Tag: Misc.

The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb

Well, here goes.

This is a post about a paper that has been a long long time coming. Today, a paper of mine is being published in PLoS One. The paper is titled “Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees” and is available at http://dx.plos.org/10.1371/journal.pone.0018011. (or if that link does not work you can get a copy here). This paper represents something I started a long time ago and I am going to try to describe the story behind the paper here.

I note – we are not doing a press release for the paper, for a few reasons. But one of them is that, well, I am starting to hate press releases. So I guess this is kind of my press release. But this will be a bit longer than most press releases. I note – my key fear here is that somehow in my communications with the press or in our text in the paper or in this post I will overstate our findings. Here is the punchline – we found some very phylogenetically novel forms of phylogenetic marker genes in metagenomic data. We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. The They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don’t know.

UPDATE: Am posting some links here to news stories/blogs about our paper





    First – a summary of what we did.

    In the paper, we searched through metagenomic data (sequences from environmental samples) for phylogenetically novel sequences for three standard phylogenetic marker genes (ss-rRNA, recA, rpoB). We focused on sequences from the Venter Global Ocean Sampling data set because, well, we started this analysis many years ago when that was the best data set available (more on this below). What we were looking for were evolutionary lineages of these genes that were separate from the branches that corresponded to the three known “Domains” of life (bacteria, archaea and eukaryotes).

    To search for such novel lineages in the metagenomic data, we built evolutionary trees using these genes where we included sequences from known organisms (and viruses) as well as sequences from metagenomic data. We then looked through the trees for groups that were both phylogenetically novel and included only environmental data (i.e., they were new compared to known organisms or viruses). This method did not work very well for rRNA sequences (largely because making high quality alignments of short phylogenetically novel rRNA sequences was difficult – more on this below). But with RecA and RpoB homologs we were able to generate what we believe to be robust phylogenetic trees. And in these trees we found evidence for phylogenetically very novel sequences in environmental data.

    Figure 1. Phylogenetic tree of the RecA superfamily. 

    Figure 3. Phylogenetic tree of the RpoB superfamily

    We then propose and discuss four potential mechanisms that could lead to the existence of such evolutionarily novel sequences. The two we consider most likely are the following

    1. The sequences could be from novel viruses
    2. The sequences could be from a fourth major branch on the tree of life

    Unfortunately, we do not actually know what is the source of these sequences. So we cannot determine which of the theories is correct. Obviously if there is a novel lineages of cellular organisms out there, well, that would be cool. But we have no evidence right now if that is what is going on. Personally, I think it is most likely that these novel sequences are from weird viruses. But as far as we can tell, they truly could be from a fourth major branch of cellular organisms and thus even though we did not have the story completely pinned down, we decided to finally write up the paper to get other people to think about this issue.

    Below I give all sorts of other details about the project in the following areas

    • The history of the project 
    • More detail on what is in the paper 
    • Follow up analysis and rapid posting with google Know 
    • Data deposition in Dryad 
    • Who was involved 
    • UPDATE: Funding for this work



    The history of the project

    Well, this is one of those projects for which the history is hard to explain. We started this work in 2004 when I was helping Venter and colleagues analyze the Sargasso Sea metagenome data. I was working at TIGR in 2003, which are the time was a sister institute to some of the institutes affiliated with the J. Craig Venter Institute (JCVI) (it was a complicated time). Craig had led a project to do a massive amount of shotgun sequencing of DNA isolated from the Sargasso Sea, which had been the site of many previous studies of uncultured microbes. And Craig, as well as some of the people working with him including John Heidelberg who was at TIGR, had asked me to help in analysis of the data. So I eventually went to a meeting about the project and got involved. It was quite exciting and I put a lot of effort into helping analyze the data.

    As part of my work on the project, I and Martin Wu and Dongying Wu did a variety of phylogenetic studies of genes and gene families. One of these, was a phylogenetic analysis of proteorhodopsin homologs showing massively more diversity in the Sargasso data than in the PCR experiments done by Delong and Beja and others.

    Figure 7 from Venter et al. 2004. 

    We also did the first “phylotyping” in metagenomic data using genes other than rRNA. We built trees of bacterial ss-rRNAs, RecAs, RpoBs, HSP70s, EF-Tus and EF-Gs and then assigned each sequence to a phylum from the trees. In this analysis we found a variety of interesting things. 

    Figure 6 from Venter et al. 2004. 
    One thing I did not include in the Sargasso paper was an analysis I did of RecA homologs where I tried to include ALL RecA-like genes from bacteria, archaea, eukaryotes and viruses. The trees I made were a bit unusual but I was not sure that the alignments I had made were robust or that I had found all the RecA-like genes of interest so I did not even show this to Craig et al. at the time.
    UPDATE: I note – our work on this project was supported by a grant from the NSF Assembling the Tree of Life program that was awarded to me and Naomi Ward and Karen Nelson. Those funds supported the development of many of the informatics tools we used in this analysis and Martin and Dongying were both working on that project.

    After the Sargasso paper was published in 2004 though, I continued to fester about the RecA trees. And I wondered – if instead of trying to classify bacterial sequences into phyla, what if I tried to look for RecAs, rRNAs and other genes that were completely new branches in the tree of life? I got the chance to start to play with this concept again when Venter and crew asked me to help analyze the data coming out of the Global Ocean Sampling project. Again, this project was very exciting and interesting.


    As part of the project, I helped Shibu Yooseph and others look into whether the GOS data revealed any completely new types of functionally interesting genes, much like I had shown for proteorhodopsin in the Sargasso data.  
    Figure 7 from Yooseph et al. 2007 . Phylogenies Illustrating the Diversity Added by GOS Data to Known Families That We Examined 






    And again my mind started wandering towards the question of “OK – so – if there are all these very unusual and novel functionally interesting genes, what about looking for unusual and very novel phylogenetic marker genes”? So finally, I got back to work on the issue.

    And so I built a better RecA tree by first pulling out all possible homologs of RecA and RecA like proteins from the GOS data and then building an alignment and a tree. And there they were. Some very f*%&$ novel RecAs – distinct from any previously known RecA like proteins as far as I could tell. And so with help from Dongying and the JCVI crew, we started building a story about novel RecAs. And then we looked at RpoBs. And found novel ones too. And in mid 2006 while Shibu and Doug worked on their papers that were to be submitted to PLoS Biology and I worked on a review paper too, I told Emma Hill (who has since changed her name to Emma Ganley due to some sort of wedding thing) at PLoS Biology about the an analysis that was consistent with the existence of a fourth domain of life. No overstating our findings really – just that we found very novel phylogenetic marker genes. And that I was working on a paper on it. But alas I never got it done, though I was happy to have convinced Venter to send the GOS papers to PLoS Biology and I think the papers that came out were good. Among the papers were my review (Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes, Doug Rusch’s diversity paper The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific and Shibu’s protein family paper The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families as well as many others as part of the Ocean Metagenomics Collection at PLoS.

    And in the midst of all of this, we had our first child and we wanted to move back to Northern California to be closer to family (my wife’s family is all in the Bay Area and my sister and brother Michael were in N. Cal too). So I applied for jobs and eventually took at job at UC Davis and we moved to Davis. Needless to say, all of that put a bit of a crimp in my work productivity. And once I was up and running at Davis, it just took a long time to get back to the searching for novel deep branches in the tree of life. But finally, we did it (with periodic prodding from Craig Venter). And we put together a paper and got it submitted to PLoS One in October. The reviews were very positive and enormously helpful. And we finally got a revision in January and it was officially accepted in February 2011. Only some seven years after my first work on the project. Whew.

    More detail of what is in the paper
    Well, I am going to be posting here some additional detail on what is in the paper.



    Why we punted on analysis of very novel rRNAs.

    The problem with rRNA is that the sequences that come from environmental samples are not complete (i.e. they only correspond to portions of the rRNA genes). Unfortunately, this makes a key step in phylogenetic analysis difficult – the alignment of sequences. We actually found about 200 rRNA sequences that seemed unusual in a phylogenetic sense. However, we were not convinced that the alignments of these fragments to other rRNAs was robust. This is because the alignment of rRNAs is best done making use of the base pairing secondary structure of the molecule and not the base sequence (i.e., primary structure).

    With only rRNA fragments, we could not use the secondary structure to do the alignments because you need to whole molecule to determine the best folding. Combined with the fact that we were searching for very distantly related ribosomal RNAs which would be hard to align even if we had the whole molecule, we were stuck for a bit. It seemed impossible to look for really novel organisms.
    So that is when we turned to other genes. The key for this is that there are protein coding genes that are universal and that for known organisms show similar patterns to rRNA in trees. In fact, in 1995 I wrote a paper showing that trees of RecA were very similar to trees of rRNA. RpoB is also considered a very robust phylogenetic marker. For organisms that we have in the lab (i.e., cultured) – many people use these other genes for phylogenetic analysis. rRNA has been very important in part because of the ease with which one can PCR amplify it from environmental samples and the fact that it is very hard to PCR amplify protein coding genes from the environment. Metagenomics changes this. With random sequencing, you get data from all genes. This means we can pick and choose genes to analyze for phylogenetic analysis and do not have to rely on rRNA.

