdis/jix141 (2017) PubMed ID: 28368463
  24. 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. 2017 Nov;409(28):6699-6708. Epub 2017 Sep 29. 10.1007/s00216-017-0628-8 (2017) PubMed ID: 28963623
  25. 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) 10.1093/nar/gkw980 (2017) PubMed ID: 27924041
  26. 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. 2017 Apr 10; 4:11 10.3389/fnut.2017.00011 (2017) PubMed ID: 28443284
  27. Cao, Y., Griffith, B., Bhomkar, P., Wishart, D.S., McDermott, M.T. Functionalized gold nanoparticle-enhanced competitive assay for sensitive small-molecule metabolite detection using surface plasmon resonance. Analyst. 2017 Dec 18; 143(1):289-296 10.1039/c7an01680h (2017) PubMed ID: 29184920
  28. 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 10.1021/acs.jproteome.6b00538 (2017) PubMed ID: 28152597
  29. Bowden, J.A., Heckert, A., Ulmer, C.Z., Jones, C.M., Koelmel, J.P., Abdullah, L., Ahonen, L., Alnouti, Y., Armando, A.M., Asara, J.M., Bamba, T., Barr, J.R., Bergquist, J., Borchers, C.H., Brandsma, J., Breitkopf, S.B., Cajka, T., Cazenave-Gassiot, A., Checa, A., Cinel, M.A., Colas, R.A., Cremers, S., Dennis, E.A., Evans, J.E., Fauland, A., Fiehn, O., Gardner, M.S., Garrett, T.J., Gotlinger, K.H., Han, J., Huang, Y., Neo, A.H., Hyötyläinen, T., Izumi, Y., Jiang, H., Jiang, H., Jiang, J., Kachman, M., Kiyonami, R., Klavins, K., Klose, C., Köfeler, H.C., Kolmert, J., Koal, T., Koster, G., Kuklenyik, Z., Kurland, I.J., Leadley, M., Lin, K., Maddipati, K.R., McDougall, D., Meikle, P.J., Mellett, N.A., Monnin, C., Moseley, M.A., Nandakumar, R., Oresic, M., Patterson, R., Peake, D., Pierce, J.S., Post, M., Postle, A.D., Pugh, R., Qiu, Y., Quehenberger, O., Ramrup, P., Rees, J., Rembiesa, B., Reynaud, D., Roth, M.R., Sales, S., Schuhmann, K., Schwartzman, M.L., Serhan, C.N., Shevchenko, A., Somerville, S.E., St John-Williams, L., Surma, M.A., Takeda, H., Thakare, R., Thompson, J.W., Torta, F., Triebl, A., Trötzmüller, M., Ubhayasekera, S.J.K., Vuckovic, D., Weir, J.M., Welti, R., Wenk, M.R., Wheelock, C.E., Yao, L., Yuan, M., Zhao, X.H., Zhou, S. Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J Lipid Res. 2017 Dec; 58(12):2275-2288 10.1194/jlr.M079012 (2017) PubMed ID: 28986437
  30. DiBattista, A., Rampersaud, D., Lee, H., Kim, M., Britz-McKibbin, P. High Throughput Screening Method for Systematic Surveillance of Drugs of Abuse by Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry. Anal Chem. 2017 Nov 7; 89(21):11853-11861 10.1021/acs.analchem.7b03590 (2017) PubMed ID: 28981253
  31. 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. 2017 Aug 4; 16(8):2975-2982 10.1021/acs.jproteome.7b00273 (2017) PubMed ID: 28616987
  32. 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 10.2337/db16-0680 (2017) PubMed ID: 27903747
  33. Blinov, N., Khorvash, M., Wishart, D.S., Cashman, N.R. and Kovalenko, A. Initial Structural Models of the Aβ42 Dimer from Replica Exchange Molecular Dynamics Simulations ACS Omega 10.1021/acsomega.7b00805 (2017)
  34. 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 10.1371/journal.pone.0177675 (2017) PubMed ID: 28531195
  35. 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)
  36. Doran, M.L., Knee, J.M., Wang, N., Rzezniczak, T.Z., Parkes, T.L., Li, L., Merritt, T.J.S. Metabolomic analysis of oxidative stress: Superoxide dismutase mutation and paraquat induced stress in Drosophila melanogaster. Free Radic Biol Med. 2017 Dec; 113:323-334 10.1016/j.freeradbiomed.2017.10.011 (2017) PubMed ID: 29031835
  37. Zhang, G., Dervishi, E., Dunn, S.M., Mandal, R., Liu, P., Han, B., Wishart, D.S., Ametaj, B. Metabotyping reveals distinct metabolic alterations in ketotic cows and identifies early predictive serum biomarkers for the risk of disease. Metabolomics. 13(4) 10.1007/s11306-017-1180-4 (2017)
  38. Zhang, G., Dervishi, E., Mandal, R., Wishart, D.S., Ametaj, B. Metallotyping of ketotic dairy cows reveals major alterations preceding, associating, and following the disease occurrence. Metabolomics. 13:97 10.1007/s11306-017-1237-4 (2017)
  39. 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 10.1186/s40168-017-0246-x (2017) PubMed ID: 28285599
  40. Hooton, K., Li, L. Nonocclusive Sweat Collection Combined with Chemical Isotope Labeling LC-MS for Human Sweat Metabolomics and Mapping the Sweat Metabolomes at Different Skin Locations. Anal Chem. 2017 Aug 1; 89(15):7847-7851 10.1021/acs.analchem.7b01988 (2017) PubMed ID: 28679039
  41. Chen, D., Han, W., Su, X., Li, L., Li, L. Overcoming Sample Matrix Effect in Quantitative Blood Metabolomics Using Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry. Anal Chem. 2017 Sep 5; 89(17):9424-31 10.1021/acs.analchem.7b02240 (2017) PubMed ID: 28787119
  42. 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
  43. Han, W., Sapkota, S., Camicioli, R., Dixon, R.A., Li, L. Profiling novel metabolic biomarkers for Parkinson's disease using in-depth metabolomic analysis. Mov Disord. 2017 Dec; 32(12):1720-1728 10.1002/mds.27173 (2017) PubMed ID: 28880465
