- Phylogenomics
Phylogenomics can be regarded as the intersection between the fields of evolution and genomics [ [http://www.biomedcentral.com/1471-2148/7/S1/S1 BioMed Central | Full text | Overview of the First Phylogenomics Conference ] ] . The term has been used in multiple ways to refer to some type of analysis involving
genome data and evolutionary reconstructions, especiallyphylogenetics . Examples of different flavors of phylogenomics include:* Prediction of the function of a gene based on its evolutionary history in a
phylogenetic tree . This was the original use of the term by Jonathan Eisen [Eisen JA, Kaiser D, Myers RL. 1997. Gastrogenomic delights: a movable feast. Nat Med. 3(10):1076-8. PMID 9334711] ] [Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8(3):163-7. PMID 9521918] ] . For reviews of this aspect of phylogenomics see [Brown D, Sjölander K. Functional classification using phylogenomic inference. PLoS Comput Biol. 2006 Jun 30;2(6):e77. PMID 16846248 ] [ Sjölander K. Bioinformatics. 2004 Jan 22;20(2):170-9. Phylogenomic inference of protein molecular function: advances and challenges. PMID 14734307 ]
* Reconstruction of aspecies tree by combining the information from many genes or entire genomes [ Delsuc F, Brinkmann H, Philippe H.Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005 6(5):361-75.] [ Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D. Mol Biol Evol. 2004 Sep;21(9):1740-52. Phylogenomics of eukaryotes: impact of missing data on large alignments. ] [Jeffroy O, Brinkmann H, Delsuc F, Philippe H.Phylogenomics: the beginning of incongruence? Trends Genet. 2006 Apr;22(4):225-31. PMID 16490279]
* The integration of genome analysis and evolutionary reconstruction [Eisen JA, Fraser CM. Phylogenomics: intersection of evolution and genomics. Science. 2003 Jun 13;300(5626):1706-7. PMID 12805538 ] [Eisen JA, Hanawalt PC. A phylogenomic study of DNA repair genes, proteins, and processes.Mutat Res. 1999 Dec 7;435(3):171-213. PMID 10606811]References
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