- Fahy E, Subramaniam S, Brown HA, et al. (2005) A comprehensive classification system for lipids. J Lipid Res 46, 839–861.
Article CAS PubMed Google Scholar
- van Meer G. (2005) Cellular lipidomics. Embo J 24, 3159–3165.
Article PubMed Google Scholar
- Wenk MR. (2006) Lipidomics of host-pathogen interactions. FEBS Lett 580, 5541–5551.
Article CAS PubMed Google Scholar
- Adibhatla RM, Hatcher JF. (2007) Role of lipids in brain injury and diseases. Future Lipidol 2, 403–422.
Article CAS PubMed Google Scholar
- Wymann MP, Schneiter R. (2008) Lipid signalling in disease. Nat Rev Mol Cell Biol 9, 162–176.
Article CAS PubMed Google Scholar
- Wenk MR. (2005) The emerging field of lipidomics. Nat Rev Drug Discov 4, 594–610.
Article CAS PubMed Google Scholar
- Mattila I, Seppanen-Laakso T, Suortti T, Oresic M. (2008) Application of lipidomics and metabolomics to the study of adipose tissue. Methods Mol Biol 456, 123–130.
Article PubMed Google Scholar
- Jia L, Wang C, Zhao S, Lu X, Xu G. (2007) Metabolomic identification of potential phospholipid biomarkers for chronic glomerulonephritis by using high performance liquid chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 860, 134–140.
Article CAS PubMed Google Scholar
- Roberts LD, McCombie G, Titman CM, Griffin JL. (2008) A matter of fat: an introduction to lipidomic profiling methods. J Chromatogr B Analyt Technol Biomed Life Sci 871, 174–181.
Article CAS PubMed Google Scholar
- Han X, Gross RW. (2005) Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 24, 367–412.
Article CAS PubMed Google Scholar
- Yetukuri L, Ekroos K, Vidal-Puig A, Oresic M. (2008) Informatics and computational strategies for the study of lipids. Mol Biosyst 4, 121–127.
Article CAS PubMed Google Scholar
- Baker CJ, Kanagasabai R, Ang WT, Veeramani A, Low HS, Wenk MR. (2008) Towards ontology-driven navigation of the lipid bibliosphere. BMC Bioinformatics 9 Suppl 1, S5.
Article PubMed Google Scholar
- Schmelzer K, Fahy E, Subramaniam S, Dennis EA. (2007) The lipid maps initiative in lipidomics. Methods Enzymol 432, 171–183.
Article CAS PubMed Google Scholar
- van Meer G, Leeflang BR, Liebisch G, Schmitz G, Goni FM. (2007) The European lipidomics initiative: enabling technologies. Methods Enzymol 432, 213–232.
Article PubMed Google Scholar
- Taguchi R, Nishijima M, Shimizu T. (2007) Basic analytical systems for lipidomics by mass spectrometry in Japan. Methods Enzymol 432, 185–211.
Article CAS PubMed Google Scholar
- Watanabe K, Yasugi E, Oshima M. (2000) How to search the glycolipid data in LIPIDBANK for Web: the newly developed lipid database. Japan Trend Glycosci Glycotechnol 12, 175–184.
CAS Google Scholar
- Fahy E, Sud M, Cotter D, Subramaniam S. (2007) LIPID MAPS online tools for lipid research. Nucleic Acids Res 35, W606–612.
Article PubMed Google Scholar
- Sud M, Fahy E, Cotter D, et al. (2007) LMSD: LIPID MAPS structure database. Nucleic Acids Res 35, D527–532.
Article CAS PubMed Google Scholar
- Cotter D, Maer A, Guda C, Saunders B, Subramaniam S. (2006) LMPD: LIPID MAPS proteome database. Nucleic Acids Res 34, D507–510.
Article CAS PubMed Google Scholar
- Kanehisa M, Araki M, Goto S, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36, D480–484.
Article CAS PubMed Google Scholar
- Kanehisa M. (1997) A database for post-genome analysis. Trends Genet 13, 375–376.
