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Items: 35

1.

A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium.

Barupal DK, Zhang Y, Shen T, Fan S, Roberts BS, Fitzgerald P, Wancewicz B, Valdiviez L, Wohlgemuth G, Byram G, Choy YY, Haffner B, Showalter MR, Vaniya A, Bloszies CS, Folz JS, Kind T, Flenniken AM, McKerlie C, Nutter LMJ, Lloyd KC, Fiehn O.

Metabolites. 2019 May 22;9(5). pii: E101. doi: 10.3390/metabo9050101.

2.

Systematic Error Removal Using Random Forest for Normalizing Large-Scale Untargeted Lipidomics Data.

Fan S, Kind T, Cajka T, Hazen SL, Tang WHW, Kaddurah-Daouk R, Irvin MR, Arnett DK, Barupal DK, Fiehn O.

Anal Chem. 2019 Mar 5;91(5):3590-3596. doi: 10.1021/acs.analchem.8b05592. Epub 2019 Feb 19.

PMID:
30758187
3.

Metabolomic analysis of serum and myocardium in compensated heart failure after myocardial infarction.

McKirnan MD, Ichikawa Y, Zhang Z, Zemljic-Harpf AE, Fan S, Barupal DK, Patel HH, Hammond HK, Roth DM.

Life Sci. 2019 Mar 15;221:212-223. doi: 10.1016/j.lfs.2019.01.040. Epub 2019 Feb 5.

PMID:
30731143
4.

Generation and quality control of lipidomics data for the alzheimer's disease neuroimaging initiative cohort.

Barupal DK, Fan S, Wancewicz B, Cajka T, Sa M, Showalter MR, Baillie R, Tenenbaum JD, Louie G; Alzheimer’s Disease Neuroimaging Initiative; Alzheimer’s Disease Metabolomics Consortium, Kaddurah-Daouk R, Fiehn O.

Sci Data. 2018 Nov 20;5:180263. doi: 10.1038/sdata.2018.263.

5.

Arginine reprogramming in ADPKD results in arginine-dependent cystogenesis.

Trott JF, Hwang VJ, Ishimaru T, Chmiel KJ, Zhou JX, Shim K, Stewart BJ, Mahjoub MR, Jen KY, Barupal DK, Li X, Weiss RH.

Am J Physiol Renal Physiol. 2018 Dec 1;315(6):F1855-F1868. doi: 10.1152/ajprenal.00025.2018. Epub 2018 Oct 3.

PMID:
30280600
6.

Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics.

Nagy-Szakal D, Barupal DK, Lee B, Che X, Williams BL, Kahn EJR, Ukaigwe JE, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Levin B, Hornig M, Fiehn O, Lipkin WI.

Sci Rep. 2018 Jul 3;8(1):10056. doi: 10.1038/s41598-018-28477-9.

7.

Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets.

Barupal DK, Fan S, Fiehn O.

Curr Opin Biotechnol. 2018 Dec;54:1-9. doi: 10.1016/j.copbio.2018.01.010. Epub 2018 Feb 6. Review.

PMID:
29413745
8.

Effects of exposure to water disinfection by-products in a swimming pool: A metabolome-wide association study.

van Veldhoven K, Keski-Rahkonen P, Barupal DK, Villanueva CM, Font-Ribera L, Scalbert A, Bodinier B, Grimalt JO, Zwiener C, Vlaanderen J, Portengen L, Vermeulen R, Vineis P, Chadeau-Hyam M, Kogevinas M.

Environ Int. 2018 Feb;111:60-70. doi: 10.1016/j.envint.2017.11.017. Epub 2017 Nov 24.

9.

Integration of metabolomics, transcriptomics, and microRNA expression profiling reveals a miR-143-HK2-glucose network underlying zinc-deficiency-associated esophageal neoplasia.

Fong LY, Jing R, Smalley KJ, Taccioli C, Fahrmann J, Barupal DK, Alder H, Farber JL, Fiehn O, Croce CM.

Oncotarget. 2017 Jun 9;8(47):81910-81925. doi: 10.18632/oncotarget.18434. eCollection 2017 Oct 10.

10.
11.

Identification of small molecules using accurate mass MS/MS search.

Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O.

Mass Spectrom Rev. 2018 Jul;37(4):513-532. doi: 10.1002/mas.21535. Epub 2017 Apr 24. Review.

PMID:
28436590
12.

The impact of ambient air pollution on the human blood metabolome.

Vlaanderen JJ, Janssen NA, Hoek G, Keski-Rahkonen P, Barupal DK, Cassee FR, Gosens I, Strak M, Steenhof M, Lan Q, Brunekreef B, Scalbert A, Vermeulen RCH.

