ISEEM:Publications, Talks & Media
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Recent news
- "Genomic Encyclopedia of Bacteria and Archaea (GEBA)" publication. The GEBA project, coordinated by Jonathan Eisen and carried out at the Joint Genome Institute, strives to improve the phylogenetic sampling of bacterial and archaeal genomes. A paper describing this effort was published in Nature recently. Some of the analysis reported in the paper was done as part of the iSEEM project. More information can be found in the New York Times article that discussed the study and in Jonathan Eisen's blog posts here and here.
Products from this project
Software
- AMPHORA
- Download here http://bobcat.genomecenter.ucdavis.edu/AMPHORA
- Described in "Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008 Oct 13; 9(10) R151. doi:10.1186/gb-2008-9-10-r151 " and available here http://genomebiology.com/2008/9/10/R151#B41
- STAP
- Download here http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/STAP_download
- Described in Wu D, Hartman A, Ward N, and Eisen JA. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 2008 Jul 2; 3(7) e2566. doi:10.1371/journal.pone.0002566 and available here http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002566
Publications
- Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, and Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24;462(7276):1056-60. DOI:10.1038/nature08656 |
- O'Dwyer JP, Lake JK, Ostling A, Savage VM, and Green JL. An integrative framework for stochastic, size-structured community assembly. Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6170-5. DOI:10.1073/pnas.0813041106 |
- O'Dwyer JP and Green JL. Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity. Ecol Lett. 2010 Jan;13(1):87-95. DOI:10.1111/j.1461-0248.2009.01404.x |
- Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008 Oct 13;9(10):R151. DOI:10.1186/gb-2008-9-10-r151 |
- Wu D, Hartman A, Ward N, and Eisen JA. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One. 2008 Jul 2;3(7):e2566. DOI:10.1371/journal.pone.0002566 |
News
Check out the blog of Jonathan Eisen