    So we went after RecA first, because it has been shown to be a good phylogenetic marker for studies of the tree of life. And we found some very novel branches in the RecA tree. And after analyzing these and convincing ourselves that they were indeed phylogenetically very novel we went after RpoB. And also found very novel branches.

    So the phylogenetic analysis I think is very robust.

    RecA and RpoB as phylogenetic markers

    Many genes have been used as alternatives to rRNA genes to build “Trees of Life” including all organisms. Each has their own flavors of advantages and drawbacks. Two commonly used ones are the RecA and RpoB superfamilies.

    The many possible explanations for finding novel forms of phylogenetic marker genes

    The phylogenetically novel phylogenetic marker genes we found could have many explanations including that they could be ancient paralogs of these genes (but not found in any genomes we have available), they could be from viruses, or they could be from a novel branch on the tree of life. Or our trees could be bad. We think the latter is somewhat unlikely as our analysis has many lines of support. For example our RecA trees are very similar to those from a comprehensive study from M. Nei’s lab except they did not include the metagenomic data. But I guess it is still a possibility that our trees are biased in some way (e.g., by long branch attraction or bad alignments)

    Follow up analysis and rapid posting via Google Knol

    Amazingly and a bit sadly, I think we rushed the paper out. We left out one thing partly by accident – we had done an analysis of the locations from which these novel RecA and RpoB sequences had come. And somehow, in our final push to get the paper out, we left this out. I will be posting this information as soon as possible here and on the PLoS One site.

    In addition, after submitting the revision of our paper, we realized that we might be able to do a deeper analysis on one aspect of the work – how RpoB homologs from unusual DNA viruses compared to our novel sequences. We had included some RpoBs from DNA viruses in our analyses but not all that were available. So Dongying Wu did a very rapid additional analysis, adding some additional RpoB homologs to our alignment and making a tree of them. We then wrote a Google Knol about this new tree and submitted the Knol to PLoS Currents “Tree of Life” where it is currently in review. We are publishing the preprint of this Knol to make it available to all even while it is in review.


    Figure 2 from Wu and Eisen submitted. 

    Data availability

    There is a move afoot to make sure all data/tools associated with publications are readily available. We used publicly available sequence data and as much as possible publicly available tools for our work . We are trying to release as much as possible to allow people to re-analyze our work and to do any of the work themselves. We have therefore made use of the Dryad Data deposition service to post some of this material (see http://datadryad.org/handle/10255/dryad.8385).

    Who was involved

    • Dongying Wu a brilliant “Project Scientist” in my lab led the project (Project Scientist is one of the UC positions that is like what others call “Senior Scientist”). Dongying is simply one of the best bioinformaticians/computational biologists I have ever met. He was first author on many key papers from my lab including the Genomic Encyclopedia paper that came out last year and the glassy winged sharpshooter symbionts paper that came out a few years ago. Dongying worked in my group at TIGR and moved with me to UC Davis and currently splits his time between UC Davis and the DOE Joint Genome Institute. 
    • Martin Wu. Martin is an Assistant Professor at the University of Virginia. Prior to that he was a Project Scientist in my lab at Davis and a post-doc in my lab at TIGR. He is also a phenomenal bioinformatician / computational biologist. He developed the AMPHORA software in my lab and also led many genome projects (back when sequencing a genome was hard …) including that of the first Wolbachia genome and that of a very unusual bug Carboxydothermus hydrogenoformans. Martin helped with some of the genome analyses as part of this work. 
    • Aaron Halpern, Doug Rusch and Shibu Yooseph are all bioinformaticians from the J. Craig Venter Institute (Aaron is no longer there). All three helped with different aspects of dealing with and analyzing the GOS data and all three have been remarkably patient as this work dragged on and on. 
    • Marv Frazier from the JCVI was helpful in the initial set up and conceptualization of the project. 
    • J. Craig Venter is, well, Craig Venter, and he was involved in multiple aspects of the project including thinking about how and where to look for unusual sequences and interpreting some of the results.

    UPDATE: Funding for this work

    Most of my labs early work on this project was supported by a grant we had from the Assembling the Tree of Life program at the National Science Foundation (grant 0228651 to me and Naomi Ward). In that project we were working on sequencing and analyzing genomes from phyla of bacteria for which genomes were not available at the time. As part of this work we were designing methods to build phylogenetic trees from metagenomic data because we thought that our new genomes would be very useful in helping analyze metagenomic reads and figure out from which phyla they came. Later work on the project was supported by a grant to me, Jessica Green and Katie Pollard from the Gordon and Betty Moore Foundation (grant 1660).

    Some questions that might be asked and some answers (based in part on questions I have gotten from reporters). Note if you have other questions please post them here or on the PLOS One site for the paper.

    • Why no press release? Well, in part, because I sent information too late (shocking I know) to the Davis Press Office. But also because they have gotten suddenly busy with some Japan earthquake related actions. But also because, well, I really hate a lot of press releases. And finally, my brother had dinner with Carl Zimmer recently and apparently they discussed the possibility of having no press releases associated with papers. So here goes …. 
    • Really – what took so long? I would like to say the US Government made us hold back on publishing this until they could look into whether Venter collected ocean data from Roswell, NM or not. But really, the story above is true. We just did not get it done earlier. 
    • Why do you not know the source of the DNA (i.e., cells, viruses, etc)? This is why there was a six year wait between discovery and writing this up. We kept thinking we would be able to find the organisms but since I moved from TIGR and started a new job, we just never got around to getting to the source. We therefore decided to open this up to others who will hunt for the source by writing up the paper. 
    • Why did you not rename the Unknown 2 group in the RecA tree? We should have renamed our group “Thaumarchaeota” or something like that. When we did the initial analysis our group was novel. And then a few years ago a few groups obtained data from what is thought to be the third major lineage of Archaea – referred to by some as Thaumarchaeota. This is to go with the Euryarchaeota and Crenarchaeota. See http://www.ncbi.nlm.nih.gov/pubmed/20598889 for example. 
    • One of the clades in the RecA tree (XRCC2) seems out of place phylogenetically. I can see how that is confusing. The XRCC2 clade is very weird and hard to figure out. It is not the “normal” eukaryotic genes – those are the Rad51/DMC1 genes. One complication with the RecA family is that there have been duplication events to go with the species evolution. And thus eukaryotes have Rad51, DMC1, Rad51B, Rad51C, Rad57, XRCC3 and XRCC2. We tried to figure out where the XRCC2 group should go but it just was hard to place. The statistical support for its position (we used a method called bootstrapping) is low (note the lack of a number on the node where the branch leading to XRCC2 connects to the base of the tree). Most likely that group should be placed with some of the other eukaryotic groups. However, it seems likely that there was a duplication in the lineage leading up to the ancestor of eukaryotes and archaea (some studies have indicated they share a common ancestor to the exclusion of bacteria). Such a duplication would explain why basically all archaea have a RadA and and RadB and all / most eukaryotes have multiple paralogs as well. 
    • The Unknown 1 group in the RpoB RecA tree seems to group with phage. What can you say about that? We think unknown 1 is potentially of viral origin but still cannot tell. The fact that is clusters with RecA superfamily members from phage suggests this but it is distant enough from known phage for us to not be confident in any predicted origin. As for derivative forms vs. independent branch – this is one of the big questions about viruses these days. Many viruses encode homologs of “housekeeping” genes found across bacteria, archaea and eukaryotes. And in many cases the viral versions of these genes appear to phylogenetically very novel. This is why the people studying mimivirus (which we refer to) suggest some viruses may in fact represent a fourth branch on the tree of life. It is possible that some viruses are in fact reduced forms of what were once cellular organisms – akin to parasitic intracellular species of bacteria possibly. 
    • Why are these phylogenetically novel sequences so low in abundance? This is a key question. I think it would be easy to come up with a theory for these being rare or these being common. They might be rare if their niche is very limited today. Or they might be rare because they could not be very competitive with other organisms. Or they could be rare because they require some unusual interactions with other taxa. In addition, we have only looked carefully at ocean water samples. If these are common somewhere else (e.g., hotsprings, deep subsurface, etc) we would not yet have figured that out. We are looking at additional metagenomic data right now to see fi we can find any locations where relatives of these genes are more common

    Some related papers by others worth looking at

    Some related papers by me possibly worth looking at

    Some related blog posts I have written over the years

      http://friendfeed.com/treeoflife/5535e8ed/story-behind-of-my-new-plosone-paper-on-stalking?embed=1

      Dongying Wu, Martin Wu, Aaron Halpern, Douglas B. Rusch, Shibu Yooseph, Marvin Frazier,, & J. Craig Venter, Jonathan A. Eisen (2011). Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees PLoS One, 6 (3) : 10.1371/journal.pone.0018011

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      I know – Ego Blogging is so 2010 – But I won. I won. I won. (The Ben Franklin Award …)

      OK so the title is a bit much. But I am really happy that I won this years Benjamin Franklin Award, given out by the Bioinformatics Organization. For more on this see …
      I found out a few days ago and am rearranging some things to go to Boston April 13 for the award ceremony at the Bio-IT World Conference and Expo.  
      From the Bioinformatics Organization web site:

      Benjamin Franklin (1706-1790) was one of the most remarkable men of his time. Scientist, inventor, statesman, he freely and openly shared his ideas and refused to patent his inventions. It is the opinion of the founders of the Bioinformatics Organization, Inc. that he embodied the best traits of a scientist, and we seek to honor those who share these virtues

      The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.

