Research library - Key Lipidomics Publications

Year published: 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017

Key Lipidomics Publications

Special issues, with significant contributions from members of the LIPID MAPS Consortium

Peer-reviewed journal articles

  • Gene-expression measurement: variance-modeling considerations for robust data analysis

    Shankar Subramaniam & Gene Hsiao

    Nature Immunology, 13,199-203 (2012)

    [ PMID: 22344273 doi: 10.1038/ni.2244 ]

  • Macrophages, Inflammation, and Insulin Resistance

    Olefsky, J, Glass, C

    Annual Review of Physiology, Volume 72 (2011)

    [ PMID: 20148674 doi: 10.1146/annurev-physiol-021909-135846 ]

  • Lipidomics reveals a remarkable diversity of lipids in human plasma.

    Quehenberger O, Armando A, Brown HA, Milne JS, Myers DS, Merrill AH, Bandyopadyhay S, Jones ND, Kelly S, Shaner RL, Sullards MC, 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

    J Lipid Res 51, 3299-3305 (2010)

    [ PMID: 20671299 ]

  • Update of the LIPID MAPS comprehensive classification system for lipids.

    Fahy E, Subramaniam S, Murphy R, Nishijima M, Raetz C, Shimizu T, Spener F, van Meer G, Wakelam M and Dennis E.

    Journal of Lipid Research 50, S9-S14 (2009)

    [ PMID:19098281 doi: 10.1194/jlr.R800095-JLR200 ]

  • LIPID MAPS online tools for lipid research.

    Fahy E, Sud M, Cotter D and Subramaniam S.

    Nucleic Acids Research 35, W606-12 (2007)

    [ PMID: 17584797 doi: 10.1093/nar/gkm324 ]

  • Parallel SUMOylation-dependent pathways mediate gene- and signal-specific transrepression by LXRs and PPARgamma.

    Ghisletti S, Huang W, Ogawa S, Pascual G, Lin M, Willson T, Rosenfeld M and Glass C.

    Molecular Cell 25, 57-70 (2007)

    [ PMID: 17218271 doi: 10.1016/j.molcel.2006.11.022 ]

  • Macrophage PPAR gamma is required for normal skeletal muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones.

    Hevener A, Olefsky J, Reichart D, Nguyen M, Bandyopadyhay G, Leung H, Watt M, Benner C, Febbraio M, Nguyen A, Folian B, Subramaniam S, Gonzalez F, Glass C and Ricote M.

    The Journal of Clinical Investigation 117, 1658-1669 (2007)

    [ PMID: 17525798 doi: 10.1172/JCI31561 ]

  • LMSD: LIPID MAPS structure database.

    Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Jr., Murphy RC, Raetz CR, Russell DW, Subramaniam S

    Nucleic Acids Research 35, D527-32 (2007)

    [ PMID: 17098933 doi: 10.1093/nar/gkl838 ]

  • Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4.

    Raetz C, Garrett T, Reynolds C, Shaw W, Moore J, Smith JD, Ribeiro A, Murphy R, Ulevitch R, Fearns C, Reichart D, Glass C, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry R, Buczynski M, Cooper J, Deems R and Dennis E.

    Journal of Lipid Research 47, 1097-1111 (2006)

    [ PMID:16479018 doi: 10.1194/jlr.M600027-JLR200 ]

  • A comprehensive classification system for lipids.

    Fahy E, Subramaniam S, Brown H, Glass C, Merrill JA, Murphy R, Raetz C, Russell D, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, Vannieuwenhze M, White S, Witztum J and Dennis E.

    Journal of Lipid Research 46, 839-861 (2005)

    [ PMID: 15722563 doi: 10.1194/jlr.E400004-JLR200 ]

  • Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP.

    Ortlund E, Lee Y, Solomon I, Hager J, Safi R, Choi Y, Guan Z, Tripathy A, Raetz C, McDonnell D, Moore D and Redinbo M.

    Nature Structural & Molecular Biology 12, 357-363 (2005)

    [ PMID: 15723037 doi: 10.1038/nsmb910 ]

  • Reconstruction of cellular signalling networks and analysis of their properties.

    Papin JA, Hunter T, Palsson BO and Subramaniam S.

