Bibliography
- Aoki-Kinoshita KF. An introduction to bioinformatics for glycomics research. PLoS computational biology. Edu Sect 2008;4(5):e1000075
- Von Der Lieth CW, Bohne-Lang A, Lohmann KK, Frank M. Bioinformatics for glycomics: status, methods, requirements and perspectives. Brief Bioinfor 2004;5(2):164-178
- Packer NH, Von Der Lieth CW, Aoki-Kinoshita KF, et al. Frontiers in glycomics: bioinformatics and biomarkers in disease. An NIH white paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11 – 13, 2006). Proteomics 2008;8(1):8-20
- Doubet S, Bock K, Smith D, et al. The complex carbohydrate structure database. Trends Biochem Sci 1989;14(12):475-7
- Doubet S, Albersheim P. CarbBank. Glycobiology 1992;2(6):505
- Hashimoto K, Goto S, Kawano S, et al. KEGG as a glycome informatics resource. Glycobiology 2006;16(5):R63-70
- Aoki KF, Yamaguchi A, Okuno Y, et al. Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform 2003;14:134-43
- Aoki KF, Yamaguchi A, Ueda N, et al. (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res 2004;32:W267-72
- Kegg Glycan Interface. Kyoto, Japan. Available from: http://www.genome.jp/kegg/glycan/ [Last accessed 20 May 2008]
- Raman R, Venkataraman M, Ramakrishnan S, et al. Advancing glycomics: implementation strategies at the consortium for functional glycomics. Glycobiology 2006;16(5):R82-90
- Glycan structure database sponsored by the CFG. Boston, MA. Available from: http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp [Last accessed 20 May 20, 2008]
- Blixt O, Razi N. Chemoenzymatic synthesis of glycan libraries. Methods Enzymol 2006;415C:137-53
- Blixt O, Head S, Mondala T, et al. Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci USA 2004;101(49):17033-8
- Comelli EM, Head SR, Gilmartin T, et al. A focused microarray approach to functional glycomics: transcriptional regulation of the glycome. Glycobiology 2006;16(2):117-31
- Haslam SM, North SJ, Dell A. Mass spectrometric analysis of N- and O-glycosylation of tissues and cells. Curr Opin Struct Biol 2006;16(5):584-91
- Berman HM, Henrick K, Nakamura H. Announcing the worldwide Protein Data Bank. Nat Struct Biol 2003;10(12):980
- wwPDB database. Available from: http://www.wwpdb.org [Last accessed 18 June 2008]
- Lütteke T, Bohne-Lang A, Loss A, et al. GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 2006;16(5):R71-81
- Glycosciences.de portal. Heidelberg, Germany. Available from: http://www.glycosciences.de/ [Last accessed 20 May 20, 2008]
- Frank M, Lütteke T, Von Der Lieth CW. GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. Nucleic Acids Res 2007;35(Database issue):287-90
- Bohne-Lang A, Von Der Lieth CW. GlyProt: in silico glycosylation of proteins. Nucleic Acids Res 2005;33(Web Server issue):W214-9
- Maass K, Ranzinger R, Geyer H, et al. “Glyco-peakfinder” – de novo composition analysis of glycoconjugates. Proteomics 2007;7(24):4435-44
- Loss A, Stenutz R, Schwarzer E, Von Der Lieth CW. GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface. Nucleic Acids Res 2006;34(Web Server issue):W733-7
- Toukach P, Joshi HJ, Ranzinger R, et al. Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de. Nucleic Acids Res 2007;35:D280-6
- Bacterial Carbohydrate Structure DataBase. Moscow, Russia. Available from: http://www.glyco.ac.ru/bcsdb/start.shtml [Last accessed 20 May 2008]
- GLYCO3D interface at the Cermav resource. Grenoble, France. Available from: http://www.cermav.cnrs.fr/glyco3d/index.php [Last accessed 20 May 2008]
- Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008;36:D480-4
- Glycan biosynthesis and metabolism pathways at KEGG. Kyoto, Japan. Available from: http://www.genome.jp/kegg/pathway.html#glycan [Last accessed 20 May 2008]
- Axelsson K, Bjorndal H. Polysaccharides elaborated by Polyporus ovinus (Schaeff). 1. Structure of a fucogalactan from the water extracts of the fruit bodies. Acta Chem Scand 1969;23(5):1815-7