      I like the general sentiment very much.  And perhaps more important – the list of prior winners is an impressive crew.  Again, from the Bioinformatics Organization web site:

      Note – my brother won the first one.

      Anyway – am thinking about what to say in the awards ceremony.  Probably going to say something about how openness is more than about being at no charge.  Also I might discuss how it would be good to have a female winner one of these days.  Speaking of which – maybe people can give suggestions for women to nominate for next year …

      UPDATE 9/25/12: See this Friendfeed discussion for some more comments about possible female candidates. I have copied the text below in case Friendfeed disappears: “maybe people can give suggestions for women to nominate for next year …”. OK, I’ll start: how about Rosie Redfield? If it weren’t for the Life Sciences focus I’d also suggest Heather Joseph. Speaking of Heathers, one H. Piwowar springs to mind whenever Open Foo is mentioned. – Bill Hooker heh, that would be cool someday 🙂 For now, how about Helen M. Berman, Judith A. Blake, Maryann E. Martone, Catherine Ball, or other pioneers in open databases? – Heather Piwowar Janet Thornton. – Heather Piwowar Agreed! – Egon Willighagen In an award speech at ISMB 2005, Janet Thornton expressed gratitude she was able to take years out-with-family and then pick up again. Inspirational. Not relevant for the Ben Franklin award, but wanted to mention it because it made such an impact. – Heather Piwowar

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      Interesting take (though not completely convincing) take on NEJM farm microbe story

      There is an interesting take in Forbes on a recent study NEJM on microbes and people growing up on farms.

      Not totally convinced of the opinion of the writer, but with a look.

      – Posted using BlogPress from my iPhone

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess

      Well, in case you did not see, yesterday I got really pissed off at Nature Publishing Group.  Short summary – many articles of mine that were supposed to be freely available on their journal sites were not.  For more information see

      People from Nature Publishing Group have responded quite quickly saying they will look into this and try to fix it and indeed they have fixed many if not all of the mistakes in accessibility I found yesterday.  Glad they responded so quickly.  However, their response raises quite a few questions.  Like “what happened?” – as in – why did access get closed off?  And why were they charging to for article use when they should not have been?
      It would be good for Nature to publish / post a full description of what went wrong.  And perhaps they will.  Apparently, it was just a glitch in the system.  Whatever the cause however, almost certainly some people paid for access for articles that were supposed to be freely available.  I am calling on Nature here to audit their systems and return all money that was paid for such access.
      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail

      Yuck.  Am getting really pissed off right now.  It is 1:30 AM.  I am tired.  And I am now angry.  I was writing a post about a recent trip, and wanted to link to an article I was a coauthor on.  The article was the paper on sequencing and analysis of the genome of Arabidopsis thaliana.  So I googled “Arabidopsis Genome Initiative” and found the link to the paper at Nature.  And much to my surprise I found this waiting for me:

      Why is that a surprise?  Because the genome paper is supposed to be freely available to all forever, under a policy Nature developed for papers reporting new genome sequence data.  I am tired or I would write more about the history of this.  But another time.

      So then I looked for other genome papers I have published in Nature.  And so I looked for the Plasmodium genome paper.  And I got this:

      Grand.  That one was supposed to be free forever too.

      And so I looked at many others.  And for most, I got the same thing.  Not freely available.  If I were not at home, I would not have noticed this because I have access at work.  And I could get access at home by setting up the UC Davis library VPN system.  But fortunately I do not do that or I would not have discovered that Nature, not for the first time mind you, has turned articles that were supposed to be freely available forever into charge for access articles.  I know.  I know.  This is probably just some glitch in their system.  They really do seem committed to trying to make these available.  But clearly, the system either does not work well.  Or they are not committed to it.  Either way this is really annoying.  In some cases, the papers were sold to communities of scientists in part with the “These will be freely available to all forever” line as part of the sell.  I am deeply worried about my recent Genomic Encyclopedia paper which is also supposed to be freely available forever.  Right now it still is, which is good.  But how long will that last?  And I note, though Nature people have said they would try and fix it, Nature still incorrectly claims Copyright to that article on the PDF.  Personally, I like most of the people I know at Nature Publishing Group and like many of the things NPG does.  But this is getting really annoying.  And it just goes to show – the ONLY way to go it seems is full, complete Open Access which the journals cannot magically then take away.

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      Norman R. Pace visit to #UCDavis; discussing microbiology of the built environment #microBEnet

      Norman R. Pace, from UC Boulder, gave a talk at UC Davis last week about microbial diversity.  In his talk he discussed some of his recent Sloan Foundation funded work on “microbiology of the built environment” including studies of shower heads, indoor swimming pools, water supplies, and hospitals.

      Pace is one of the pioneers of DNA based studies of microbes in the environment.  His initial work on studies of ribosomal RNA from uncultured organisms (started more than 20 years ago) helped launch the field.  For more information on his work see his lab page here

      If you are interested in the microbes that are found in showerheads, his PNAS paper on this (which can be found here) on this from 2 years ago got a lot of press.  See for example this Science Friday
      and this New York Times article by Nicholas Wade.

      Pace was at UC Davis as part of the Storer Major Issues in Modern Biology Lecture Series.

      I note, I have written about Pace before a few times including this:
      Here’s hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine

      I note we have a new project as part of this Sloan program to facilitate communication and networking and sharing information as part of this project.  My lab is creating something called “microBEnet” – the microbiology of the built environment network.  We are just getting our real site up and running.  For now you can find out some information at a temporary page http://microbenet.blogspot.com/

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      The Microbe Project – A Portal to Federal Efforts in Microbial Research #microBEnet

      For those interested in what the US Government is doing in areas relating to microbiology, there is a useful site to check out called “The Microbe Project“. The goal of this project is to “to maximize the opportunities offered by genome-enabled microbial science to benefit science and society, through coordinated interagency efforts to promote research, infrastructure development, education and outreach.” There is a lot of information there on different agencies and their funding opportunities.

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      A bit upset by @NYTimes article on twitter>>blogging so I posted 140 characters to my blog

      A recent NYTimes article discusses how twitter/facebook are on rise vs. blogs-the key isn’t to pick one over others but to use each smartly.

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      Open Access Pioneer Award: George Garrity for his work on Standards in Genomic Sciences journal

      A few days ago I got a message that made a big impact on my publication record in PubMed Central.  My number of publications there went up by 85 in one fell swoop (see below for the list …).  Did I publish 85 new papers yesterday?  No.  But a journal in which I have been a co-author on many papers recently finally showed up in Pubmed Central.  The journal is called Standards in Genomic Sciences.  The journal’s scope is:

      The goal of SIGS is to serve as an open-access, standards-supportive publication for rapid dissemination of concise genome and metagenome reports that comply with the emerging MIGS/MIMS standards, detailed standard operating procedures, meeting reports, reviews and commentaries, data policies, white papers and other gray literature that is relevant to genome sciences but currently absent from the scholarly literature.

      Lots of jargon, I know.  But you can ignore that.  The reason I am writing here is that this journal is a place to publish what could be called “genome sequencing data reports.”  These reports are a way for data producers to describe, in a formal manner, their sequencing project – and to share – in a formal manner – not only the data but also metadata about the organism(s) sequenced and the methods used.  As sequencing gets cheaper and easier, we need places for people to publish these types of “data papers” to both produce a citable unit with a DOI relating to the data, and to also share the details of the data production in a way that a simple Genbank entry does not.

      One aspect of the papers in this “SIGS” journal is that they are being done in a way that is compliant with sets of standards for sharing metadata about the organism and the project.  I confess, when I first heard about these standards developments, I was bored almost to tears.  But now I realize that this is a very important aspect of getting the most out of genome data.  If people who sequence a genome not only release the sequence data, but also a table of information about the project, such as information about the organism (e.g., aerobic vs anaerobic, location of isolation) and about the data production (e.g., sequencing methods used) then people will be able to do high throughput analyses of these features.  Then we will not just be looking at sequence but also connecting these sequences to organismal features.  Right now that is very hard to do since genome data is rarely accompanied by machine usable information about the organism that has been sequenced.

      Anyway – long story short – there will be a paper published in this journal for each genome being produced as part of the “Genomic Encyclopedia of Bacteria and Archaea” project that I have been coordinating at the DOE Joint Genome Institute in collaboration with the DSMZ.