    Nature Reviews Molecular Cell Biology 6, 99-111 (2005)

    [ PMID: 15654321 doi: 10.1038/nrm1570 ]

Other key publications relevant to the field of lipidomics

Books Peer-reviewed journal articles
  • MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

    Nature methods (2015)

    doi: 10.1038/nmeth.3393

  • Lysophospholipid Acyltransferases Mediate Phosphatidylcholine Diversification to Achieve the Physical Properties Required In Vivo

    Cell Metabolomism (2015)

    doi: 10.1016/j.cmet.2014.05.019

  • Dysregulation of soluble epoxide hydrolase and lipidomic profiles in anorexia nervosa.

    Mol Psychiatry (2015)

    doi: 10.1038/mp.2015.26

  • HIF-2α promotes degradation of mammalian peroxisomes by selective autophagy

    Cell Metabolomism (2014)

    doi:10.1016/j.cmet.2014.09.017

  • Cannabidiol exerts sebostatic and antiinflammatory effects on human sebocytes.

    J Clin Invest (2014)

    doi: 10.1172/JCI64628

  • A community-driven global reconstruction of human metabolism.

    Nature Biotechnology (2013)

    doi: 10.1038/nbt.2488

  • LipidBlast in silico tandem mass spectrometry database for lipid identification.

    Nature methods (2013)

    doi: 10.1038/nmeth.2551

  • Heat generates a family of oxidized linoleic acid metabolites that activate TRPV1 and produce pain in rodents.

    J Clin Invest (2010)

    doi: 10.1172/JCI41678

  • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules.

    Weininger D

    J Chem Inf Comput Sci 28, 31-36 (1988)

    doi: [10.1021/ci00057a005]

  • Plasma lipid profiling by liquid chromatography with chloride-attachment mass spectrometry.

    Kuksis A, Marai L, Myher JJ.

    Lipids 26, 240-246 (1991)

    doi: [10.1007/BF02543979]

  • Nondestructive quantification of neutral lipids by thin-layer chromatography and laser-fluorescent scanning: Suitable methods for 'lipidome' analysis.

    Kishimoto,K., Urade,R., Ogawa,T. and Moriyama T.

    Biochem. Biophys. Res. Commun. 281, 657-662 (2001)

    doi: [10.1006/bbrc.2001.4404]

  • Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression.

    Alvin Berger, David M Mutch, J Bruce German, Matthew A Roberts

    Lipids in Health and Disease 1, (2002)

    doi: [10.1186/1476-511X-1-2]

  • Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics.

    Han, X. and Gross, R.W.

    J. Lipid Res. 44, 1071-1079 (2003)

    PMID: 12671038

  • Editorial: What is lipidomics?

    Spener, F., Lagarde, M., Géloên, A. and Record, M.

    Eur. J. Lipid Sci. Technol. 105, 481-482 (2003)

    doi: [10.1002/ejlt.200390101]

  • Computational Lipidomics: A multiplexed analysis of dynamic changes in membrane lipid composition during signal transduction.

    Forrester JS, Milne SB, Ivanova PT, and Brown HA.

    Molecular Pharmacology 65, 813-821 (2004)

    PMID: 15044609

  • Processing methods for differential analysis of LC/MS profile data.

    Mikko Katajamaa, Matej Orešič

    BMC Bioinformatics 6, (2005)

    doi: [10.1186/1471-2105-6-179]

  • Cellular lipidomics.

    van Meer G

    EMBO J 24, 3159-3164 (2005)

    PMID: 16138081

  • The emerging field of lipidomics.

    Wenk, M.R.

    Nat. Rev. Drug Discov. 4, 594-610 (2005)

    PMID: 16052242

  • Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems.

    Watson, AD

    J. Lipid Res. 47, 2101-2111 (2006)

    doi: [10.1194/jlr.R600022-JLR200]

  • Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis.

    Laxman Yetukuri, Mikko Katajamaa, Gema Medina-Gomez, Tuulikki Seppänen-Laakso, Antonio Vidal-Puig, Matej Orešič

    BMC Systems Biology 1, (2007)

    doi: [10.1186/1752-0509-1-12]

  • Normalization method for metabolomics data using optimal selection of multiple internal standards.

    Marko Sysi-Aho, Mikko Katajamaa, Laxman Yetukuri, Matej Orešič

    BMC Bioinformatics 8, (2007)

    doi: [10.1186/1471-2105-8-93]

  • An analysis of the epitope knowledge related to Mycobacteria.

    Martin J Blythe, Qing Zhang, Kerrie Vaughan, Romulo de Castro, Nima Salimi, Huynh-Hoa Bui, David M Lewinsohn, Joel D Ernst, Bjoern Peters, Alessandro Sette

    Immunome Research 3, (2007)

    doi: [10.1186/1745-7580-3-10]

  • Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis.

