ISEEM:Publications, Talks & Media

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The iSEEM Project
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[[iSEEM | <font face="trebuchet ms" style="color:#55778D"> '''Home''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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= Recent news =
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[[iSEEM:Who We Are | <font face="trebuchet ms" style="color:#55778D"> '''Who We Are''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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* "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 [http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html 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 [http://www.nytimes.com/2009/12/29/science/29microbes.html New York Times article that discussed the study] and in Jonathan Eisen's blog posts [http://phylogenomics.blogspot.com/2009/12/more-coverage-of-geba-phylogeny-driven.html here] and [http://phylogenomics.blogspot.com/2009/12/story-behind-nature-paper-on-phylogeny.html here].
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[[iSEEM:What We Do | <font face="trebuchet ms" style="color:#55778D"> '''What We Do''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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[[iSEEM:Lab Members | <font face="trebuchet ms" style="color:#55778D"> '''Lab Members''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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= Products from this project  =
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[[iSEEM:Publications, Talks & Media | <font face="trebuchet ms" style="color:#55778D"> '''Publications, Talks & Media''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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== Software ==
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[[iSEEM:Lab Members Only | <font face="trebuchet ms" style="color:#55778D"> '''Lab Members Only''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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#[[AMPHORA]]
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#* Download here http://bobcat.genomecenter.ucdavis.edu/AMPHORA
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#* 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
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#[[STAP]]
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#* Download here http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/STAP_download
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#* 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
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== Publications ==
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<biblio>
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#Wu-2009 pmid=20033048
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#ODwyer-2009 pmid=19336583
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#ODwyer-2009 pmid=19909313
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#Wu-2008b pmid=18851752
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#Wu-2008 pmid=18596968
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</biblio>
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==News==
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Check out the blog of [http://phylogenomics.blogspot.com Jonathan Eisen]

Current revision

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Contents

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

  1. AMPHORA
  2. STAP

Publications

  1. 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. . pmid:20033048. PubMed HubMed [Wu-2009]
  2. O'Dwyer JP, Lake JK, Ostling A, Savage VM, and Green JL. . pmid:19336583. PubMed HubMed [ODwyer-2009]
  3. O'Dwyer JP and Green JL. . pmid:19909313. PubMed HubMed [ODwyer-2009]
  4. Wu M and Eisen JA. . pmid:18851752. PubMed HubMed [Wu-2008b]
  5. Wu D, Hartman A, Ward N, and Eisen JA. . pmid:18596968. PubMed HubMed [Wu-2008]
All Medline abstracts: PubMed HubMed

News

Check out the blog of Jonathan Eisen
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