      Today I am writing to recognize the people connected to this movement – the people who created the standards, the people who created and run the journal, and the people writing papers for this journal.  All of them are to be commended for their vision and their dedication to openness.  Thus I am giving George Garrity the EIC of SIGS  my “Open Access Pioneer Award” for creating SIGS, making it an open access journal,  for keeping it running and for getting its papers into Pubmed Central and soon Pubmed.   Many others should be recognized too for their contribution to SIGS (see the whole list of founding members here).  I also should recognize Nikos Kyrpides from the DOE JGI who helped coordinate the writing and submission of these papers along with Hans Peter Klenk from the DSMZ.  Without them, these papers would never have gotten out there.  Plus I think some credit goes to Michigan State University and the Department of Energy which apparently are sponsors of SIGS

      ————————————





      1:
      Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
      Jack A. Gilbert, Folker Meyer, Dion Antonopoulos, Pavan Balaji, C. Titus Brown, Christopher T. Brown, Narayan Desai, Jonathan A Eisen, Dirk Evers, Dawn Field, Wu Feng, Daniel Huson, Janet Jansson, Rob Knight, James Knight, Eugene Kolker, Kostas Konstantindis, Joel Kostka, Nikos Kyrpides, Rachel Mackelprang, Alice McHardy, Christopher Quince, Jeroen Raes, Alexander Sczyrba, Ashley Shade, and Rick Stevens

      Stand Genomic Sci. 2010 December 31; 3(3): 243–248. Published online 2010 December 25. doi: 10.4056/sigs.1433550.

      PMCID: PMC3035311
      2:
      Complete genome sequence of Thermaerobacter marianensis type strain (7p75aT)
      Cliff Han, Wei Gu, Xiaojing Zhang, Alla Lapidus, Matt Nolan, Alex Copeland, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxane Tapia, Lynne Goodwin, Sam Pitluck, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Susanne Schneider, Manfred Rohde, Markus Göker, Rüdiger Pukall, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and John C. Detter

      Stand Genomic Sci. 2010 December 31; 3(3): 337–345. Published online 2010 December 15. doi: 10.4056/sigs.1373474.

      PMCID: PMC3035304
      3:
      Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1T)
      Olivier Duplex Ngatchou Djao, Xiaojing Zhang, Susan Lucas, Alla Lapidus, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Jan-Fang Cheng, Cliff Han, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Galina Ovchinnikova, Amrita Pati, Evelyne Brambilla, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Johannes Sikorski, Stefan Spring, Markus Göker, John C. Detter, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 December 31; 3(3): 268–275. Published online 2010 December 15. doi: 10.4056/sigs.1233249.

      PMCID: PMC3035303
      4:
      Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1T)
      Johannes Sikorski, Olga Chertkov, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxane Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Evelyne Brambilla, Montri Yasawong, Manfred Rohde, Rüdiger Pukall, Stefan Spring, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 December 31; 3(3): 304–314. Published online 2010 December 15. doi: 10.4056/sigs.1273360.

      PMCID: PMC3035301
      5:
      Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509T)
      Hui Sun, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxane Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Olivier Duplex Ngatchou Djao, Manfred Rohde, Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 December 31; 3(3): 325–336. Published online 2010 November 30. doi: 10.4056/sigs.1363462.

      PMCID: PMC3035300
      6:
      Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3)
      Sam Pitluck, Montri Yasawong, Brittany Held, Alla Lapidus, Matt Nolan, Alex Copeland, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Olga Chertkov, Lynne Goodwin, Roxane Tapia, Cliff Han, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Rüdiger Pukall, Stefan Spring, Manfred Rohde, Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 December 31; 3(3): 285–293. Published online 2010 November 20. doi: 10.4056/sigs.1253298.

      PMCID: PMC3035310
      7:
      Complete genome sequence of Methanothermus fervidus type strain (V24ST)
      Iain Anderson, Olivier Duplex Ngatchou Djao, Monica Misra, Olga Chertkov, Matt Nolan, Susan Lucas, Alla Lapidus, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Evelyne Brambilla, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Johannes Sikorski, Stefan Spring, Manfred Rohde, Konrad Eichinger, Harald Huber, Reinhard Wirth, Markus Göker, John C. Detter, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 December 31; 3(3): 315–324. Published online 2010 November 20. doi: 10.4056/sigs.1283367.

      PMCID: PMC3035299
      8:
      Complete genome sequence of Desulfarculus baarsii type strain (2st14T)
      Hui Sun, Stefan Spring, Alla Lapidus, Karen Davenport, Tijana Glavina Del Rio, Hope Tice, Matt Nolan, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Ionna Pagani, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, John C. Detter, Cliff Han, Manfred Rohde, Evelyne Brambilla, Markus Göker, Tanja Woyke, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, and Miriam Land

      Stand Genomic Sci. 2010 December 31; 3(3): 276–284. Published online 2010 November 20. doi: 10.4056/sigs.1243258.

      PMCID: PMC3035298
      9:
      Complete genome sequence of Intrasporangium calvum type strain (7 KIPT)
      Tijana Glavina Del Rio, Olga Chertkov, Montri Yasawong, Susan Lucas, Shweta Deshpande, Jan-Fang Cheng, Chris Detter, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Rüdiger Pukall, Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 December 31; 3(3): 294–303. Published online 2010 November 16. doi: 10.4056/sigs.1263355.

      PMCID: PMC3035309
      10:
      Complete genome sequence of Sulfurimonas autotrophica type strain (OK10T)
      Johannes Sikorski, Christine Munk, Alla Lapidus, Olivier Duplex Ngatchou Djao, Susan Lucas, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Cliff Han, Jan-Fang Cheng, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, David Sims, Linda Meincke, Thomas Brettin, John C. Detter, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Elke Lang, Stefan Spring, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 October 31; 3(2): 194–202. Published online 2010 October 27. doi: 10.4056/sigs.1173118.

      PMCID: PMC3035374
      11:
      Complete genome sequence of Ferrimonas balearica type strain (PATT)
      Matt Nolan, Johannes Sikorski, Karen Davenport, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Roxanne Tapia, Thomas Brettin, John C. Detter, Cliff Han, Montri Yasawong, Manfred Rohde, Brian J Tindall, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 October 31; 3(2): 174–182. Published online 2010 October 27. doi: 10.4056/sigs.1161239.

      PMCID: PMC3035368
      12:
      Complete genome sequence of Candidatus Ruthia magnifica
      Guus Roeselers, Irene L. G. Newton, Tanja Woyke, Thomas A. Auchtung, Geoffrey F. Dilly, Rachel J. Dutton, Meredith C. Fisher, Kristina M. Fontanez, Evan Lau, Frank J. Stewart, Paul M. Richardson, Kerrie W. Barry, Elizabeth Saunders, John C. Detter, Dongying Wu, Jonathan A. Eisen, and Colleen M. Cavanaugh

      Stand Genomic Sci. 2010 October 31; 3(2): 163–173. Published online 2010 October 27. doi: 10.4056/sigs.1103048.

      PMCID: PMC3035367
      13:
      Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T)
      Hajnalka Kiss, David Cleland, Alla Lapidus, Susan Lucas, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Megan Lu, Thomas Brettin, John C. Detter, Markus Göker, Brian J. Tindall, Brian Beck, Timothy R. McDermott, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Jan-Fang Cheng

      Stand Genomic Sci. 2010 October 31; 3(2): 153–162. Published online 2010 October 27. doi: 10.4056/sigs.1153107.

      PMCID: PMC3035366
      14:
      Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847T)
      Evelyne Brambilla, Olivier Duplex Ngatchou Djao, Hajnalka Daligault, Alla Lapidus, Susan Lucas, Nancy Hammon, Matt Nolan, Hope Tice, Jan-Fang Cheng, Cliff Han, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 October 31; 3(2): 203–211. Published online 2010 October 27. doi: 10.4056/sigs.1183143.

      PMCID: PMC3035365
      15:
      Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228T)
      Konstantinos Mavromatis, Montri Yasawong, Olga Chertkov, Alla Lapidus, Susan Lucas, Matt Nolan, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Roxanne Tapia, Cliff Han, David Bruce, Lynne Goodwin, Amrita Pati, Ami Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, John C. Detter, Manfred Rohde, Evelyne Brambilla, Stefan Spring, Markus Göker, Johannes Sikorski, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 October 31; 3(2): 136–144. Published online 2010 October 18. doi: 10.4056/sigs.1143106.

      PMCID: PMC3035371
      16:
      Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)
      Montri Yasawong, Hazuki Teshima, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Johannes Sikorski, Rüdiger Pukall, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 October 31; 3(2): 126–135. Published online 2010 September 28. doi: 10.4056/sigs.1123072.

      PMCID: PMC3035375
      17:
      Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT)
      Sam Pitluck, Montri Yasawong, Christine Munk, Matt Nolan, Alla Lapidus, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Lynne Goodwin, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 October 31; 3(2): 108–116. Published online 2010 September 28. doi: 10.4056/sigs.1133078.

      PMCID: PMC3035372
      18:
      Complete genome sequence of Vulcanisaeta distributa type strain (IC-017T)
      Konstantinos Mavromatis, Johannes Sikorski, Elke Pabst, Hazuki Teshima, Alla Lapidus, Susan Lucas, Matt Nolan, Tijana Glavina Del Rio, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Markus Göker, Reinhard Wirth, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 October 31; 3(2): 117–125. Published online 2010 September 28. doi: 10.4056/sigs.1113067.