    Robert Kleemann, Lars Verschuren, Marjan J van Erk, Yuri Nikolsky, Nicole HP Cnubben, Elwin R Verheij, Age K Smilde, Henk FJ Hendriks, Susanne Zadelaar, Graham J Smith, Valery Kaznacheev, Tatiana Nikolskaya, Anton Melnikov, Eva Hurt-Camejo, Jan van der Greef, Ben van Ommen, Teake Kooistra

    Genome Biology 8, (2007)

    doi: [10.1186/gb-2007-8-9-r200]

  • Bench-to-bedside review: Mitochondrial injury, oxidative stress and apoptosis: there is nothing more practical than a good theory.

    Hülya Bayir, Valerian E Kagan

    Critical Care 12, (2008)

    doi: [10.1186/cc6779]

  • The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.

    Intawat Nookaew, Michael C Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana

    BMC Systems Biology 2, (2008)

    doi: [10.1186/1752-0509-2-71]

  • Technological developments in lipidomics.

    Weimin Hou, Hu Zhou, Fred Elisma, Steffany A. L. Bennett, and Daniel Figeys

    Briefings in Functional Genomics and Proteomics 7, 395-409 (2008)

    doi: [10.1093/bfgp/eln042]

  • Genetics of asthma: a molecular biologist perspective.

    Amrendra Kumar, Balaram Ghosh

    Clinical and Molecular Allergy 7, (2009)

    doi: [10.1186/1476-7961-7-7]

  • Systems medicine: the future of medical genomics and healthcare.

    Charles Auffray, Zhu Chen, Leroy Hood

    Genome Medicine 1, (2009)

    doi: [10.1186/gm2]

  • Improving the analysis of designed studies by combining statistical modelling with study design information.

    Uwe Thissen, Suzan Wopereis, Sjoerd AA van den Berg, Ivana Bobeldijk, Robert Kleemann, Teake Kooistra, Ko Willems van Dijk, Ben van Ommen, Age K Smilde

    BMC Bioinformatics 10, (2009)

    doi: [10.1186/1471-2105-10-52]

  • Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis.

    Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, Masanori Arita

    BMC Bioinformatics 11, (2010)

    doi: [10.1186/1471-2105-11-214]

  • Role of platelets in neuroinflammation: a wide-angle perspective.

    Lawrence L Horstman, Wenche Jy, Yeon S Ahn, Robert Zivadinov, Amir H Maghzi, Masoud Etemadifar, J Steven Alexander, Alireza Minagar

    Journal of Neuroinflammation 7, (2010)

    doi: [10.1186/1742-2094-7-10]

  • LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB.

    Sheng He, Juan Mei, Guiyang Shi, Zhengxiang Wang, Weijiang Li

    BMC Bioinformatics 11, (2010)

    doi: [10.1186/1471-2105-11-31]

  • Evaluation of bioactive sphingolipids in 4-HPR-resistant leukemia cells.

    Aintzane Apraiz, Jolanta K Idkowiak-Baldys, María Boyano, Gorka Pérez-Yarza, Yusuf A Hannun, Aintzane Asumendi

    BMC Cancer 11, (2011)

    doi: [10.1186/1471-2407-11-477]

  • Contribution of bacterial outer membrane vesicles to innate bacterial defense.

    Andrew J Manning, Meta J Kuehn

    BMC Microbiology 11, (2011)

    doi: [10.1186/1471-2180-11-258]

  • The Protein Lipidation and Its Analysis.

    Gemma Triola

    J Glycom Lipidom S2, (2011)

    doi: [10.4172/2153-0637.S2-001]

  • Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data.

    Jan Krumsiek, Karsten Suhre, Thomas Illig, Jerzy Adamski, Fabian J Theis

    BMC Systems Biology 5, (2011)

    doi: [10.1186/1752-0509-5-21]

  • Review: Accurate Quantification of Lipid Species by Electrospray Ionization Mass Spectrometry — Meets a Key Challenge in Lipidomics.

    Kui Yang and Xianlin Han

    Metabolites 1, 21-40 (2011)

    doi: [10.3390/metabo1010021]

  • Metabolome in schizophrenia and other psychotic disorders: a general population-based study.

    Matej Orešič, Jing Tang, Tuulikki Seppänen-Laakso, Ismo Mattila, Suoma E Saarni, Samuli I Saarni, Jouko Lönnqvist, Marko Sysi-Aho, Tuulia Hyötyläinen, Jonna Perälä, Jaana Suvisaari

    Genome Medicine 3, (2011)

    doi: [10.1186/gm233]

  • Methods in Comprehensive Mass Spectrometry-Based Measurement of Sphingolipids.