  44. Ryan, P.M., Patterson, E., Kent, R.M., Stack, H., O'Connor, P.M., Murphy, K., Peterson, V.L., Mandal, R., Wishart, D.S., Dinan, T.G., Cryan, J.F., Seeley, R.J., Stanton, C., Ross, R.P. Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents Sci Rep. 2017 Oct 19; 7(1):13523 10.1038/s41598-017-14010-x (2017) PubMed ID: 29051554
  45. 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. 2017 Jul 28. pii: AEM.01148-17 10.1128/AEM.01148-17 (2017) PubMed ID: 28754707
  46. 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 10.1021/acs.analchem.6b03934 (2017)
  47. Wilson, HJ., Palk, G., Sheehan, MC., Wishart, D., Watson, B. Steering Clear of Driving After Drinking: a Tailored e-Health Intervention for Reducing Repeat Offending and Modifying Alcohol Use in a High-Risk Cohort Int J Behav Med 10.1007/s12529-017-9664-1 (2017) PubMed ID: 28600704
  48. 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 10.1021/acs.jproteome.7b00157 (2017) PubMed ID: 28608686
  49. 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 10.1021/acs.analchem.7b01727 (2017) PubMed ID: 28648083
  50. Pagadala, NS., Bjorndahl, TC., Joyce, M., Wishart, DS., Syed, K., Landi, A. The compound (3-{5-[(2,5-dimethoxyphenyl)amino]-1,3,4-thiadiazolidin-2-yl}-5,8-methoxy-2H-chromen-2-one) inhibits the prion protein conversion from PrPC to PrPSc with lower IC50 in ScN2a cells. Bioorg Med Chem 10.1016/j.bmc.2017.09.024 (2017) PubMed ID: 28951092
  51. 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 10.1155/2017/3167985 (2017) PubMed ID: 29230249
  52. 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. 2017 Aug 23; 3(8):904-913 10.1021/acscentsci.7b00299 (2017) PubMed ID: 28852705
  53. Adutwum, L.A., Abel, R.J., Harynuk, J.J. Total Ion Spectra versus Segmented Total Ion Spectra as Preprocessing Tools for Gas Chromatography - Mass Spectrometry Data. J Forensic Sci. 2017 Oct 10 10.1111/1556-4029.13657 (2017) PubMed ID: 29023723
  54. 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 10.1139/gen-2016-0111 (2017) PubMed ID: 28045337
  55. Berjanskii, MV., Wishart, DS. Unraveling the meaning of chemical shifts in protein NMR Biochim. Biophys. Acta. 10.1016/j.bbapap.2017.07.005 (2017) PubMed ID: 28716441
  56. Blydt-Hansen, T.D., Sharma, A., Gibson, I.W., 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. 2017 Oct; 101(10):2553-2561 10.1097/TP.0000000000001662 (2017) PubMed ID: 28121909
  57. 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 10.1093/nar/gkw1058 (2017) PubMed ID: 27899612

2016

  1. Bahado-Signh, R.O., Syngelaki, A., Mandal, R., Bjondahl, T.C., Li, L., Maulik, D., Dong, H.B., Turkoglu, O., Zeb, A., Redman, M, Wishart, D.S., Nicolaides, K.H. 132: First-trimester metabolomics prediction of subsequent stillbirth American Journal of Obstetrics & Gynecology doi.org/10.1016/j.ajog.2015.10.168 (2016)
  2. 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
  3. 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)
  4. Wishart, D.S., Mandal, R., Stanislaus, A. & Ramirez-Gaona, M. Cancer Metabolomics and the Human Metabolome Database. Metabolites 6, 1 10.3390/metabo6010010 (2016) PubMed ID: 26950159
  5. 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.org/10.1074/jbc.M116.756973 (2016) PubMed ID: 27621312
  6. 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
  7. Allen, F., Greiner, R., Wishart, D.S. CFM-ID applied to CASMI 2014 Current Metabolomics, June 2016 (2016)
  8. 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 10.1021/acs.analchem.6b02967 (2016) PubMed ID: 27690392
  9. 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
  10. 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 10.1186/s13321-016-0174-y (2016) PubMed ID: 27867422
  11. 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
  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 10.1016/j.ebiom.2016.04.025 (2016) PubMed ID: 27428442
  13. 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 10.1021/acs.analchem.6b01930 (2016) PubMed ID: 27351466
  14. 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. 10.1007/s00216-016-0137-1 (2016) PubMed ID: 28028595
  15. 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
  16. 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) 10.3390/metabo6040046 (2016) PubMed ID: 27983674
  17. 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 10.1016/j.aca.2015.11.027 (2016) PubMed ID: 26709303
  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) 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 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 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 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. 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
  25. 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 10.1056/NEJMoa1515792 (2016) PubMed ID: 27276562
  26. 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)
  27. 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)
  28. 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 10.1093/nar/gkw 419 (2016) PubMed ID: 27190236
  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 10.1021/acs.jproteome.6b00070 (2016) PubMed ID: 26947805
  30. 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 10.1007/s11306-016-0957-1 (2016)
