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For: Edmands WMB, Barupal DK, Scalbert A. MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets. Bioinformatics 2015;31:788-90. [PMID: 25348215 PMCID: PMC4341062 DOI: 10.1093/bioinformatics/btu705] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 09/24/2014] [Accepted: 10/21/2014] [Indexed: 01/05/2023]  Open
Number Cited by Other Article(s)
1
Yin J, Huang M, Zeng Z, Zhang Y, Tan Z, Xia Y. Atrazine exposure induces abnormal swimming behavior of tadpoles under light and/or dark stimuli: A comprehensive multi-omics insights from eyes and brain. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2025;284:107396. [PMID: 40344973 DOI: 10.1016/j.aquatox.2025.107396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2025] [Revised: 04/16/2025] [Accepted: 05/03/2025] [Indexed: 05/11/2025]
2
Huang M, Yin J, Wan Y, Duan R. The influences of pulse exposure versus continuous exposure to cadmium are different: Mechanisms elucidated from motor behavior and brain in amphibian larvae. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2025;299:118412. [PMID: 40424726 DOI: 10.1016/j.ecoenv.2025.118412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2025] [Revised: 05/11/2025] [Accepted: 05/23/2025] [Indexed: 05/29/2025]
3
Guo C, Zhang Y, Bai D, Zhen W, Ma P, Wang Z, Zhao X, Ma X, Xie X, Ito K, Zhang B, Yang Y, Li J, Ma Y. Aspirin Eugenol Ester Alleviates Energy Metabolism Disorders by Reducing Oxidative Damage and Inflammation in the Livers of Broilers Under High-Stocking-Density Stress. Int J Mol Sci 2025;26:1877. [PMID: 40076504 PMCID: PMC11899955 DOI: 10.3390/ijms26051877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 02/14/2025] [Accepted: 02/19/2025] [Indexed: 03/14/2025]  Open
4
Liao J, Zhang Y, Zhang W, Zeng Y, Zhao J, Zhang J, Yao T, Li H, Shen X, Wu G, Zhang W. Different software processing affects the peak picking and metabolic pathway recognition of metabolomics data. J Chromatogr A 2023;1687:463700. [PMID: 36508769 DOI: 10.1016/j.chroma.2022.463700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
5
Duan R, Lin Y, Yang L, Zhang Y, Hu W, Du Y, Huang M. Effects of antimony stress on growth, structure, enzyme activity and metabolism of Nipponbare rice (Oryza sativa L.) roots. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023;249:114409. [PMID: 36508805 DOI: 10.1016/j.ecoenv.2022.114409] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
6
Loftfield E, Stepien M, Viallon V, Trijsburg L, Rothwell JA, Robinot N, Biessy C, Bergdahl IA, Bodén S, Schulze MB, Bergman M, Weiderpass E, Schmidt JA, Zamora-Ros R, Nøst TH, Sandanger TM, Sonestedt E, Ohlsson B, Katzke V, Kaaks R, Ricceri F, Tjønneland A, Dahm CC, Sánchez MJ, Trichopoulou A, Tumino R, Chirlaque MD, Masala G, Ardanaz E, Vermeulen R, Brennan P, Albanes D, Weinstein SJ, Scalbert A, Freedman ND, Gunter MJ, Jenab M, Sinha R, Keski-Rahkonen P, Ferrari P. Novel Biomarkers of Habitual Alcohol Intake and Associations With Risk of Pancreatic and Liver Cancers and Liver Disease Mortality. J Natl Cancer Inst 2021;113:1542-1550. [PMID: 34010397 PMCID: PMC8562969 DOI: 10.1093/jnci/djab078] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/24/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022]  Open
7
Viallon V, His M, Rinaldi S, Breeur M, Gicquiau A, Hemon B, Overvad K, Tjønneland A, Rostgaard-Hansen AL, Rothwell JA, Lecuyer L, Severi G, Kaaks R, Johnson T, Schulze MB, Palli D, Agnoli C, Panico S, Tumino R, Ricceri F, Verschuren WMM, Engelfriet P, Onland-Moret C, Vermeulen R, Nøst TH, Urbarova I, Zamora-Ros R, Rodriguez-Barranco M, Amiano P, Huerta JM, Ardanaz E, Melander O, Ottoson F, Vidman L, Rentoft M, Schmidt JA, Travis RC, Weiderpass E, Johansson M, Dossus L, Jenab M, Gunter MJ, Lorenzo Bermejo J, Scherer D, Salek RM, Keski-Rahkonen P, Ferrari P. A New Pipeline for the Normalization and Pooling of Metabolomics Data. Metabolites 2021;11:631. [PMID: 34564446 PMCID: PMC8467830 DOI: 10.3390/metabo11090631] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/10/2023]  Open
8
Mengdi X, Haibo D, Jiaxin L, Zhe X, Yi C, Xuan L, Haiyan M, Hui S, Tianqi A, Yunzhen L, Wenqing C. Metabolomics reveals the "Invisible" detoxification mechanisms of Amaranthus hypochondriacus at three ages upon exposure to different levels of cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020;195:110520. [PMID: 32213366 DOI: 10.1016/j.ecoenv.2020.110520] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 05/15/2023]