    Nikolaus Gassler

    J Glycom Lipidom S2, (2011)

    doi: [10.4172/2153-0637.S2-002]

  • Allergy as an epithelial barrier disease.

    Pirkko Mattila, Sakari Joenväärä, Jutta Renkonen, Sanna Toppila-Salmi, Risto Renkonen

    Clinical and Translational Allergy 1, (2011)

    doi: [10.1186/2045-7022-1-5]

  • Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism.

    Shakti Gupta, Mano R Maurya, Alfred H Merrill Jr, Christopher K Glass, Shankar Subramaniam

    BMC Systems Biology 5, (2011)

    doi: [10.1186/1752-0509-5-26]

  • Clinical review: Exogenous surfactant therapy for acute lung injury/acute respiratory distress syndrome - where do we go from here?

    Ahilanandan Dushianthan, Rebecca Cusack, Victoria Goss, Anthony D Postle, Mike PW Grocott

    Critical Care 16, (2012)

    doi: [10.1186/cc11512]

  • On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies.

    Ann-Kristin Petersen, Jan Krumsiek, Brigitte Wägele, Fabian J Theis, H-Erich Wichmann, Christian Gieger, Karsten Suhre

    BMC Bioinformatics 13, (2012)

    doi: [10.1186/1471-2105-13-120]

  • Review: Perturbations of Lipid Metabolism Indexed by Lipidomic Biomarkers.

    Antonin Lamaziere, Claude Wolf and Peter J. Quinn

    Metabolites 2, 1-18 (2012)

    doi: [10.3390/metabo2010001]

  • Article: Shotgun Lipidomics by Sequential Precursor Ion Fragmentation on a Hybrid Quadrupole Time-of-Flight Mass Spectrometer.

    Brigitte Simons, Dimple Kauhanen, Tuulia Sylvänne, Kirill Tarasov, Eva Duchoslav and Kim Ekroos

    Metabolites 2, 195-213 (2012)

    doi: [10.3390/metabo2010195]

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

    Carsten Denkert, Elmar Bucher, Mika Hilvo, Reza Salek, Matej Orešič, Julian Griffin, Scarlet Brockmöller, Frederick Klauschen, Sibylle Loibl, Dinesh Barupal, Jan Budczies, Kristiina Iljin, Valentina Nekljudova, Oliver Fiehn

    Genome Medicine 4, (2012)

    doi: [10.1186/gm336]

  • Article: Comparative Lipidomic Profiling of S. cerevisiae and Four Other Hemiascomycetous Yeasts.

    Eva-Maria Hein and Heiko Hayen

    Metabolites 2, 254-267 (2012)

    doi: [10.3390/metabo2010254]

  • Article: Metabolomic and Lipidomic Analysis of the Heart of Peroxisome Proliferator-Activated Receptor-γ Coactivator 1-β Knock Out Mice on a High Fat Diet.

    Gregor McCombie, Gema Medina-Gomez, Christopher J Lelliott, Antonio Vidal-Puig and Julian L Griffin

    Metabolites 2, 366-381 (2012)

    doi: [10.3390/metabo2020366]

  • Review: Lipidomics of Glycosphingolipids.

    Hany Farwanah and Thomas Kolter

    Metabolites 2, 134-164 (2012)

    doi: [10.3390/metabo2010134]

  • Review: Mass Spectrometry Based Lipidomics: An Overview of Technological Platforms.

    Harald C. Köfeler, Alexander Fauland, Gerald N. Rechberger and Martin Trötzmüller

    Metabolites 2, 19-38 (2012)

    doi: [10.3390/metabo2010019]

  • VANTED v2: a framework for systems biology applications.

    Hendrik Rohn, Astrid Junker, Anja Hartmann, Eva Grafahrend-Belau, Hendrik Treutler, Matthias Klapperstück, Tobias Czauderna, Christian Klukas, Falk Schreiber

    BMC Systems Biology 6, (2012)

    doi: [10.1186/1752-0509-6-139]

  • Structure-based classification and ontology in chemistry.

    Janna Hastings, Despoina Magka, Colin Batchelor, Lian Duan, Robert Stevens, Marcus Ennis, Christoph Steinbeck

    Journal of Cheminformatics 4, (2012)

    doi: [10.1186/1758-2946-4-8]

  • Genome-wide association studies with metabolomics.

    Jerzy Adamski

    Genome Medicine 4, (2012)

    doi: [10.1186/gm333]

  • Self-organizing ontology of biochemically relevant small molecules.