- Glycan structure pathways provided by the CFG. Boston, MA. Available from: http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/geMolecule.jsp [Last accessed: 20 May 2008]
- Barthelmes J, Ebeling C, Chang A, et al. BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res 2007;35:D511-4
- Main page for the BRENDA database of enzymes. Braunschweig, Germany. Available from: http://www.brenda-enzymes.info/ [Last accessed 20 May 2008]
- Merril AH. SphinGOMAP – a web-based biosynthetic pathway map of sphingolipids and glycosphingolipids. Glycobiology 2005;15(6):G15-6
- SphinGOMAP© resource web site. Atlanta, GA. Available from: http://www.sphingomap.org/ [Last access 20 May 2008]
- GBP database provided by the CFG. Boston, MA. Available from: http://www.functionalglycomics.org/glycomics/molecule/jsp/gbpMolecule-home.jsp [Last accessed 20 May 2008]
- Wheeler DL, Barrett T, Benson DA, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008;36(Database issue):D13-21
- NCBI. Bethesda MD. Available from: http://ncbi.nlm.nih.gov/ [Last accessed 18 June 2008]
- The Gene Ontology Consortium: The Gene Ontology project in 2008. Nucleic Acids Res 2008;36(Database issue):D440-4
- The Gene Ontology (GO) database. Available from: http://www.geneontology.org/ [Last accessed 18 June 2008]
- Johnson M, Zaretskaya I, Raytselis Y, et al. NCBI BLAST: a better web interface. 2008; Web server issue
- CAZy database. Marseille, France. Available from: http://www.cazy.org/ [Last accessed 20 May 20, 2008]
- Coutinho PM, Henrissat B. Carbohydrate-active enzymes: an integrated database approach. In: Gilbert HJ, Davies G, Henrissat B, Svensson B, editors, Recent advances in carbohydrate bioengineering. The Royal Society of Chemistry: Cambridge; 1999. p. 3-12
- Hierarchy of orthologous groups of glycan binding proteins at KEGG. Kyoto, Japan. Available from: http://www.genome.jp/kegg-bin/get_htext?ko04091.keg [Last accessed 20 May 2008]
- Krengel U, Imberty A. Crystallography and Lectin Structure Database. In: Nillson CL, editor, Lectins: analytical technologies. Elsevier; 2007. p. 15-50
- Lectines database. Grenoble, France. Available from: http://www.cermav.cnrs.fr/lectines/ [Last accessed 20 May 2008]
- 3D-glycosyltransferase database of GLYCO3D. Grenoble, France. Available from: http://www.cermav.cnrs.fr/cgi-bin/rxgt/rxgt.cgi [Last accessed 20 May 2008]
- GAGPROT database. Grenoble, France. Available from: http://www.cermav.cnrs.fr/cgi-bin/gag/gag.cgi [Last accessed 20 May 2008]
- Chandra NR, Kumar N, Jeyakani J, et al. Lectindb: a plant lectin database. Glycobiology 2006;16(10):938-46
- LectinDB. Bangalore, India. Available from: http://nscdb.bic.physics.iisc.ernet.in [Last accessed 11 May 2008]
- Damodaran D, Jeyakani J, Chauhan A, et al. CancerLectinDB: a database of lectins relevant to cancer. Glycoconj J 2008;25(3):191-8
- CancerLectinDB. Bangalore, India. Available from: http://proline.physics.iisc.ernet.in/cancerdb [Last accessed 20 May 2008]
- Animal Lectin DB. London, UK. Available from: http://www.imperial.ac.uk/research/animallectins/ [Last accessed 20 May 2008]
- Lata S, Raghava GP. PRRDB: a comprehensive database of pattern-recognition receptors and their ligands. BMC Genomics 2008;9:180
- PRRDB. Chandigarh, India. Available from: http://www.imtech.res.in/raghava/prrdb/ [Last accessed 20 May 2008]
- ECODAB database. Stockholm, Sweden. Available from: http://www.casper.organ.su.se/ECODAB/ [Last accessed 20 May 2008]
- Kawasaki T, Nakao, H, Takahashi E, Tominaga T. GlycoEpitope: the Integrated Database of Carbohydrate Antigens and Antibodies. Trends Glycosci Glycotechnol 2006;18(102):267-72
- GlycoEpitope database. Kyoto, Japan. Available from: http://www.glyco. is.ritsumei.ac.jp/epitope/ [Last accessed 20 May 2008]
- Yang IS, Ryu C, Cho KJ, et al. IDBD: infectious disease biomarker database. Nucleic Acids Res 2008;36(Database issue):D455-60