9
Rothwell JA, Keski-Rahkonen P, Robinot N, Assi N, Casagrande C, Jenab M, Ferrari P, Boutron-Ruault MC, Mahamat-Saleh Y, Mancini FR, Boeing H, Katzke V, Kühn T, Niforou K, Trichopoulou A, Valanou E, Krogh V, Mattiello A, Palli D, Sacerdote C, Tumino R, Scalbert A. A Metabolomic Study of Biomarkers of Habitual Coffee Intake in Four European Countries. Mol Nutr Food Res 2019;63:e1900659. [PMID: 31483556 DOI: 10.1002/mnfr.201900659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/23/2019] [Indexed: 11/07/2022]
10
Edmands WMB, Hayes J, Rappaport SM. SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis. Bioinformatics 2019;34:3589-3590. [PMID: 29790936 DOI: 10.1093/bioinformatics/bty218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 05/18/2018] [Indexed: 11/12/2022]  Open
11
Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites 2019;9:E200. [PMID: 31548506 PMCID: PMC6835268 DOI: 10.3390/metabo9100200] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 11/17/2022]  Open
12
Aszyk J, Byliński H, Namieśnik J, Kot-Wasik A. Main strategies, analytical trends and challenges in LC-MS and ambient mass spectrometry–based metabolomics. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
13
Park Y, Noda I, Jung YM. Smooth Factor Analysis (SFA) to Effectively Remove High Levels of Noise from Spectral Data Sets. APPLIED SPECTROSCOPY 2018;72:765-775. [PMID: 29264945 DOI: 10.1177/0003702817752126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
14
Perez de Souza L, Naake T, Tohge T, Fernie AR. From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience 2017;6:1-20. [PMID: 28520864 PMCID: PMC5499862 DOI: 10.1093/gigascience/gix037] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 01/19/2023]  Open
15
Edmands WMB, Petrick L, Barupal DK, Scalbert A, Wilson MJ, Wickliffe JK, Rappaport SM. compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets. Anal Chem 2017;89:3919-3928. [PMID: 28225587 PMCID: PMC6338221 DOI: 10.1021/acs.analchem.6b02394] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
16
Wen B, Mei Z, Zeng C, Liu S. metaX: a flexible and comprehensive software for processing metabolomics data. BMC Bioinformatics 2017;18:183. [PMID: 28327092 PMCID: PMC5361702 DOI: 10.1186/s12859-017-1579-y] [Citation(s) in RCA: 537] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/03/2017] [Indexed: 12/14/2022]  Open
17
Petrick L, Edmands W, Schiffman C, Grigoryan H, Perttula K, Yano Y, Dudoit S, Whitehead T, Metayer C, Rappaport S. An untargeted metabolomics method for archived newborn dried blood spots in epidemiologic studies. Metabolomics 2017;13:27. [PMID: 29706849 PMCID: PMC5918689 DOI: 10.1007/s11306-016-1153-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022]
18
Gagnebin Y, Tonoli D, Lescuyer P, Ponte B, de Seigneux S, Martin PY, Schappler J, Boccard J, Rudaz S. Metabolomic analysis of urine samples by UHPLC-QTOF-MS: Impact of normalization strategies. Anal Chim Acta 2017;955:27-35. [DOI: 10.1016/j.aca.2016.12.029] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 12/08/2016] [Accepted: 12/20/2016] [Indexed: 10/20/2022]
19
Supporting metabolomics with adaptable software: design architectures for the end-user. Curr Opin Biotechnol 2017;43:110-117. [DOI: 10.1016/j.copbio.2016.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 02/07/2023]
20
Uppal K, Walker DI, Liu K, Li S, Go YM, Jones DP. Computational Metabolomics: A Framework for the Million Metabolome. Chem Res Toxicol 2016;29:1956-1975. [PMID: 27629808 DOI: 10.1021/acs.chemrestox.6b00179] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
21
Misra BB, van der Hooft JJJ. Updates in metabolomics tools and resources: 2014-2015. Electrophoresis 2015;37:86-110. [DOI: 10.1002/elps.201500417] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/04/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022]
22
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. Polyphenol metabolome in human urine and its association with intake of polyphenol-rich foods across European countries. Am J Clin Nutr 2015;102:905-13. [PMID: 26269369 DOI: 10.3945/ajcn.114.101881] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 07/21/2015] [Indexed: 02/05/2023]  Open
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