    Leonid L Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck, Michel Dumontier

    BMC Bioinformatics 13, (2012)

    doi: [10.1186/1471-2105-13-3]

  • Glycosphingolipid Mediated Caveolin-1 Oligomerization.

    Liming Shu and James A. Shayman

    J Glycom Lipidom S2, (2012)

    doi: [10.4172/2153-0637.S2-003]

  • New perspectives on central and peripheral immune responses to acute traumatic brain injury.

    Mahasweta Das, Subhra Mohapatra, Shyam S Mohapatra

    Journal of Neuroinflammation 9, (2012)

    doi: [10.1186/1742-2094-9-236]

  • Phospholipids and insulin resistance in psychosis: a lipidomics study of twin pairs discordant for schizophrenia.

    Matej Orešič, Tuulikki Seppänen-Laakso, Daqiang Sun, Jing Tang, Sebastian Therman, Rachael Viehman, Ulla Mustonen, Theo G van Erp, Tuulia Hyötyläinen, Paul Thompson, Arthur W Toga, Matti O Huttunen, Jaana Suvisaari, Jaakko Kaprio, Jouko Lönnqvist, Tyrone D Cannon

    Genome Medicine 4, (2012)

    doi: [10.1186/gm300]

  • Article: Quantification of Signaling Lipids by Nano-Electrospray Ionization Tandem Mass Spectrometry (Nano-ESI MS/MS).

    Mathias Haag, Angelika Schmidt, Timo Sachsenheimer and Britta Brügger

    Metabolites 2, 57-76 (2012)

    doi: [10.3390/metabo2010057]

  • A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica.

    Nicolas Loira, Thierry Dulermo, Jean-Marc Nicaud, David Sherman

    BMC Systems Biology 6, (2012)

    doi: [10.1186/1752-0509-6-35]

  • Lipidomics of Alzheimer's disease: current status.

    Paul L Wood

    Alzheimer's Research & Therapy 4, (2012)

    doi: [10.1186/alzrt103]

  • Ceramide Profiles of Human Serum Gangliosides GM2 and GD1a exhibit Cancer-associated Alterations.

    Stephan Kirsch, Jamal Souady, Michael Mormann, Laura Bindila and JasnaPeter-Katalinić

    J Glycom Lipidom S2, (2012)

    doi: [10.4172/2153-0637.S2-005]

  • Imaging Technology of Complex Lipid Molecular Species by a Combination of TLC-Blot and MALDI-TOF –Special Reference to Human Brain Ganglioside Molecular Species.

    Tania Valdes-Gonzalez, Naoko Goto-Inoue, Takahiro Hayasaka, Hironobu Ishiyama, Mitsutoshi Setou and Takao Taki

    J Glycom Lipidom S2, (2012)

    doi: [10.4172/2153-0637.S2-004]

  • Resolvin D1 attenuates inflammation in lipopolysaccharide-induced acute lung injury through a process involving the PPAR_/NF-κB pathway.

    Zenglin Liao, Jiajia Dong, Wei Wu, Ting Yang, Tao Wang, Lingli Guo, Lei Chen, Dan Xu, Fuqiang Wen

    Respiratory Research 13, (2012)

    doi: [10.1186/1465-9921-13-110]

  • Applications of metabolomics for understanding the action of peroxisome proliferator-activated receptors (PPARs) in diabetes, obesity and cancer.

    Zsuzsanna Ament, Mojgan Masoodi, Julian L Griffin

    Genome Medicine 4, (2012)

    doi: [10.1186/gm331]

  • Clinical, imaging, and pathological heterogeneity of the Alzheimer's disease syndrome.

    Benjamin Lam, Mario Masellis, Morris Freedman, Donald T Stuss, Sandra E Black

    Alzheimer's Research & Therapy 5, (2013)

    doi: [10.1186/alzrt155]

  • MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

    Brian L LaMarche, Kevin L Crowell, Navdeep Jaitly, Vladislav A Petyuk, Anuj R Shah, Ashoka D Polpitiya, John D Sandoval, Gary R Kiebel, Matthew E Monroe, Stephen J Callister, Thomas O Metz, Gordon A Anderson, Richard D Smith

    BMC Bioinformatics 14, (2013)

    doi: [10.1186/1471-2105-14-49]

  • Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics.

    Kiersten A Liddy, Melanie Y White, Stuart J Cordwell

    Genome Medicine 5, (2013)

    doi: [10.1186/gm424]