Tag: Genomics

Playing around with CloVR – cloud computing bioinformatics system

Nice new tool/resource available out there for metagenomic and genomic analysis called CloVR: CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
It is available at http://clovr.org and it should be useful to many people out there doing genomics and metagenomics if you want to make use of cloud computing resources.

CloVR is brought to us by Florian Fricke and Owen White and Sam Angiuoli and others from the University of Maryland (full disclosure – many of the authors are ex-colleagues of mine from TIGR).

Not only is Clovr available openly and freely but they even have a Clovr blog: http://clovr.org/category/blog/ … though it does not seem to be heavily used.  Kudos to this team for producing and releasing this software for others to use.  And kudos to NSF, USDA and NIH for funding its development — I have a feeling many people will use it.

——–
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.

——–

What is in a name? A case study of genomic epidemiology w/ Bacillus cereus and Bacillus anthracis

ResearchBlogging.org There is a very interesting new paper that just came online in the Archives of Pathology: Rapidly Progressive, Fatal, Inhalation Anthrax-Like Infection in a Human: Case Report, Pathogen Genome Sequencing, Pathology, and Coordinated Response

I was alerted to the paper by Eileen Choffnes of the National Academy of Sciences Institute of Medicine Forum on Microbial Threats (which I am a member of).  In the paper, James Musser, Angela Wright and colleagues, the authors discuss the use of genome sequencing in the characterization of a fatal infection with a bacterium that appeared to be a species of Bacillus.  Their summary is below and pretty much sums it up:

Context.—Ten years ago a bioterrorism event involving Bacillus anthracis spores captured the nation’s interest, stimulated extensive new research on this pathogen, and heightened concern about illegitimate release of infectious agents. Sporadic reports have described rare, fulminant, and sometimes fatal cases of pneumonia in humans and nonhuman primates caused by strains of Bacillus cereus, a species closely related to Bacillus anthracis.

Objectives.—To describe and investigate a case of rapidly progressive, fatal, anthrax-like pneumonia and the overwhelming infection caused by a Bacillus species of uncertain provenance in a patient residing in rural Texas.

Design.—We characterized the genome of the causative strain within days of its recovery from antemortem cul- tures using next-generation sequencing and performed immunohistochemistry on tissues obtained at autopsy with antibodies directed against virulence proteins of B. anthracis and B. cereus.

Results.—We discovered that the infection was caused by a previously unknown strain of B. cereus that was closely related to, but genetically distinct from, B. anthracis. The strain contains a plasmid similar to pXO1, a genetic element encoding anthrax toxin and other known virulence factors. Immunohistochemistry demonstrated that several homologs of B. anthracis virulence proteins were made in infected tissues, likely contributing to the patient’s death.

Conclusions.—Rapid genome sequence analysis permit- ted us to genetically define this strain, rule out the like- lihood of bioterrorism, and contribute effectively to the institutional response to this event. Our experience strongly reinforced the critical value of deploying a well- integrated, anatomic, clinical, and genomic strategy to respond rapidly to a potential emerging, infectious threat to public health.

The part in which I am interested, not surprisingly, is the genomic-evolution part.  This is of interest since Bacillus anthracis is in a way a subspecies of a larger clade of bacterial types that includes Bacillus cereus and Bacillus thuringensis.  These two generally do not cause fatal disease in humans, though I believe there are prior cases (see for example, Anthrax, but not Bacillus anthracis?).  Also, I note, B. thuringensis is also known as Bt and is used extensively in agriculture to kill pests.  Anyway, though Bt abd Bc are known to occasionally cause humans trouble, without a doubt, if you say you have found a case of Bacillus anthracis in people, some serious freaking out will occur at some level.  People will want to know things – like is this a natural occurrence or a purposeful attack?  And in the end, there is a lot associated with the name since of course “anthrax” scares people.

