Tuesday, December 29, 2009

More coverage of the GEBA "Phylogeny Driven Genomic Encyclopedia"

Just a quick note here to post some links to additional stories about my new paper on "A phylogeny driven genomic encyclopedia of bacteria and archaea" which was published last week in Nature (with a Creative Commons license - which is rare in Nature but is what they use for genome sequencing papers).

Carl Zimmer has an article today in the New York Times "Scientists Start a Genomic Catalog of Earth’s Abundant Microbes"  about the paper and the project.  In the article he interviews me and Hans-Peter Klenk, who was a co-author and led the culturing part of the project.  A few things to note about this:
  • It is rare to have archaea mentioned in the New York Times.
  • There is a tree that goes along with the article which is a modified version of the tree we had in our paper.  I think theirs is very nice. Kudos to their artist
  • There is a quote by Norm Pace generally supportive of the project 
  • The article mentions the JGI Adopt a Microbe program and even has a shout out to Malcolm Campbell at Davidson College and his recent PLoS One paper where they discuss results from a project where they took one of the genomes from our project and used it as part of a course on genome annotation/analysis. 
For some of the story behind the paper see my recent blog post "Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution"

Other discussions worth checking out
Also see


Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656

Bakke, P., Carney, N., DeLoache, W., Gearing, M., Ingvorsen, K., Lotz, M., McNair, J., Penumetcha, P., Simpson, S., Voss, L., Win, M., Heyer, L., & Campbell, A. (2009). Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis PLoS ONE, 4 (7) DOI: 10.1371/journal.pone.0006291


  1. There is also a nice post about it at the Brazilian scienceblogs. There is just a small mistake about the number of species/number of microbes.

    I didn't even know that the word "nonillion" existed...

  2. I had never heard of the word before either

  3. Is there any slightly higher res image available (with legible names), by any chance? Otherwise it's tortiously tantalising...

    [threat]Otherwise I'll just use Cavalier-Smith's bacterial taxonomy [/threat] =P

  4. PSI - You can get the Adobe Illustrator versions of the figures here: http://bobcat.genomecenter.ucdavis.edu/geba/GEBAAI.zip

  5. Thank you so much! I love this tree! =D

    (took my friend at Dal about a week to convert this thing to JPEG..)

    Ok, I'm now gonna spend -weeks- googling these organisms...

  6. Thanks for telling us about the science and history of this project Dr. E., it was a cool perspective that I didn't have before, congrats again to the whole team on this vital contribution to the field(s)


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