Eoin Fahy

Title(s)CMPTL AND DATA SCI RSCH SPEC 4, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    LIPID Metabolites And Pathways Strategy (LIPID MAPS)
    NIH R24GM107784Sep 1, 2013 - Jul 31, 2017
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Enabling pan-repository reanalysis for big data science of public metabolomics data. Nat Commun. 2025 May 24; 16(1):4838. El Abiead Y, Strobel M, Payne T, Fahy E, O'Donovan C, Subramamiam S, Vizcaíno JA, Yurekten O, Deleray V, Zuffa S, Xing S, Mannochio-Russo H, Mohanty I, Zhao HN, Caraballo-Rodriguez AM, P Gomes PW, Avalon NE, Northen TR, Bowen BP, Louie KB, Dorrestein PC, Wang M. PMID: 40413169; PMCID: PMC12103507.
      View in: PubMed   Mentions:    Fields:    
    2. MetGENE: gene-centric metabolomics information retrieval tool. Gigascience. 2022 12 28; 12. Srinivasan S, Maurya MR, Ramachandran S, Fahy E, Subramaniam S. PMID: 37983749; PMCID: PMC10659118.
      View in: PubMed   Mentions: 1     Fields:    
    3. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods. 2022 02; 19(2):134-136. Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M. PMID: 34862502; PMCID: PMC8831450.
      View in: PubMed   Mentions: 27     Fields:    
    4. RefMet: a reference nomenclature for metabolomics. Nat Methods. 2020 12; 17(12):1173-1174. Fahy E, Subramaniam S. PMID: 33199890.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    5. LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics. Bioinformatics. 2019 02 15; 35(4):685-687. Fahy E, Alvarez-Jarreta J, Brasher CJ, Nguyen A, Hawksworth JI, Rodrigues P, Meckelmann S, Allen SM, O'Donnell VB. PMID: 30101336; PMCID: PMC6378932.
      View in: PubMed   Mentions: 17     Fields:    
    6. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res. 2016 Jan 04; 44(D1):D463-70. Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C, Edison A, Fiehn O, Higashi R, Nair KS, Sumner S, Subramaniam S. PMID: 26467476; PMCID: PMC4702780.
      View in: PubMed   Mentions: 381     Fields:    Translation:HumansAnimalsCells
    7. A combined omics study on activated macrophages--enhanced role of STATs in apoptosis, immunity and lipid metabolism. Bioinformatics. 2013 Nov 01; 29(21):2735-43. Dinasarapu AR, Gupta S, Ram Maurya M, Fahy E, Min J, Sud M, Gersten MJ, Glass CK, Subramaniam S. PMID: 23981351; PMCID: PMC3799469.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    8. Analysis of inflammatory and lipid metabolic networks across RAW264.7 and thioglycolate-elicited macrophages. J Lipid Res. 2013 Sep; 54(9):2525-42. Maurya MR, Gupta S, Li X, Fahy E, Dinasarapu AR, Sud M, Brown HA, Glass CK, Murphy RC, Russell DW, Dennis EA, Subramaniam S. PMID: 23776196; PMCID: PMC3735949.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    9. Regulated accumulation of desmosterol integrates macrophage lipid metabolism and inflammatory responses. Cell. 2012 Sep 28; 151(1):138-52. Spann NJ, Garmire LX, McDonald JG, Myers DS, Milne SB, Shibata N, Reichart D, Fox JN, Shaked I, Heudobler D, Raetz CR, Wang EW, Kelly SL, Sullards MC, Murphy RC, Merrill AH, Brown HA, Dennis EA, Li AC, Ley K, Tsimikas S, Fahy E, Subramaniam S, Quehenberger O, Russell DW, Glass CK. PMID: 23021221; PMCID: PMC3464914.
      View in: PubMed   Mentions: 274     Fields:    Translation:AnimalsCells
    10. Template-based combinatorial enumeration of virtual compound libraries for lipids. J Cheminform. 2012 Sep 25; 4(1):23. Sud M, Fahy E, Subramaniam S. PMID: 23006594; PMCID: PMC3545849.
      View in: PubMed   Mentions: 8  
    11. LIPID MAPS-Nature Lipidomics Gateway: An Online Resource for Students and Educators Interested in Lipids. J Chem Educ. 2012 Jan 10; 89(2):291-292. Sud M, Fahy E, Cotter D, Dennis EA, Subramaniam S. PMID: 24764601; PMCID: PMC3995124.
      View in: PubMed   Mentions: 23     Fields:    
    12. Bioinformatics and systems biology of the lipidome. Chem Rev. 2011 Oct 12; 111(10):6452-90. Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR. PMID: 21939287; PMCID: PMC3383319.