So the authors here basically sequenced the genome of this isolate and then did some detailed phylogenomic analysis to place it in the Bacillus cereus/thuringensis/anthracis group.  See below:

And it turns out, this strain is not in the anthrax portion of the tree.  It is in the Bacillus cereus part.  The key thing here is that this strain is clearly, phylogenetically, in the Bacillus cereus/thuringensis part of this clade.  Not so sure if the genomics was necessary here.  I think some detailed MLST and/or phylogenetics of other variable markers might have done the same trick.  But still, the resolution one gets from the phylogenomics is pretty good.  This is of course nothing really new.  There have been some nice genomic epidemiological studies done in the last year or two such as in the German E. coli and in some other cases (see for example, Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology and Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany and The 2011 Shiga toxin-producing Escherichia coli O104:H4 German outbreak: a lesson in genomic plasticity and Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4 and Pathogens: Genes and Genomes).
Though this is not per se new, this paper focuses a bit more on the pathology part of the story and even ends by linking to a new paper from one of the authors on how this type of work changes how we should conceive of pathology training: 

One of us recently proposed the inception of a third, training track in pathology termed genomic pathology, designed to complement the traditional anatomic and clinical pathology tracks. As the introgression of genome- scale analyses proceeds rapidly and inexorably into con- temporary patient care and pathology practice, the career opportunities for this new type of trainee will increase considerably, and new patient-care niches will be created. We believe cases such as this highlight the need for, and potential utility of, a cadre of pathologists trained and facile in genomic pathology.

The paper on Genomic Pathology (thank goodness they did not invent a new omics word) can be found here.  There is no doubt we are in a new era.  Genomic sequencing is certainly going to be used in more and more cases like this and we definitely need to change the training paradigm if we want more people to use and understand it.
Some other reading worth checking out:
Some videos of interest

Reference:
Wright AM, Beres SB, Consamus EN, Long SW, Flores AR, Barrios R, Richter GS, Oh SY, Garufi G, Maier H, Drews AL, Stockbauer KE, Cernoch P, Schneewind O, Olsen RJ, & Musser JM (2011). Rapidly Progressive, Fatal, Inhalation Anthraxlike Infection in a Human: Case Report, Pathogen Genome Sequencing, Pathology, and Coordinated Response. Archives of pathology & laboratory medicine PMID: 21827220

——–
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.

——–

Notes from a trip to Woods Hole, MA to teach #genomics at the MBL Microbial Diversity Course

Here are some notes from my recent trip to Woods Hole, MA where I went to give a talk for the Marine Biological Lab “Microbial Diversity Course”.

Day 1:  Thursday

My trip started quite poorly.  I wrote a whole post on the first day so if you want more detail go here: A squatter’s journey to the Marine Biological Lab (MBL).  I posted (of course) to twitter along the way.  Here are some of my posts:

  • Heading to Woods Hole/MBL-giving talk for symposium for the Microbial Diversity Class  
  • Anyone out there recommend best way to get from Logon to Woods Hole after 10:30 PM (no Peter Pan bus) w/o renting car? 
  • Thank you Delta for out early arrival in MSP- not so many thanks for sitting on runway for 20 minutes ad more waiting for gate
  • Yhgtbfkm – we finally got to a gate at MSP and the gate agents keep missing our door with jetway
  •  maybe I’ll see you as I head to my connection
    • Had a long twitter conversation with her about the fact that both of our flights were becoming disasters
  • Plane was very late bit now in a nice Prius from Green Shuttles on way to Woods Hole  
  • UGGGH – arrived Woods Hole/MBL; got dorm room key at 1am; woman in room not very happy; finally got other hot crummy dorm room; Ahh MBL

Day 2: Friday: Hanging out at MBL

Woke up at the Swope Dorms and, thanks to the lovely reception I got from the Housing Staff (see A squatter’s journey to the Marine Biological Lab (MBL) again for more detail) I was not very happy.  I went in to town to get a latte and something to eat and then made it over to the Microbial Diversity Course to hear a few talks and see some of the folks there.  Then I went back to my dorm room, packed up my stuff and abandoned Swope and went to the Sleepy Hollow Motor Inn just up the road, a bit out of town.  I had already called and they held a room for me (I tried the one place actually in town but they were full).  So I checked in, dumped my stuff and then walked back in to town.  I eventually ended up going to dinner with some of the course TAs and other personnel.

