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

• John Timmer’s article for Ars Technica on “Presenting a genomic encyclopedia of bacteria (and archaea)” 
• The Department of Energy is featuring the project as part of their “National Impact” Series” Scientists Launch the Genomic Encyclopedia of Bacteria and Archaea
• NYTimes Science Times discussion from Charlie Petit at the Knight Science Journalism tracker

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

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis View all posts by Jonathan Eisen