      PMCID: PMC3035369
      19:
      Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1T)
      Markus Göker, Brittany Held, Alla Lapidus, Matt Nolan, Stefan Spring, Montri Yasawong, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Lynne Goodwin, Roxanne Tapia, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Evelyne Brambilla, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, John C. Detter, Cliff Han, Manfred Rohde, Johannes Sikorski, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 August 30; 3(1): 66–75. Published online 2010 August 20. doi: 10.4056/sigs.1072907.

      PMCID: PMC3035270
      20:
      Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)
      Markus Göker, Brittany Held, Susan Lucas, Matt Nolan, Montri Yasawong, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, David Bruce, John C. Detter, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Johannes Sikorski, Rüdiger Pukall, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 August 30; 3(1): 76–84. Published online 2010 August 20. doi: 10.4056/sigs.1082860.

      PMCID: PMC3035265
      21:
      Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T)
      Johannes Sikorski, Alla Lapidus, Olga Chertkov, Susan Lucas, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Jan-Fang Cheng, Cliff Han, Evelyne Brambilla, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, David Bruce, Chris Detter, Roxanne Tapia, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Markus Göker, Stefan Spring, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 August 30; 3(1): 57–65. Published online 2010 August 20. doi: 10.4056/sigs.1062906.

      PMCID: PMC3035264
      22:
      Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)
      Kurt LaButti, Shanmugam Mayilraj, Alicia Clum, Susan Lucas, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Jan-Fang Cheng, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 August 30; 3(1): 85–92. Published online 2010 August 20. doi: 10.4056/sigs.1092865.

      PMCID: PMC3035263
      23:
      Complete genome sequence of Meiothermus silvanus type strain (VI-R2T)
      Johannes Sikorski, Brian J Tindall, Stephen Lowry, Susan Lucas, Matt Nolan, Alex Copeland, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Cliff Han, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 August 30; 3(1): 37–46. Published online 2010 July 29. doi: 10.4056/sigs.1042812.

      PMCID: PMC3035272
      24:
      Complete genome sequence of Planctomyces limnophilus type strain (Mü 290T)
      Kurt LaButti, Johannes Sikorski, Susanne Schneider, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Brian J Tindall, Manfred Rohde, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 August 30; 3(1): 47–56. Published online 2010 July 29. doi: 10.4056/sigs.1052813.

      PMCID: PMC3035269
      25:
      Complete genome sequence of Meiothermus ruber type strain (21T)
      Brian J Tindall, Johannes Sikorski, Susan Lucas, Eugene Goltsman, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Jan-Fang Cheng, Cliff Han, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Regine Fähnrich, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 August 30; 3(1): 26–36. Published online 2010 July 29. doi: 10.4056/sigs.1032748.

      PMCID: PMC3035268
      26:
      Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)
      Yun-Juan Chang, Rüdiger Pukall, Elizabeth Saunders, Alla Lapidus, Alex Copeland, Matt Nolan, Tijana Glavina Del Rio, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Mikhailova, Konstantinos Liolios, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, Thomas Brettin, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 August 30; 3(1): 1–14. Published online 2010 July 29. doi: 10.4056/sigs.1002553.

      PMCID: PMC3035267
      27:
      Complete genome sequence of Cellulomonas flavigena type strain (134T)
      Birte Abt, Brian Foster, Alla Lapidus, Alicia Clum, Hui Sun, Rüdiger Pukall, Susan Lucas, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Jan-Fang Cheng, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Lynne Goodwin, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 August 30; 3(1): 15–25. Published online 2010 July 29. doi: 10.4056/sigs.1012662.

      PMCID: PMC3035266
      28:
      Erratum to: Complete genome sequence of Atopobium parvulum type strain (IPP 1246T)
      Alex Copeland, Johannes Sikorski, Alla Lapidus, Matt Nolan, Tijana Glavina, Del Rio, Susan Lucas, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Rüdiger Pukall, Olga Chertkov, Thomas Brettin, Cliff Han, Cheryl Kuske, David Bruce, Lynne Goodwin, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Patrick Chain, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and John C. Detter

      Stand Genomic Sci. 2010 June 30; 2(3): 361–362. Published online 2010 June 15. doi: 10.4056/sigs.992408.

      PMCID: PMC3035296
      29:
      Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T)
      Olga Chertkov, Johannes Sikorski, Evelyne Brambilla, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, David Bruce, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Stefan Spring, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 June 30; 2(3): 280–289. Published online 2010 June 15. doi: 10.4056/sigs.902116.

      PMCID: PMC3035294
      30:
      Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)
      Hajnalka Kiss, Elke Lang, Alla Lapidus, Alex Copeland, Matt Nolan, Tijana Glavina Del Rio, Feng Chen, Susan Lucas, Hope Tice, Jan-Fang Cheng, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, John C. Detter, Thomas Brettin, Stefan Spring, Manfred Rohde, Markus Göker, Tanja Woyke, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 June 30; 2(3): 270–279. Published online 2010 June 15. doi: 10.4056/sigs.892105.

      PMCID: PMC3035293
      31:
      Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)
      Stefan Spring, Reinhard Rachel, Alla Lapidus, Karen Davenport, Hope Tice, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia C. Jeffries, Thomas Brettin, John C. Detter, Roxanne Tapia, Cliff Han, Thomas Heimerl, Fabian Weikl, Evelyne Brambilla, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 June 30; 2(3): 245–259. Published online 2010 June 15. doi: 10.4056/sigs.821804.

      PMCID: PMC3035292
      32:
      Complete genome sequence of Thermobispora bispora type strain (R51T)
      Konstantinos Liolios, Johannes Sikorski, Marlen Jando, Alla Lapidus, Alex Copeland, Tijana Glavina, Del Rio, Matt Nolan, Susan Lucas, Hope Tice, Jan-Fang Cheng, Cliff Han, Tanja Woyke, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Olga Chertkov, Cheryl Kuske, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 June 30; 2(3): 318–326. Published online 2010 June 15. doi: 10.4056/sigs.962171.

      PMCID: PMC3035289
      33:
      Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)
      Amrita Pati, Sabine Gronow, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Hope Tice, Jan-Fang Cheng, Cliff Han, Olga Chertkov, David Bruce, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, John C. Detter, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 June 30; 2(3): 300–308. Published online 2010 June 15. doi: 10.4056/sigs.912121.

      PMCID: PMC3035288
      34:
      Complete genome sequence of Brachyspira murdochii type strain (56-150T)
      Amrita Pati, Johannes Sikorski, Sabine Gronow, Christine Munk, Alla Lapidus, Alex Copeland, Tijana Glavina Del Tio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, David Bruce, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Stefan Spring, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 June 30; 2(3): 260–269. Published online 2010 June 15. doi: 10.4056/sigs.831993.

      PMCID: PMC3035287
      35:
      Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)
      Konstantinos Mavromatis, Birte Abt, Evelyne Brambilla, Alla Lapidus, Alex Copeland, Shweta Deshpande, Matt Nolan, Susan Lucas, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, Tanja Woyke, Lynne Goodwin, Sam Pitluck, Brittany Held, Thomas Brettin, Roxanne Tapia, Natalia Ivanova, Natalia Mikhailova, Amrita Pati, Konstantinos Liolios, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 June 30; 2(3): 290–299. Published online 2010 June 15. doi: 10.4056/sigs.952166.

      PMCID: PMC3035286
      36:
      Complete genome sequence of Archaeoglobus profundus type strain (AV18T)
      Mathias von Jan, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, Lynne Goodwin, Cliff Han, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Olga Chertkov, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Elizabeth Saunders, Thomas Brettin, John C. Detter, Patrick Chain, Konrad Eichinger, Harald Huber, Stefan Spring, Manfred Rohde, Markus Göker, Reinhard Wirth, Tanja Woyke, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 June 30; 2(3): 327–346. Published online 2010 June 15. doi: 10.4056/sigs.942153.

      PMCID: PMC3035285
      37:
      Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)
      Alicia Clum, Brian J. Tindall, Johannes Sikorski, Natalia Ivanova, Konstantinos Mavromatis, Susan Lucas, Tijana Glavina Del Rio, Matt Nolan, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Olga Chertkov, Thomas Brettin, Cliff Han, John C. Detter, Cheryl Kuske, David Bruce, Lynne Goodwin, Galina Ovchinikova, Amrita Pati, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 April 30; 2(2): 228–288. Published online 2010 May 15. doi: 10.4056/sigs.881234.

      PMCID: PMC3035276
      38:
      Complete genome sequence of Spirosoma linguale type strain (1T)
      Kathleen Lail, Johannes Sikorski, Elizabeth Saunders, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Thomas Brettin, John C. Detter, Andrea Schütze, Manfred Rohde, Brian J. Tindall, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Feng Chen

      Stand Genomic Sci. 2010 April 30; 2(2): 176–185. Published online 2010 March 30. doi: 10.4056/sigs.741334.