Here are some tweets from the day

Alas, was quite a bit tired from the horrible trip and bad housing experience so did not tweet much the whole day.  Here are some pics from the day:

View from my second room at Swope
View from my room of Eel Pond
View from my room – nice view – but room was unbearably
hot even on a cool day.
Microbial Diversity course lab

Microbial Diversity course lab
Microbial Diversity course lab

Microbial Diversity course lab

Microbial Diversity course lab
Eel Pond again
Eel Pond again
The Kidd
Art around MBL

Art around MBL
Art around MBL
Fun chairs in the Candle House
Fun chairs in the Candle House
Squid on a fence
Squid on a fence
More eel pond
Magical berries
Microbial mat

Microbial mat
Magical berries
Magical berries
Magical berries

Microbial mat 
Skate babies

Day 3: Symposium

Saturday was the day for the genomics symposium I had come for.  The symposium was hosted by the Microbial Diversity Course and was focused on microbial genomics.  There were four speakers – me, Howard Ochman, Nancy Moran and Eugene Koonin.  I thought the symposium went quite well — each speaker did a good job of not both complimenting and complementing the other speakers.   I hope the students liked it.

I spent many hours the night before and in the AM working on my talk, trying to fine tune it for the audience.  I grabbed a latte in the morning at a nice Woods Hole place, and eventually walked on over towards the lab.



I headed over to Swope and fortunately found a person from the course who told me where the talks were.  I gabbed some breakfast in the dining hall and then went to the room next door where the Symposium was going to be held.  I set up my laptop and alas noticed I had forgotten my Apple remote.  So I did a App store search to see if my iPhone could serve as a remote for Keynote and it can (for 99 cents).  So I downloaded the App and got it working and was ready to go.
I got a nice introduction from Dan Buckley, one of the Course organizers and then gave my talk.  I think I went a bit fast in parts but people seemed to like it.  I got some good questions and then it was time for a break.  Anyway – here are my slides, which I posted on Slideshare: Eisen Talk for MBL Microbial Diversity Course
View more presentations from Jonathan Eisen Then Howard Ochman gave a talk.  Here are some tweets from his talk:

  • Done with my talk at MBL for the Microbial Diversity course Symposium on Microbial Genomics – now listening to Howard Ochman
  • Howard Ochman discussing how genes in a bacterial genome w/ atypical composition are considered likely to have entered by lateral transfer
  • Ochman referencing classic paper by Sueoka “ON THE GENETIC BASIS OF VARIATION & HETEROGENEITY OF DNA BASE COMPOSITION” 
  • Ochman showing time course of the plot of genome size vs. # of genes for bacteria – all looked good 1kb=1 gene until M. leprae genome
  • Ochman quotes “Less than half of the genome contains functional genes but pseudogenes …. abound” 
  • Ochman: Why aren’t there lots of pseudogenes in most bacterial genomes? B/c there is a mutation bias towards deletions
  • Ochman referencing “Bacterial genome size reduction by experimental evolution”  re: deletion bias
  • Ochman making genetic drift personal: sometimes you pull out just the blue M&Ms, which of course you really don’t like 
  • Ochman referencing “The consequences of genetic drift for bacterial genome complexity” 
  • Ochman: an increase in genetic drift from reduced effective population size can lead to increase in Ka/Ks
  • Ochman discussing how effect of drift on bacterial genome size is opposite trend predicted in Lynch and Conery 2003

Then there was a little break for Lunch.  After lunch I had an entertaining conversation with Howard Ochman about various topics.  And then we were back to talks.

Nancy Moran.  Here are my tweets:

  • Listening to talk by Nancy Moran about tiny bacterial genomes – she is discussing her work w/ now retired  prof. Paul Baumann 
  • Moran – discussing work of Allison Hansen in her lab on bacterial gene expression in bacteria containing cells in aphid gut
  • Moran discussing incredible diversity of insect symbionts that help hosts obtain nutrients from nutrient poor diets 
  • Moran discussing the Tremblaya genome which has recently shown up in Genbank 
    • : @phylogenomics Tremblaya is awesome. John McCutchoen is the man – hope this is published soon.
    • : @phylogenomics 58% GC in an insect symbiont – simply weird. McCutcheon talked about this at SGM Insect Symbiosis in Harrogate, UK in April.
    •  yes, high GC but it is related to organisms with even higher GC