  31. 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 10.3389/fmicb.2016.00828 (2016) PubMed ID: 27375567
  32. 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) 10.1146/annurev-publhealth-082516-012737 (2016) PubMed ID: 28068484
  33. 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)
  34. Wishart, D.S. Introduction to Cheminformatics. Curr Protoc Bioinformatics. 53:14.1.1-14.1.21 10.1002/0471250953.bi1401s18 (2016) PubMed ID: 27010335
  35. 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)
  36. 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 10.1016/j.bbadis.2016.06.007 (2016) PubMed ID: 27288730
  37. 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 10.1038/srep32272 (2016) PubMed ID: 27578275
  38. 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
  39. 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 10.1016/j.bbapap.2016.12.012 (2016) PubMed ID: 28017863
  40. 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 10.1007/s11306-016-1094-6 (2016) PubMed ID: 27642271
  41. 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 10.1002/elps.201600250 (2016) PubMed ID: 27667503
  42. 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 10.1021/acs.nanolett.6b03066 (2016) PubMed ID: 27749074
  43. 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 10.1038/srep38718 (2016) PubMed ID: 27966539
  44. 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
  45. 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 10.1002/jssc.201600307 (2016) PubMed ID: 27159197
  46. 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 10.1002/elps.201600150 (2016) PubMed ID: 27120558
  47. 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 10.1016/j.copbio.2016.09.003 (2016) PubMed ID: 27690313
  48. 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 10.1021/acs.jproteome.5b00885 (2016) PubMed ID: 26745651
  49. 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. 2016 Jan 12; 23(1):179-93 10.1016/j.cmet.2015.10.016 (2016) PubMed ID: 26626461
  50. Wu, Y., Li, L. Sample normalization methods in quantitative metabolomics. J Chromatogr A. 2016 Jan 22; 1430:80-95 10.1016/j.chroma.2015.12.007 (2016) PubMed ID: 26763302
  51. 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 10.1039/c6an01210h (2016) PubMed ID: 27390787
  52. 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)
  53. 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)
  54. 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 10.1038/nbt.3689 (2016) PubMed ID: 27824832
  55. 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 10.2527/jam2016-0150 (2016)
  56. 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 10.1016/j.copbio.2016.08.001 (2016) PubMed ID: 27580257
  57. 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)
  58. 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
  59. Xia, J., Wishart, D.S. Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis. Curr Protoc Bioinformatics. 55:14.10.1-14.10.91 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 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 10.1038/ncomms8806 (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 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 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 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 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 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 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) 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. 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
  30. 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
  31. 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
  32. 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 10.1007/s11306-014-0746-7 (2015) PubMed ID: 26109927
  33. 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
  34. 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 10.1016/j.clinbiochem.2015.02.004 (2015) PubMed ID: 25697106
  35. 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)
  36. 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
  37. 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 10.1111/cbdd.12132 (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 6βhydroxycortisol 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
  18. 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) PubMed ID: 21848803
  19. 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) PubMed ID: 21360156
  20. 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) PubMed ID: 21338760
  21. 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)
  22. 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) PubMed ID: 21637195

0

  1. Cassiede, M., Mercier, P., Shipley, P.R., Dueck, M., Kamravaei, S., Nair, S., Mino, J., Pei, L., Broadhurst, D., Lacy, P., Quémerais, B. Comparison of computational approaches for identification and quantification of urinary 5 metabolites in 1H NMR spectra Analytical Methods (0)
  2. Li, L.  MALDI Mass Spectrometry for Polymer Characterization "A Practical Guide to MALDI MS, 2nd Edition" F. Hillenkam, Ed., Wiley-VCH, Germany (2013) (0)