      View in: PubMed   Mentions: 47     Fields:    
    13. Lipid classification, structures and tools. Biochim Biophys Acta. 2011 Nov; 1811(11):637-47. Fahy E, Cotter D, Sud M, Subramaniam S. PMID: 21704189; PMCID: PMC3995129.
      View in: PubMed   Mentions: 197     Fields:    Translation:HumansAnimals
    14. A mouse macrophage lipidome. J Biol Chem. 2010 Dec 17; 285(51):39976-85. Dennis EA, Deems RA, Harkewicz R, Quehenberger O, Brown HA, Milne SB, Myers DS, Glass CK, Hardiman G, Reichart D, Merrill AH, Sullards MC, Wang E, Murphy RC, Raetz CR, Garrett TA, Guan Z, Ryan AC, Russell DW, McDonald JG, Thompson BM, Shaw WA, Sud M, Zhao Y, Gupta S, Maurya MR, Fahy E, Subramaniam S. PMID: 20923771; PMCID: PMC3000979.
      View in: PubMed   Mentions: 136     Fields:    Translation:AnimalsCells
    15. Lipidomics reveals a remarkable diversity of lipids in human plasma. J Lipid Res. 2010 Nov; 51(11):3299-305. Quehenberger O, Armando AM, Brown AH, Milne SB, Myers DS, Merrill AH, Bandyopadhyay S, Jones KN, Kelly S, Shaner RL, Sullards CM, Wang E, Murphy RC, Barkley RM, Leiker TJ, Raetz CR, Guan Z, Laird GM, Six DA, Russell DW, McDonald JG, Subramaniam S, Fahy E, Dennis EA. PMID: 20671299; PMCID: PMC2952570.
      View in: PubMed   Mentions: 507     Fields:    Translation:Humans
    16. Subcellular organelle lipidomics in TLR-4-activated macrophages. J Lipid Res. 2010 Sep; 51(9):2785-97. Andreyev AY, Fahy E, Guan Z, Kelly S, Li X, McDonald JG, Milne S, Myers D, Park H, Ryan A, Thompson BM, Wang E, Zhao Y, Brown HA, Merrill AH, Raetz CR, Russell DW, Subramaniam S, Dennis EA. PMID: 20574076; PMCID: PMC2918461.
      View in: PubMed   Mentions: 85     Fields:    Translation:AnimalsCells
    17. Application of proteomic marker ensembles to subcellular organelle identification. Mol Cell Proteomics. 2010 Feb; 9(2):388-402. Andreyev AY, Shen Z, Guan Z, Ryan A, Fahy E, Subramaniam S, Raetz CR, Briggs S, Dennis EA. PMID: 19884172; PMCID: PMC2830848.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    18. Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res. 2009 Apr; 50 Suppl:S9-14. Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR, Shimizu T, Spener F, van Meer G, Wakelam MJ, Dennis EA. PMID: 19098281; PMCID: PMC2674711.
      View in: PubMed   Mentions: 601     Fields:    
    19. LIPID MAPS online tools for lipid research. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W606-12. Fahy E, Sud M, Cotter D, Subramaniam S. PMID: 17584797; PMCID: PMC1933166.
      View in: PubMed   Mentions: 343     Fields:    Translation:HumansCells
    20. The lipid maps initiative in lipidomics. Methods Enzymol. 2007; 432:171-83. Schmelzer K, Fahy E, Subramaniam S, Dennis EA. PMID: 17954217.
      View in: PubMed   Mentions: 52     Fields:    
    21. Bioinformatics for lipidomics. Methods Enzymol. 2007; 432:247-73. Fahy E, Cotter D, Byrnes R, Sud M, Maer A, Li J, Nadeau D, Zhau Y, Subramaniam S. PMID: 17954221.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    22. Arachidonate-derived dihomoprostaglandin production observed in endotoxin-stimulated macrophage-like cells. J Biol Chem. 2007 Feb 02; 282(5):2899-910. Harkewicz R, Fahy E, Andreyev A, Dennis EA. PMID: 17135246.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    23. A comprehensive classification system for lipids. J Lipid Res. 2005 May; 46(5):839-61. Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH, Murphy RC, Raetz CR, Russell DW, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, VanNieuwenhze MS, White SH, Witztum JL, Dennis EA. PMID: 15722563.
      View in: PubMed   Mentions: 504     Fields:    Translation:Cells
    24. MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W372-4. Guda C, Guda P, Fahy E, Subramaniam S. PMID: 15215413; PMCID: PMC441512.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimalsCells
    25. MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics. 2004 Jul 22; 20(11):1785-94. Guda C, Fahy E, Subramaniam S. PMID: 15037509.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansAnimalsCells
    26. MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D463-7. Cotter D, Guda P, Fahy E, Subramaniam S. PMID: 14681458; PMCID: PMC308782.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansCells
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