Environ Res. 2017 Jul;156:341-348. doi: 10.1016/j.envres.2017.03.042. Epub 2017 Apr 6.

PMID:
28391173
13.

compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets.

Edmands WM, Petrick L, Barupal DK, Scalbert A, Wilson MJ, Wickliffe JK, Rappaport SM.

Anal Chem. 2017 Apr 4;89(7):3919-3928. doi: 10.1021/acs.analchem.6b02394. Epub 2017 Mar 27.

14.

Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration.

Wanichthanarak K, Fan S, Grapov D, Barupal DK, Fiehn O.

PLoS One. 2017 Jan 31;12(1):e0171046. doi: 10.1371/journal.pone.0171046. eCollection 2017.

15.

Dietary flavonoid intake and colorectal cancer risk in the European prospective investigation into cancer and nutrition (EPIC) cohort.

Zamora-Ros R, Barupal DK, Rothwell JA, Jenab M, Fedirko V, Romieu I, Aleksandrova K, Overvad K, Kyrø C, Tjønneland A, Affret A, His M, Boutron-Ruault MC, Katzke V, Kühn T, Boeing H, Trichopoulou A, Naska A, Kritikou M, Saieva C, Agnoli C, Santucci de Magistris M, Tumino R, Fasanelli F, Weiderpass E, Skeie G, Merino S, Jakszyn P, Sánchez MJ, Dorronsoro M, Navarro C, Ardanaz E, Sonestedt E, Ericson U, Maria Nilsson L, Bodén S, Bueno-de-Mesquita HB, Peeters PH, Perez-Cornago A, Wareham NJ, Khaw KT, Freisling H, Cross AJ, Riboli E, Scalbert A.

Int J Cancer. 2017 Apr 15;140(8):1836-1844. doi: 10.1002/ijc.30582. Epub 2017 Jan 19.

16.

Environmental Tobacco Smoke Alters Metabolic Systems in Adult Rats.

Barupal DK, Pinkerton KE, Hood C, Kind T, Fiehn O.

Chem Res Toxicol. 2016 Nov 21;29(11):1818-1827. Epub 2016 Nov 9.

PMID:
27788581
17.

Prioritizing Chemicals for Risk Assessment Using Chemoinformatics: Examples from the IARC Monographs on Pesticides.

Guha N, Guyton KZ, Loomis D, Barupal DK.

Environ Health Perspect. 2016 Dec;124(12):1823-1829. Epub 2016 May 10.

18.

Systematic analysis of the polyphenol metabolome using the Phenol-Explorer database.

Rothwell JA, Urpi-Sarda M, Boto-Ordoñez M, Llorach R, Farran-Codina A, Barupal DK, Neveu V, Manach C, Andres-Lacueva C, Scalbert A.

Mol Nutr Food Res. 2016 Jan;60(1):203-11. doi: 10.1002/mnfr.201500435. Epub 2015 Oct 15.

19.

Polyphenol metabolome in human urine and its association with intake of polyphenol-rich foods across European countries.

Edmands WM, Ferrari P, Rothwell JA, Rinaldi S, Slimani N, Barupal DK, Biessy C, Jenab M, Clavel-Chapelon F, Fagherazzi G, Boutron-Ruault MC, Katzke VA, Kühn T, Boeing H, Trichopoulou A, Lagiou P, Trichopoulos D, Palli D, Grioni S, Tumino R, Vineis P, Mattiello A, Romieu I, Scalbert A.

Am J Clin Nutr. 2015 Oct;102(4):905-13. doi: 10.3945/ajcn.114.101881. Epub 2015 Aug 12.

PMID:
26269369
20.

Alteration of amino acid and biogenic amine metabolism in hepatobiliary cancers: Findings from a prospective cohort study.

Stepien M, Duarte-Salles T, Fedirko V, Floegel A, Barupal DK, Rinaldi S, Achaintre D, Assi N, Tjønneland A, Overvad K, Bastide N, Boutron-Ruault MC, Severi G, Kühn T, Kaaks R, Aleksandrova K, Boeing H, Trichopoulou A, Bamia C, Lagiou P, Saieva C, Agnoli C, Panico S, Tumino R, Naccarati A, Bueno-de-Mesquita HB, Peeters PH, Weiderpass E, Quirós JR, Agudo A, Sánchez MJ, Dorronsoro M, Gavrila D, Barricarte A, Ohlsson B, Sjöberg K, Werner M, Sund M, Wareham N, Khaw KT, Travis RC, Schmidt JA, Gunter M, Cross A, Vineis P, Romieu I, Scalbert A, Jenab M.