      PMCID: PMC3035282
      39:
      Complete genome sequence of Geodermatophilus obscurus type strain (G-20T)
      Natalia Ivanova, Johannes Sikorski, Marlen Jando, Christine Munk, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Linda Meincke, Thomas Brettin, John C. Detter, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 April 30; 2(2): 158–167. Published online 2010 March 30. doi: 10.4056/sigs.711311.

      PMCID: PMC3035280
      40:
      Complete genome sequence of Thermocrinis albus type strain (HI 11/12T)
      Reinhard Wirth, Johannes Sikorski, Evelyne Brambilla, Monica Misra, Alla Lapidus, Alex Copeland, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, Roxane Tapia, David Bruce, Lynne Goodwin, Sam Pitluck, Amrita Pati, Iain Anderson, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Yvonne Bilek, Thomas Hader, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Brian J. Tindall, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 April 30; 2(2): 194–202. Published online 2010 March 30. doi: 10.4056/sigs.761490.

      PMCID: PMC3035279
      41:
      Complete genome sequence of Conexibacter woesei type strain (ID131577T)
      Rüdiger Pukall, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Konstantinos Mavromatis, Natalia Ivanova, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Linda Meincke, David Sims, Thomas Brettin, John C. Detter, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Nikos C. Kyrpides, Hans-Peter Klenk, and Philip Hugenholtz

      Stand Genomic Sci. 2010 April 30; 2(2): 212–219. Published online 2010 March 30. doi: 10.4056/sigs.751339.

      PMCID: PMC3035278
      42:
      Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T)
      Johannes Sikorski, Alla Lapidus, Alex Copeland, Monica Misra, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Marlen Jando, Susanne Schneider, David Bruce, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Mikhailova, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Olga Chertkov, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, John C. Detter, Cliff Han, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 April 30; 2(2): 203–211. Published online 2010 March 30. doi: 10.4056/sigs.791633.

      PMCID: PMC3035277
      43:
      Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T)
      Miranda Harmon-Smith, Laura Celia, Olga Chertkov, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Sam Pitluck, Amrita Pati, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, Markus Göker, Brian Beck, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Feng Chen

      Stand Genomic Sci. 2010 April 30; 2(2): 220–227. Published online 2010 March 30. doi: 10.4056/sigs.811799.

      PMCID: PMC3035275
      44:
      Complete genome sequence of Kribbella flavida type strain (IFO 14399T)
      Rüdiger Pukall, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, Kurt LaButti, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Sam Pitluck, David Bruce, Lynne Goodwin, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Amy Chen, Krishna Palaniappan, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Thomas Brettin

      Stand Genomic Sci. 2010 April 30; 2(2): 186–193. Published online 2010 March 30. doi: 10.4056/sigs.731321.

      PMCID: PMC3035274
      45:
      Complete genome sequence of Nakamurella multipartita type strain (Y-104T)
      Hope Tice, Shanmugam Mayilraj, David Sims, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Alex Copeland, Jan-Fang Cheng, Linda Meincke, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Feng Chen

      Stand Genomic Sci. 2010 April 30; 2(2): 168–175. Published online 2010 March 30. doi: 10.4056/sigs.721316.

      PMCID: PMC3035273
      46:
      Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)
      Johannes Sikorski, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Elizabeth Saunders, David Bruce, Lynne Goodwin, Sam Pitluck, Galina Ovchinnikova, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Patrick Chain, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, John C. Detter, Cliff Han, Manfred Rohde, Elke Lang, Stefan Spring, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 April 30; 2(2): 149–157. Published online 2010 March 24. doi: 10.4056/sigs.671209.

      PMCID: PMC3035281
      47:
      Complete genome sequence of Haloterrigena turkmenica type strain (4kT)
      Elisabeth Saunders, Brian J. Tindall, Regine Fähnrich, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Patrick Chain, Sam Pitluck, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, Manfred Rohde, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 February 282010 February 28; 2(1): 107–116. Published online 2010 February 28. doi: 10.4056/sigs.681272.

      PMCID: PMC3035258
      48:
      Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T)
      Tijana Glavina Del Rio, Birte Abt, Stefan Spring, Alla Lapidus, Matt Nolan, Hope Tice, Alex Copeland, Jan-Fang Cheng, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Susan Lucas

      Stand Genomic Sci. 2010 February 28; 2(1): 87–95. Published online 2010 February 28. doi: 10.4056/sigs.661199.

      PMCID: PMC3035255
      49:
      Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T)
      Amrita Pati, Kurt LaButti, Rüdiger Pukall, Matt Nolan, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Alex Copeland, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Sam Pitluck, David Bruce, Lynne Goodwin, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Amy Chen, Krishna Palaniappan, Patrick Chain, Thomas Brettin, Johannes Sikorski, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 February 28; 2(1): 49–56. Published online 2010 January 28. doi: 10.4056/sigs.601105.

      PMCID: PMC3035262
      50:
      Complete genome sequence of Veillonella parvula type strain (Te3T)
      Sabine Gronow, Sabine Welnitz, Alla Lapidus, Matt Nolan, Natalia Ivanova, Tijana Glavina Del Rio, Alex Copeland, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Elizabeth Saunders, Thomas Brettin, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Amrita Pati, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Susan Lucas

      Stand Genomic Sci. 2010 February 28; 2(1): 57–65. Published online 2010 January 28. doi: 10.4056/sigs.521107.

      PMCID: PMC3035260
      51:
      Complete genome sequence of Gordonia bronchialis type strain (3410T)
      Natalia Ivanova, Johannes Sikorski, Marlen Jando, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, Cliff Han, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 February 28; 2(1): 19–28. Published online 2010 January 28. doi: 10.4056/sigs.611106.

      PMCID: PMC3035257
      52:
      Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)
      Stefan Spring, Matt Nolan, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Miriam Land, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Christine Munk, Hajnalka Kiss, Patrick Chain, Cliff Han, Thomas Brettin, John C. Detter, Esther Schüler, Markus Göker, Manfred Rohde, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 February 28; 2(1): 38–48. Published online 2010 January 28. doi: 10.4056/sigs.581048.

      PMCID: PMC3035252
      53:
      Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)
      Matt Nolan, Johannes Sikorski, Marlen Jando, Susan Lucas, Alla Lapidus, Tijana Glavina Del Rio, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Olga Chertkov, David Sims, Linda Meincke, Thomas Brettin, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 February 28; 2(1): 29–37. Published online 2010 January 28. doi: 10.4056/sigs.631049.

      PMCID: PMC3035251
      54:
      Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)
      Natalia Ivanova, Chris Daum, Elke Lang, Birte Abt, Markus Kopitz, Elizabeth Saunders, Alla Lapidus, Susan Lucas, Tijana Glavina Del Rio, Matt Nolan, Hope Tice, Alex Copeland, Jan-Fang Cheng, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Konstantinos Mavromatis, Amrita Pati, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Jim Bristow, Victor Markowitz, Jonathan A. Eisen, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2010 February 28; 2(1): 96–106. Published online 2010 January 28. doi: 10.4056/sigs.69.1277.

      PMCID: PMC3035250
      55:
      Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)
      Brian Foster, Rüdiger Pukall, Birte Abt, Matt Nolan, Tijana Glavina Del Rio, Feng Chen, Susan Lucas, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Olga Chertkov, Thomas Brettin, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Natalia Ivanova, Konstantinos Mavromatis, Amrita Pati, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2010 February 28; 2(1): 1–8. Published online 2010 January 28. doi: 10.4056/sigs.571102.

      PMCID: PMC3035249
      56:
      Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)
      Konstantinos Mavromatis, Johannes Sikorski, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Linda Meincke, David Sims, Olga Chertkov, Cliff Han, Thomas Brettin, John C. Detter, Claudia Wahrenburg, Manfred Rohde, Rüdiger Pukall, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2010 February 28; 2(1): 9–18. Published online 2010 January 28. doi: 10.4056/sigs.591104.

      PMCID: PMC3035248
      57:
      Complete genome sequence of Streptobacillus moniliformis type strain (9901T)
      Matt Nolan, Sabine Gronow, Alla Lapidus, Natalia Ivanova, Alex Copeland, Susan Lucas, Tijana Glavina Del Rio, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, David Sims, Linda Meincke, David Bruce, Lynne Goodwin, Thomas Brettin, Cliff Han, John C. Detter, Galina Ovchinikova, Amrita Pati, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Manfred Rohde, Cathrin Spröer, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Patrick Chain

      Stand Genomic Sci. 2009 December 31; 1(3): 300–307. Published online 2009 December 30. doi: 10.4056/sigs.48727.

      PMCID: PMC3035246
      58:
      Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T)
      Chris Munk, Alla Lapidus, Alex Copeland, Marlen Jando, Shanmugam Mayilraj, Tijana Glavina Del Rio, Matt Nolan, Feng Chen, Susan Lucas, Hope Tice, Jan-Fang Cheng, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Patrick Chain, Sam Pitluck, Markus Göker, Galina Ovchinikova, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 December 31; 1(3): 234–241. Published online 2009 December 30. doi: 10.4056/sigs.47643.