- IDBD. Seoul, Korea. Available from: http://biomarker.cdc.go.kr [Last accessed 20 May 2008]
- Alternative site for IDBD. Seoul, Korea. Available from: http://biomarker.korea.ac.kr [Last accessed 20 May 2008]
- LÜtteke T, Frank M, Von Der Lieth CW. Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. Nucleic Acids Res 2005;33(Database issue):D242-246
- Umana P, Bailey JE. A mathematical model of N-linked glycoform biosynthesis. Biotechnol Bioeng 1997;55(6):890-908
- Krambeck FJ, Betenbaugh MJ. A mathematical model of N-linked glycosylation. Biotechnol Bioeng 2005;92(6):711-28
- Scholkopf B, Smola AJ. Learning with kernels: support vector machines, regularization, optimization and beyond. MIT Press: Cambridge, MA; 2002
- Hizukuri Y, Yamanishi Y, Nakamura O, et al. Extraction of leukemia specific glycan motifs in humans by computational glycomics. Carbohydr Res 2005;340(14):2270-8
- Kuboyama T, Hirata K, Aoki-Kinoshita KF, et al. A gram distribution kernel applied to glycan classification and motif extraction. Genome Inform 2006;17(2):25-34
- Yamanishi Y, Bach F, Vert JP. Glycan classification with tree kernels. Bioinformatics 2007;23(10):1211-6
- Aoki KF, Ueda N, Yamaguchi A, et al. Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics 2004;20:i6-14
- Ueda N, Aoki KF, Mamitsuka H. A general probabilistic framework for mining labeled ordered trees. Proceedings of the Fourth SIAM International Conference on Data Mining (SDM 2004). 2004:357-68
- Aoki-Kinoshita KF, Ueda N, Mamitsuka H, Kanehisa M. ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics 2006;22:e25-34
- BioMOBY Consortium; Wilkinson MD, Senger M, et al. Interoperability with Moby 1.0 – it's better than sharing your toothbrush! Brief Bioinform 2008;9(3):220-31
- Oinn T, Addis M, Ferris J, et al. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004;20(17):3045-54
- Kerhornou A, Guigo R. BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations. Bioinformatics 2007;23(14):1831-3
- Kappler MA. Software for rapid prototyping in the pharmaceutical and biotechnology industries. Curr Opin Drug Discov Devel 2008;11(3):389-92
- Shriver Z, Raguram S, Sasisekharan R. Glycomics: a pathway to a class of new and improved therapeutics. Nat Rev Drug Discov 2004;3(10):863-73
- Bertozzi CR, Kiessling LL. Chemical glycobiology. Science 2001;291(5512):2357
- Luallen RJ, Lin J, Fu H, et al. An engineered Saccharomyces cerevisiae strain binds the broadly neutralizing HIV-1 antibody 2G12 and elicits mannose-specific, gp120 binding antibodies. J Virol 2008;82(13):6447-57
- Wei CJ, Xu L, Kong WP, et al. Comparative efficacy of neutralizing antibodies elicited by recombinant hemagglutinin proteins from avian H5N1 influenza virus. J Virol 2008
- Von Der Lieth CW, LÜtteke T, Frank M. The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra. Biochim Biophys Acta 2006;1760(4):568-77
- Goldberg D, Bern MW, Parry S, et al. Automated N-Glycopeptide identification using a combination of single- and tandem-MS. J Proteome Res 2007;6(10):3995-4005
- Goldberg D, Sutton-Smith M, Paulson J, Dell A. Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra. Proteomics 2005;5(4):865-75
- Goldberg D, Bern MW, Li B, Lebrilla CB. Automatic determination of O-glycan structure from fragmentation spectra. J Proteome Res5:1429-34
- Werz DB, Ranzinger R, Herget S, et al. Exploring the structural diversity of mammalian carbohydrates (“glycospace”) by statistical databank analysis. ACS Chem Biol 2007;2(10):685-91
- Neerincx PB, Leunissen JA. Evolution of web services in bioinformatics. Brief Bioinform 2005;6(2):178-88
- Marenco L, Nadkarni P, Martone M, Gupta A. Interoperability across neuroscience databases. Methods Mol Biol 2007;401:23-36
- Curcin V, Ghanem M, Guo Y. Web services in the life sciences. Drug Discov Today 2005;10(12):865-71