Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Oh, S June ^a   Joung, Je Gun ^b   Chang, Jeong Ho ^b   Zhang, Byoung Tak ^b  

^a Inje University   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONAL RELATIONSHIP; GENETIC RELATIONSHIPS; HIERARCHICAL CLUSTERING ALGORITHMS; KERNEL BASED APPROACH; METABOLIC INFORMATION; PHYLOGENETIC ANALYSIS; PHYSIOLOGICAL CONDITION; SEQUENCE INFORMATIONS;

BIOINFORMATICS; MICROORGANISMS; PHYSIOLOGY; POLYNOMIAL APPROXIMATION; TREES (MATHEMATICS);

METABOLISM;

BUTYRIC ACID; CITRIC ACID; DICARBOXYLIC ACID; FRUCTOSE; GALACTOSE; GLYOXYLIC ACID; MANNOSE; PENTOSE PHOSPHATE; PROPIONIC ACID; PYRUVIC ACID; RIBOSOME RNA; ARCHAEAL PROTEIN;

ALGORITHM; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CARBOHYDRATE METABOLISM; CLUSTER ANALYSIS; CONTROLLED STUDY; EUKARYOTE; FUNCTIONAL ASSESSMENT; GENE TRANSFER; GENETIC ANALYSIS; GENOMICS; GLUCONEOGENESIS; GLYCOLYSIS; INTERMETHOD COMPARISON; NONHUMAN; PHYLOGENY; PROKARYOTE; SEQUENCE ANALYSIS; STATISTICAL MODEL; TAXONOMY; ARCHAEAL GENE; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; METABOLISM; PROCEDURES; PROTEOMICS;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

ARCHAEAL PROTEINS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENES, ARCHAEAL; GLYCOLYSIS; METABOLISM; MODELS, BIOLOGICAL; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; PROTEOMICS;

EID: 33746956892     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-284     Document Type: Article

References (44)

1. Whiting MF, Carpenter JC, Wheeler QD, Wheeler WC: The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Syst Biol 1997, 46:1-68.
2. Delsuc F, Brinkmann H, Philippe H: Phylogenomics and the reconstruction of the tree of life. Nature Rev Genet 2005, 6:361-375.
3. Fitz-Gibbon ST, House CH: Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 1999, 27:4218-4222.
4. Lin J, Gerstein M: Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels. Genome Res 2000, 10:808-818.
5. Otu HH, Sayood K: A new sequence distance measure for phylogenetic tree construction. Bloinformatics 2003, 19:2122-2130.
6. Forst CV, Schulten K: Evolution of metabolisms: A new method for the comparison of metabolic pathways using genomics information. J Comp Biol 1999, 6:343-360.
7. Forst CV, Schulten K: Phylgenetic analysis of metabolic pathways. J Mol Evol 2001, 52:471-489.
8. Schuster Dandekar TT, Snel B, Huynen M, Bork P: Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J 1999, 343:115-124.
9. Moret BME, Wang LS, Warnow T, Wyman SK: New approaches for reconstructing phylogenies from gene order data. Bioinformatics 2001, 17:S165-S173.
10. Liao L, Kim S, Tomb JF: Genome comparisons based on profiles of metabolic pathways. Proceedings of the Sixth Intemational Conference on Knowledge-based Intelligent Information & Engineering Systems 2002:469-476.
11. Heymans M, Singh AK: Deriving phylogenetic trees from the similarity analysis of metabolic pathways. Bioinfonnatics 2003, 19:i138-i146.
12. Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV: Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 2001, 1:8.
13. Korbel JO, Snel B, Huynen MA, Bork P: SHOT: a web server for the construction of genome phylogenies. Trends Genet 2002, 18:158-162.
14. Tekaia F, Lazcano A, Dujon B: The genomic tree as revealed from whole proteome comparison. Genome Res 1999, 9:550-557.
15. Grishin NV, Wolf YI, Koonin EV: From complete genomes to measures of substitution rate variability within and between proteins. Genome Res 2000, 10:991-1000.
16. Henz SK, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC: Whole-genome prokaryotic phylogeny. Bioinformatics 2005, 21:2329-2335.
17. Qi J, Wang B, Hao BI: Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 2004, 58:1-11.
18. Daubin V, Gouy M, Perriere G: A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 2002, 12:1080-1090.
19. Rokas A, Williams BL, King L, Carroll SB: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
20. Woese CR, Kandler O, L WM: Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990, 87:4576-4579.
21. Doolittle WF: Phylogenetic classification and the universal tree. Science 1999, 284:2124-2128.
22. Lake JA, Moore JE: Phylogenetic analysis and comparative genomics. Trends Guide to Bioinformatics 1998.
23. Podani J, Oltvai ZN, Jeong H, Tombor B, Barabasi AL: Comparable system-level organization of Archaea and Eukaryotes. Nat Genet 2001, 29:54-56.
24. Rivera MC, Jain R, Moore JE, Lake JA: Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA 1998, 95:6239-6244.
25. Canback B, Andersson SGE, Kurland CG: The global phylogeny of glycolytic enzymes. Proc Natl Acad Sci USA 2002, 99:6097-6102.
26. Jain R, Rivera MC, Lake JA: Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 1999, 96:3801-3806.
27. Doolittle WF Lateral genomics. Trends Cell Biol 1999,9:M5-M8.
28. Li M, Badger JH, Chen X, Kwong S, Kearney P. Zhang H: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001, 17:149-154.
29. Keeling PJ, Palmer JD: Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc Natl Acad Sci USA 2001, 98:10745-10750.
30. Nye TMW, Lio P, Gilks WR: A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 2006, 22:117-119.
31. Zhang K, Wang JTL, Shasha D: On the editing distance between undirected acyclic graphs. Int J Foundations Comput Sci 1996, 7:43-57.
32. Fritz B, Raczniak GA: Bacterial genomics: potential for antimicrobial drug discovery. Biodrugs 2002, 16:331-337.
33. Doolittle WF, Brown JR: Tempo, mode, the progenote, and the universal root. Proc Natl Acad Sci USA 1994, 91:6721-6728.
34. Doolittle WF, Logsdon JM Jr: Archaeal genomics: Do archaea have a mixed heritage? Curr Biol 1998, 8:R209-R211.
35. Wolf YI, Rogozin IB, Grishin NV, Koonin EV: Genome trees and the tree of life. Trends Genet 2002, 18:472-479.
36. Tree of Life [http://tolweb.org]
37. Ogata H, Goto SK, Fujibuchi H, Bono H, Kanehisa M: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999, 27:29-34.
38. Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M: LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res 2002, 30:402-404.
39. Gärtner T: Exponential and Geometric Kernels for Graphs. NIPS 2002 Workshop on Unreal Data: Principles of Modeling Nonvectorial Data 2002.
40. Kondor RI, Lafferty J: Diffusion kernels on graphs and other discrete input spaces. Proceedings of 19th International Conference on Machine Learning 2002:315-322.
41. Jain AK, Dubes RC: Algorithms for Clustering Data 2nd edition. address in USA: Prentice Hall; 1988.
42. Durbin R, Eddy SR, Krogh A, Mitchison G: Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids Cambridge University Press; 1998.
43. Page RDM: TREEVIEW: An application to display phylogenetic trees on personal computers. CABIOS 1996, 12:357-358.
44. NCBI taxonomy [http://www.ncbi.nlm.nih.gov/Taxonomy/]