      PMCID: PMC3035245
      59:
      Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)
      Alicia Clum, Brian J. Tindall, Johannes Sikorski, Natalia Ivanova, Konstantinos Mavrommatis, Susan Lucas, Tijana Glavina, Del Rio, Matt Nolan, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Olga Chertkov, Thomas Brettin, Cliff Han, John C. Detter, Cheryl Kuske, David Bruce, Lynne Goodwin, Galina Ovchinikova, Amrita Pati, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2009 December 31; 1(3): 308–316. Published online 2009 December 30. doi: 10.4056/sigs.51657.

      PMCID: PMC3035237
      60:
      Complete genome sequence of Rhodothermus marinus type strain (R-10T)
      Matt Nolan, Brian J. Tindall, Helga Pomrenke, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Elizabeth Saunders, Cliff Han, David Bruce, Lynne Goodwin, Patrick Chain, Sam Pitluck, Galina Ovchinikova, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and John C. Detter

      Stand Genomic Sci. 2009 December 31; 1(3): 283–290. Published online 2009 December 29. doi: 10.4056/sigs.46736.

      PMCID: PMC3035238
      61:
      Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T)
      Stefan Spring, Alla Lapidus, Maren Schröder, Dorothea Gleim, David Sims, Linda Meincke, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, Thomas Brettin, John C. Detter, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, and Cliff Han

      Stand Genomic Sci. 2009 December 31; 1(3): 242–253. Published online 2009 November 22. doi: 10.4056/sigs.39508.

      PMCID: PMC3035247
      62:
      Complete genome sequence of Kangiella koreensis type strain (SW-125T)
      Cliff Han, Johannes Sikorski, Alla Lapidus, Matt Nolan, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Alex Copeland, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, David Bruce, Lynne Goodwin, Sam Pitluck, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, Thomas Brettin, Markus Göker, Brian J. Tindall, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and John C. Detter

      Stand Genomic Sci. 2009 December 31; 1(3): 226–233. Published online 2009 November 22. doi: 10.4056/sigs.36635.

      PMCID: PMC3035244
      63:
      Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1T)
      Rüdiger Pukall, Alla Lapidus, Matt Nolan, Alex Copeland, Tijana Glavina Del Rio, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Olga Chertkov, David Bruce, Lynne Goodwin, Cheryl Kuske, Thomas Brettin, John C. Detter, Cliff Han, Sam Pitluck, Amrita Pati, Konstantinos Mavrommatis, Natalia Ivanova, Galina Ovchinnikova, Amy Chen, Krishna Palaniappan, Susanne Schneider, Manfred Rohde, Patrick Chain, Patrik D’haeseleer, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Nikos C. Kyrpides, Hans-Peter Klenk, and Philip Hugenholtz

      Stand Genomic Sci. 2009 December 31; 1(3): 234–241. Published online 2009 November 22. doi: 10.4056/sigs.37633.

      PMCID: PMC3035243
      64:
      Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T)
      Mansi Chovatia, Johannes Sikorski, Maren Schröder, Alla Lapidus, Matt Nolan, Hope Tice, Tijana Glavina Del Rio, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Stefan Spring, Jim Bristow, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Jonathan A. Eisen

      Stand Genomic Sci. 2009 December 31; 1(3): 254–261. Published online 2009 November 22. doi: 10.4056/sigs.40645.

      PMCID: PMC3035242
      65:
      Complete genome sequence of Halorhabdus utahensis type strain (AX-2T)
      Iain Anderson, Brian J. Tindall, Helga Pomrenke, Markus Göker, Alla Lapidus, Matt Nolan, Alex Copeland, Tijana Glavina Del Rio, Feng Chen, Hope Tice, Jan-Fang Cheng, Susan Lucas, Olga Chertkov, David Bruce, Thomas Brettin, John C. Detter, Cliff Han, Lynne Goodwin, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Sam Pitluck, Amrita Pati, Konstantinos Mavromatis, Natalia Ivanova, Galina Ovchinnikova, Amy Chen, Krishna Palaniappan, Patrick Chain, Manfred Rohde, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 December 31; 1(3): 218–225. Published online 2009 November 22. doi: 10.4056/sigs.31864.

      PMCID: PMC3035240
      66:
      Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T)
      Brian J. Tindall, Susanne Schneider, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Elizabeth Saunders, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Mikhailova, Amrita Pati, Natalia Ivanova, Konstantinos Mavrommatis, Amy Chen, Krishna Palaniappan, Patrick Chain, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, Cliff Han, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, Nikos C. Kyrpides, and John C. Detter

      Stand Genomic Sci. 2009 December 31; 1(3): 270–277. Published online 2009 November 22. doi: 10.4056/sigs.42644.

      PMCID: PMC3035239
      67:
      Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T)
      Rüdiger Pukall, Gabriele Gehrich-Schröter, Alla Lapidus, Matt Nolan, Tijana Glavina Del Rio, Susan Lucas, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Alex Copeland, Elizabeth Saunders, Thomas Brettin, John C. Detter, David Bruce, Lynne Goodwin, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Cliff Han

      Stand Genomic Sci. 2009 December 31; 1(3): 262–269. Published online 2009 November 22. doi: 10.4056/sigs.41646.

      PMCID: PMC3035236
      68:
      Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T)
      Elizabeth Saunders, Rüdiger Pukall, Birte Abt, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Linda Meincke, David Sims, Thomas Brettin, John C. Detter, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Cliff Han

      Stand Genomic Sci. 2009 September 29; 1(2): 174–182. Published online 2009 September 28. doi: 10.4056/sigs.33592.

      PMCID: PMC3035228
      69:
      Complete genome sequence of Saccharomonospora viridis type strain (P101T)
      Amrita Pati, Johannes Sikorski, Matt Nolan, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Susan Lucas, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Olga Chertkov, Thomas Brettin, Cliff Han, John C. Detter, Cheryl Kuske, David Bruce, Lynne Goodwin, Patrick Chain, Patrik D’haeseleer, Amy Chen, Krishna Palaniappan, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Manfred Rohde, Brian J. Tindall, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 September 29; 1(2): 141–149. Published online 2009 September 24. doi: 10.4056/sigs.20263.

      PMCID: PMC3035233
      70:
      Complete genome sequence of Dyadobacter fermentans type strain (NS114T)
      Elke Lang, Alla Lapidus, Olga Chertkov, Thomas Brettin, John C. Detter, Cliff Han, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Feng Chen, Susan Lucas, Hope Tice, Jan-Fang Cheng, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Marcus Kopitz, David Bruce, Lynne Goodwin, Sam Pitluck, Galina Ovchinnikova, Amrita Pati, Natalia Ivanova, Konstantinos Mavrommatis, Amy Chen, Krishna Palaniappan, Patrick Chain, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Markus Göker, Manfred Rohde, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 September 29; 1(2): 133–140. Published online 2009 September 24. doi: 10.4056/sigs.19262.

      PMCID: PMC3035232
      71:
      Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T)
      Alex Copeland, Alla Lapidus, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Mikhailova, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Patrick Chain, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Olga Chertkov, Thomas Brettin, John C. Detter, Cliff Han, Zahid Ali, Brian J. Tindall, Markus Göker, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 September 29; 1(2): 119–125. Published online 2009 September 24. doi: 10.4056/sigs.17259.

      PMCID: PMC3035231
      72:
      Complete genome sequence of Anaerococcus prevotii type strain (PC1T)
      Kurt LaButti, Rudiger Pukall, Katja Steenblock, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, Thomas Brettin, John C. Detter, Cliff Han, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2009 September 29; 1(2): 159–165. Published online 2009 September 24. doi: 10.4056/sigs.24194.

      PMCID: PMC3035230
      73:
      Complete genome sequence of Halogeometricum borinquense type strain (PR3T)
      Stephanie Malfatti, Brian J. Tindall, Susanne Schneider, Regine Fähnrich, Alla Lapidus, Kurt LaButtii, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Feng Chen, Susan Lucas, Hope Tice, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Iain Anderson, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Patrik D’haeseleer, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Patrick Chain

      Stand Genomic Sci. 2009 September 29; 1(2): 150–159. Published online 2009 September 24. doi: 10.4056/sigs.23264.

      PMCID: PMC3035229
      74:
      Complete genome sequence of Cryptobacterium curtum type strain (12-3T)
      Konstantinos Mavrommatis, Rüdiger Pukall, Christine Rohde, Feng Chen, David Sims, Thomas Brettin, Cheryl Kuske, John C. Detter, Cliff Han, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Hope Tice, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Galina Ovchinnikova, Amrita Pati, Natalia Ivanova, Amy Chen, Krishna Palaniappan, Patrick Chain, Patrik D’haeseleer, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Manfred Rohde, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2009 September 29; 1(2): 93–100. Published online 2009 September 24. doi: 10.4056/sigs.12260.

      PMCID: PMC3035227
      75:
      Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)
      Konstantinos Mavrommatis, Sabine Gronow, Elizabeth Saunders, Miriam Land, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Amrita Pati, Natalia Ivanova, Amy Chen, Krishna Palaniappan, Patrick Chain, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Thomas Brettin, John C. Detter, Cliff Han, James Bristow, Markus Göker, Manfred Rohde, Jonathan A. Eisen, Victor Markowitz, Nikos C. Kyrpides, Hans-Peter Klenk, and Philip Hugenholtz

      Stand Genomic Sci. 2009 September 29; 1(2): 101–109. Published online 2009 September 24. doi: 10.4056/sigs.15195.

