Phylogenomics (Eisen) 2009

• Eisen.Bodega.2009.part1.pdf
  

• Eisen.Bodega.2009.part2.pdf

• Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. PMID: 12805538. Eisen.Fraser.2003.Phylogenomics.pdf

• Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucl Acids Res 23: 2715-2723. PMID: 7651832. This is the first paper where I showed that phylogenetics is an important tool in protein functional prediction. PDF
  

• Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nature Medicine 3: 1076-1078. PMID: 9334711. This is the first paper where I defined "phylogenomics" in terms of integrating genome and evolutionary analyses. PDF
  

• Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8: 163-167. PMID: 9521918. This paper outlines the use of character state reconstruction methods to predict protein function. http://genome.cshlp.org/content/8/3/163
  

• Eisen JA. 1998. A phylogenomic study of the MutS family of proteins. Nucl Acids Res 26: 4291-4300. PMID: 9722651. An example of phylogenetic prediction of protein function. PDF
  

• Eisen JA, Wu M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Pop Biol 61: 481-487. PMID: 12167367. A review on phylogenetics and functional prediction. PDF
  

• Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA. 2005. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genetics 1: e65. PMID: 16729848. The genome paper I discussed in class where we used phylogenetic profiling. Free online

• Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3): e82. PMID: 17355177. PDF
  

• Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson JD, Hoffman J, Parsons R, Baden-Tillson H, Pfannkock C, Rogers Y-H, and Smith HO. 2004. Environmental whole genome shotgun sequencing: the Sargasso Sea. Science 304: 66-74. PMID: 15001713. PDF
  

• Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 2008, 9:R151. PMID: 18851752 Free online

• Wu D, Hartman A, Ward N, Eisen JA. 2008. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 3(7): e2566. PMID: 18596968 Free online

• Eisen JA. 2001. Gastrogenomics. Nature 409: 463-465. PMID: 11206526. PDF
  

• Eisen JA. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genetics Dev 10: 606-611. PMID: 11088009. PDF
  

• Eisen JA. 2000. Assessing evolutionary relationships among microbes from whole genome analysis. Curr Opin Microbiol 3: 475-480. PMID: 11050445. PDF

* My blog: http://phylogenomics.blogspot.com
* My evolution textbook: http://evolution-textbook.org
* My lab page: http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page