Article CAS PubMed Google Scholar
- Fleischmann RD, Adams MD, White O, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.
Article CAS PubMed Google Scholar
- Goto S, Nishioka T, Kanehisa M. (1998) LIGAND: chemical database for enzyme reactions. Bioinformatics 14, 591–599.
Article CAS PubMed Google Scholar
- Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M. (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res 30, 402–404.
Article CAS PubMed Google Scholar
- Hashimoto K, Yoshizawa AC, Okuda S, Kuma K, Goto S, Kanehisa M. (2008) The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J Lipid Res 49, 183–191.
Article CAS PubMed Google Scholar
- Smith TF, Waterman MS. (1981) Identification of common molecular subsequences. J Mol Biol 147, 195–197.
Article CAS PubMed Google Scholar
- Fujibuchi W, Goto S, Migimatsu H, et al. (1998) DBGET/LinkDB: an integrated database retrieval system. Pac Symp Biocomput 683–694.
Google Scholar
- Klukas C, Schreiber F. (2007) Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics 23, 344–350.
Article CAS PubMed Google Scholar
- Suderman M, Hallett M. (2007) Tools for visually exploring biological networks. Bioinformatics 23, 2651–2659.
Article CAS PubMed Google Scholar
- Junker BH, Klukas C, Schreiber F. (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7, 109.
Article PubMed Google Scholar
- Klukas C, Junker BH, Schreiber F. (2006) The VANTED software system for transcriptomics, proteomics and metabolomics analysis. J Pestic Sci 31, 289–292.
Article CAS Google Scholar
- Yoshida K, Kobayashi K, Miwa Y, et al. (2001) Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res 29, 683–692.
Article CAS PubMed Google Scholar
- Fahy E, Cotter D, Byrnes R, et al. (2007) Bioinformatics for lipidomics. Methods Enzymol 432, 247–273.
Article CAS PubMed Google Scholar
- Lu Y, Hong S, Serhan C. (2006) Lipid mediator informatics-lipidomics: novel pathways in mapping resolution. AAPS Journal 8, E284–E297.
Article PubMed Google Scholar
- Ejsing CS, Duchoslav E, Sampaio J, et al. (2006) Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning. Anal Chem 78, 6202–6214.
Article CAS PubMed Google Scholar
- Kurvinen J-P, Aaltonan J, Kuksis A, H. Kallio. (2002) Software algorithm for automatic interpretation of mass spectra of glycerolipids. Rapid Commun Mass Spectrom 16, 1812–18201.
Article CAS PubMed Google Scholar
- Hermansson M, Uphoff A, Kakela R, Somerharju P. (2005) Automated quantitative analysis of complex lipidomes by liquid chromatography/mass spectrometry. Anal Chem 77, 2166–2175.
Article CAS PubMed Google Scholar
- Katajamaa M, Orešič M. (2005) Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6, 179–190.
Article PubMed Google Scholar
- Yetukuri L, Katajamaa M, Medina-Gomez G, Seppanen-Laakso T, Vidal-Puig A, Orešič M. (2007) Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. BMC Systems Biology 1, 12.
Article PubMed Google Scholar
- Katajamaa M, Miettinen J, Orešič M. (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22, 634–636.
Article CAS PubMed Google Scholar
- Krieger CJ, Zhang P, Mueller LA, et al. (2004) MetaCyc: a multiorganism database of metabolic pathways and enzymes 10.1093/nar/gkh100. Nucl Acids Res 32, D438–442.
Article CAS PubMed Google Scholar
- Gopalacharyulu PV, Lindfors E, Bounsaythip C, et al. (2005) Data integration and visualization system for enabling conceptual biology. Bioinformatics 21, i177–185.
Article CAS PubMed Google Scholar
- Wheelock CE, Wheelock AM, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggström JZ, Goto S. (2009) Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol Biosyst. 5(6), 588–602.
Article CAS PubMed Google Scholar