      PMCID: PMC3035226
      76:
      Complete genome sequence of Sanguibacter keddieii type strain (ST-74T)
      Natalia Ivanova, Johannes Sikorski, David Sims, Thomas Brettin, John C. Detter, Cliff Han, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Feng Chen, Susan Lucas, Hope Tice, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Amrita Pati, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Patrik D’haeseleer, Patrick Chain, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Markus Göker, Rüdiger Pukall, Hans-Peter Klenk, and Nikos C. Kyrpides

      Stand Genomic Sci. 2009 September 29; 1(2): 110–118. Published online 2009 September 24. doi: 10.4056/sigs.16197.

      PMCID: PMC3035225
      77:
      Complete genome sequence of Leptotrichia buccalis type strain (C-1013-bT)
      Natalia Ivanova, Sabine Gronow, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng, Elizabeth Saunders, David Bruce, Lynne Goodwin, Thomas Brettin, John C. Detter, Cliff Han, Sam Pitluck, Natalia Mikhailova, Amrita Pati, Konstantinos Mavrommatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Christine Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 September 29; 1(2): 126–132. Published online 2009 September 24. doi: 10.4056/sigs.1854.

      PMCID: PMC3035221
      78:
      Complete genome sequence of Atopobium parvulum type strain (IPP 1246T)
      Alex Copeland, Johannes Sikorski, Alla Lapidus, Matt Nolan, Tijana Glavina Del Rio, Susan Lucas, Feng Chen, Hope Tice, Sam Pitluck, Jan-Fang Cheng, Rüdiger Pukall, Olga Chertkov, Thomas Brettin, Cliff Han, John C. Detter, Cheryl Kuske, David Bruce, Lynne Goodwin, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amy Chen, Krishna Palaniappan, Patrick Chain, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and John C. Detter

      Stand Genomic Sci. 2009 September 29; 1(2): 166–173. Published online 2009 September 23. doi: 10.4056/sigs.29547.

      PMCID: PMC3035223
      79:
      Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)
      Alicia Clum, Matt Nolan, Elke Lang, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavrommatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Markus Göker, Stefan Spring, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia C. Jeffries, Patrick Chain, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2009 July 20; 1(1): 38–45. Published online 2009 July 20. doi: 10.4056/sigs.1463.

      PMCID: PMC3035218
      80:
      Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T)
      Miriam Land, Rüdiger Pukall, Birte Abt, Markus Göker, Manfred Rohde, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Loren Hauser, Yun-Juan Chang, Cynthia C. Jefferies, Elizabeth Saunders, Thomas Brettin, John C. Detter, Cliff Han, Patrick Chain, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Alla Lapidus

      Stand Genomic Sci. 2009 July 20; 1(1): 21–28. Published online 2009 July 20. doi: 10.4056/sigs.1162.

      PMCID: PMC3035217
      81:
      Complete genome sequence of Desulfomicrobium baculatum type strain (XT)
      Alex Copeland, Stefan Spring, Markus Göker, Susanne Schneider, Alla Lapidus, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavrommatis, Galina Ovchinnikova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia C. Jeffries, Linda Meincke, David Sims, Thomas Brettin, John C. Detter, Cliff Han, Patrick Chain, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and Susan Lucas

      Stand Genomic Sci. 2009 July 20; 1(1): 29–37. Published online 2009 July 20. doi: 10.4056/sigs.13134.

      PMCID: PMC3035215
      82:
      Complete genome sequence of Kytococcus sedentarius type strain (541T)
      David Sims, Thomas Brettin, John C. Detter, Cliff Han, Alla Lapidus, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Feng Chen, Susan Lucas, Hope Tice, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Galina Ovchinnikova, Amrita Pati, Natalia Ivanova, Konstantinos Mavrommatis, Amy Chen, Krishna Palaniappan, Patrik D’haeseleer, Patrick Chain, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Susanne Schneider, Markus Göker, Rüdiger Pukall, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 July 20; 1(1): 12–20. Published online 2009 July 20. doi: 10.4056/sigs.761.

      PMCID: PMC3035214
      83:
      Complete genome sequence of Actinosynnema mirum type strain (101T)
      Miriam Land, Alla Lapidus, Shanmugam Mayilraj, Feng Chen, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Hope Tice, Jan-Fang Cheng, Olga Chertkov, David Bruce, Lynne Goodwin, Sam Pitluck, Manfred Rohde, Markus Göker, Amrita Pati, Natalia Ivanova, Konstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Loren Hauser, Yun-Juan Chang, Cynthia C. Jeffries, Thomas Brettin, John C. Detter, Cliff Han, Patrick Chain, Brian J. Tindall, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 July 20; 1(1): 46–53. Published online 2009 July 20. doi: 10.4056/sigs.21137.

      PMCID: PMC3035213
      84:
      Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)
      Cliff Han, Stefan Spring, Alla Lapidus, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia C. Jeffries, Elizabeth Saunders, Olga Chertkov, Thomas Brettin, Markus Göker, Manfred Rohde, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, and John C. Detter

      Stand Genomic Sci. 2009 July 20; 1(1): 54–62. Published online 2009 July 20. doi: 10.4056/sigs.22138.

      PMCID: PMC3035210
      85:
      Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10T)
      Alla Lapidus, Rüdiger Pukall, Kurt LaButtii, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Feng Chen, Susan Lucas, Hope Tice, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Sam Pitluck, Manfred Rohde, Markus Göker, Amrita Pati, Natalia Ivanova, Konstantinos Mavrommatis, Amy Chen, Krishna Palaniappan, Patrik D’haeseleer, Patrick Chain, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, and Hans-Peter Klenk

      Stand Genomic Sci. 2009 July 20; 1(1): 3–11. Published online 2009 July 20. doi: 10.4056/sigs.492.

      PMCID: PMC3035206

      ——–
      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

      ——–

      STAMPS: good course for those interested in molecular surveys of microbial diversity

      This looks like a good course to take for those interested ion molecular studies of microbial diversity

      STAMPS: Marine Biological Laboratory

      From the course website:

      Strategies and Techniques for Analyzing Microbial Population Structures
      Directors: Mitchell L. Sogin and David B. Mark Welch

      Course Dates: August 3 – August 13, 2011.
      Online Application Form | Deadline: April 15, 2011
      Deep DNA sequencing using massively-parallel, next-generation technology has enabled nearly comprehensive environmental surveys that can describe the different kinds of microbes in a community and their relative abundance. These descriptions of richness and evenness make possible estimates of microbial diversity, but the size of the required data sets pose enormous computational challenges. The rapidly expanding flow of information from next generation DNA sequencing platforms has fueled healthy debate about best practices for data analysis while at the same time building a user demand for tools that can address important ecological questions. The STAMPS course will promote dialogue and the exchange of ideas between experts in analysis of metagenomic data and offer interdisciplinary bioinformatic and statistical training to practitioners of molecular microbial ecology and genomics.

      Topics to be covered include but are not limited to next-generation strategies for analysis of microbial communities; acquisition and organization of next generation sequence data; principles of quality control of sequence data; the theory of cluster and rarefaction analyses; taxonomic assignments for high-throughput data; statistical models for estimating microbial diversity; microbial community comparison methodology and metrics; and analysis of shotgun metagenomic data. The lectures will be augmented by a computer laboratory where students will have the opportunity to use state of the art facilities to test theoretical concepts described in the lectures series. Guided by authors of ARB, CatchAll, Esprit, Mothur, Pyronoise, RDP, Silva, UClust, and Pyronoise for cluster analyses; mother, QIIME, Unifrac, and VAMPS for community analysis; and METAREP and MG-RAST for shotgun metagenomics analysis, participants in the workshop will have the opportunity to compare different analysis techniques for molecular data.

      The course is designed for established investigators, postdoctoral fellows and advanced graduate students from diverse biological fields. The Workshop Participants will also be given priority for acceptance into the MBL’s Workshop in Molecular Evolution that will meet the preceding week. This option will provide an opportunity to develop a stronger conceptual framework for understanding the basis of analytical tools in the STAMPS workshop.

      Faculty for 2011 will include:
      Gary Anderson, Lawrence Berkeley National Lab
      John Bunge, Cornell University
      James Cole, Michigan State University
      Robert Edgar, gentleman scholar
      Jed Fuhrman, University of Southern California
      Susan Huse, Marine Biological Laboratory
      Rob Knight, University of Colorado at Boulder
      Hilary Morrison, Marine Biological Laboratory
      Elmer Pruesse, Max Planck Institute for Marine Microbiology
      Chris Quince, University of Glasgow
      Antonis Rokas, Vanderbilt University
      Patrick Schloss, University of Michigan
      Yijun Sun, University of Florida
      Peter Turnbaugh, Harvard University

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      This is from the “Tree of Life Blog”
      of Jonathan Eisen, an evolutionary biologist and Open Access advocate
      at the University of California, Davis. For short updates, follow me on Twitter.

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