Phylogenomics.html
 
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Phylogenomics can be regarded as the intersection between the fields of evolution and genomics 1. The term has been used in multiple ways to refer to some type of analysis involving genome data and evolutionary reconstructions, especially phylogenetics. 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 23. For reviews of this aspect of phylogenomics see 45
  • Reconstruction of a species tree by combining the information from many genes or entire genomes 678
  • The integration of genome analysis and evolutionary reconstruction 9 10


References

  1. ^ BioMed Central | Full text | Overview of the First Phylogenomics Conference
  2. ^ Eisen JA, Kaiser D, Myers RL. 1997. Gastrogenomic delights: a movable feast. Nat Med. 3(10):1076-8. PMID 9334711
  3. ^ Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8(3):163-7. PMID 9521918
  4. ^ Brown D, Sjölander K. Functional classification using phylogenomic inference. PLoS Comput Biol. 2006 Jun 30;2(6):e77. PMID 16846248
  5. ^ Sjölander K. Bioinformatics. 2004 Jan 22;20(2):170-9. Phylogenomic inference of protein molecular function: advances and challenges. PMID 14734307
  6. ^ Delsuc F, Brinkmann H, Philippe H.Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005 6(5):361-75.
  7. ^ 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.
  8. ^ Jeffroy O, Brinkmann H, Delsuc F, Philippe H. Phylogenomics: the beginning of incongruence? Trends Genet. 2006 Apr;22(4):225-31. PMID 16490279
  9. ^ Eisen JA, Fraser CM. Phylogenomics: intersection of evolution and genomics. Science. 2003 Jun 13;300(5626):1706-7. PMID 12805538
  10. ^ 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


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