Int J Cancer. 2016 Jan 15;138(2):348-60. doi: 10.1002/ijc.29718. Epub 2015 Aug 21.

21.

Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry.

Miyamoto S, Taylor SL, Barupal DK, Taguchi A, Wohlgemuth G, Wikoff WR, Yoneda KY, Gandara DR, Hanash SM, Kim K, Fiehn O.

Metabolites. 2015 Apr 9;5(2):192-210. doi: 10.3390/metabo5020192.

22.

MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets.

Edmands WM, Barupal DK, Scalbert A.

Bioinformatics. 2015 Mar 1;31(5):788-90. doi: 10.1093/bioinformatics/btu705. Epub 2014 Oct 27.

23.

The blood exposome and its role in discovering causes of disease.

Rappaport SM, Barupal DK, Wishart D, Vineis P, Scalbert A.

Environ Health Perspect. 2014 Aug;122(8):769-74. doi: 10.1289/ehp.1308015. Epub 2014 Mar 21.

24.

Inactivation of metabolic genes causes short- and long-range dys-regulation in Escherichia coli metabolic network.

Barupal DK, Lee SJ, Karoly ED, Adhya S.

PLoS One. 2013 Dec 5;8(12):e78360. doi: 10.1371/journal.pone.0078360. eCollection 2013.

25.

Comparative metabolomics of estrogen receptor positive and estrogen receptor negative breast cancer: alterations in glutamine and beta-alanine metabolism.

Budczies J, Brockmöller SF, Müller BM, Barupal DK, Richter-Ehrenstein C, Kleine-Tebbe A, Griffin JL, Orešič M, Dietel M, Denkert C, Fiehn O.

J Proteomics. 2013 Dec 6;94:279-88. doi: 10.1016/j.jprot.2013.10.002. Epub 2013 Oct 11.

PMID:
24125731
26.

Pharmacometabolomic signature of ataxia SCA1 mouse model and lithium effects.

Perroud B, Jafar-Nejad P, Wikoff WR, Gatchel JR, Wang L, Barupal DK, Crespo-Barreto J, Fiehn O, Zoghbi HY, Kaddurah-Daouk R.

PLoS One. 2013 Aug 2;8(8):e70610. doi: 10.1371/journal.pone.0070610. Print 2013.

27.

A new metabolomic workflow for early detection of Alzheimer's disease.

Ibáñez C, Simó C, Barupal DK, Fiehn O, Kivipelto M, Cedazo-Mínguez A, Cifuentes A.

J Chromatogr A. 2013 Aug 9;1302:65-71. doi: 10.1016/j.chroma.2013.06.005. Epub 2013 Jun 14.

PMID:
23827464
28.

Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolism.

Meissen JK, Yuen BT, Kind T, Riggs JW, Barupal DK, Knoepfler PS, Fiehn O.

PLoS One. 2012;7(10):e46770. doi: 10.1371/journal.pone.0046770. Epub 2012 Oct 15.

29.

System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium.

Lee DY, Park JJ, Barupal DK, Fiehn O.

Mol Cell Proteomics. 2012 Oct;11(10):973-88. Epub 2012 Jul 10.

30.

MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity.

Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL, Pinkerton KE, Fiehn O.

BMC Bioinformatics. 2012 May 16;13:99.

31.

Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery.

Denkert C, Bucher E, Hilvo M, Salek R, Orešič M, Griffin J, Brockmöller S, Klauschen F, Loibl S, Barupal DK, Budczies J, Iljin K, Nekljudova V, Fiehn O.

Genome Med. 2012 Apr 30;4(4):37.

32.

The volatile compound BinBase mass spectral database.

Skogerson K, Wohlgemuth G, Barupal DK, Fiehn O.

BMC Bioinformatics. 2011 Aug 4;12:321. doi: 10.1186/1471-2105-12-321.

33.

Extending biochemical databases by metabolomic surveys.

Fiehn O, Barupal DK, Kind T.

J Biol Chem. 2011 Jul 8;286(27):23637-43. doi: 10.1074/jbc.R110.173617. Epub 2011 May 12. Review. Erratum in: J Biol Chem. 2011 Aug 26;286(34):30244.

34.

Hydrocarbon phenotyping of algal species using pyrolysis-gas chromatography mass spectrometry.

Barupal DK, Kind T, Kothari SL, Lee DY, Fiehn O.

BMC Biotechnol. 2010 May 21;10:40. doi: 10.1186/1472-6750-10-40.

35.

Human gut microbiome adopts an alternative state following small bowel transplantation.

Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA.

Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17187-92. doi: 10.1073/pnas.0904847106. Epub 2009 Sep 17.

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