Then Eugene Koonin. Here are my tweets from his talk:

  • Now listening to the one and only Eugene Koonin discussing evolution of archaea/bacteria at MBL Microbial Diversity course 
  • I note my start in genome evolution really came from reading papers by Koonin on helicases
  • Koonin showing figures from one of my favorite papers of his: … the emerging dynamic view of the prokaryotic world 
  • Koonin: Archaeal genomes are even more gene dense than bacterial genomes
  • Koonin: the majority of genes in bacterial and Archaeal genomes are part of conserved families
  • Koonin: most gene families show patchy phyletic patterns across bacterial and Archaeal genomes
  • Note – Koonin has more than 500 papers listed in Pubmed
  • Koonin : most of the universal genes in bacteria and archaea are involved in translation
  • Koonin describes “bureaucratic ceiling” to genome size b/c of exponential incr. in regulators vs. genome size – can’t get too big
    •  @phylogenomics Limit on “genome size”. He means gene number (which does correlate in bact/arch but not euk)
    •  Sorry .. He is only discussing bacteria and archaea … So here it does correlated w/ genome size
    •  indeed .. He was using gene number as his key feature
  • Koonin describing 1998 Aravind et al paper on Aquifex which was 1st report of massive gene transfer between bacteria / archaea
  • Side story: when Thermotoga genome paper came out (I was buried as middle author) Koonin called me, POd that we had not refd Aquifex paper
    •  yes but this was a bit of a big deal … Press coverage … Nature paper, etc etc …
    •  The funny part was . He was POd at me even though I was buried in the middle b/c he said I should know better …
  • I must say Koonin is giving a damn excellent talk on bacteria and Archaeal evolution
  • Koonin discussions how there is a central tree-like structure in the “forest of life” of trees of conserved genes
  • Koonin discussions this: Comparison of phylogenetic trees and search for a … 
  • Koonin: there is a strong signal of vertical evolution even among much lateral gene transfer, b/c transfer is mostly random
  • ATGC: a DB of orthologous genes from closely related prokaryotic genomes & a research platform for microevolution
  • Koonin: “There is such a thing as a prokaryote” (gives many reasons)
  • Koonin discussing my favorite topic these days: CRISPR-CAS system
  • Koonin discussing his paper on early finding of crispr elements
  • Prediction: A Nobel in the near future will go for work on CRISPR/CAS system of adaptive immunity in bacteria / archaea
  • Koonin discussing the journal he helped start called Biology Direct which is both  and has open review
  • Koonin has a new Book: The Logic of Chance: The Nature and Origin of Biological Evolution: ProQuest Tech Books

After Koonin was done, everyone dispersed.  I wandered around and took some pics:

Magical mushrooms
Sloan Urinal (inside joke about http://microbe.net
????

I went back to my motel room for a little bit and then headed down to Eel Pond for a Course BBQ.

Deck for party
Deck for party

Photosynth stiched together pic
Eel pond

Party
Party
Party

I then headed in to town where my friend Nipam Patel was having a party for the Embryology Course he was teaching.  And I hung out as his house for a bit and then went back to my room.

Day 4: Home

Got up late.  Checked out.  Wandered into town with my suitcase.  Took some pics.

And after some internal debate, decided to switch my flight to return that day rather than go visit relatives in Boston (sorry Diana, Hal — just wanted to get home).  So I took the Bonanza Bus to Logan – discovered that Karl Stetter was also going on the bus to Logan.  I tried to watch the US-Brasil women’s soccer game on my iPad using the wireless they have on the bus but it was choppy.  So I just followed updates on the game – and even that was exciting.

Here are my tweets from the day:

——–
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.

——–

Fun with a scanner – 1998 press release from Wellcome Trust re: Celera

Just found this in an old folder on a different topic.  It is a press release from the Wellcome Trust that was handed out at the Cold Spring Harbor Genomes Meeting in 1998 in response to the announcement from Venter et al. that they were starting a company to sequence the human genome.

——–
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.

——–

#UCDavis to partner with the Beijing Genome Institute (BGI)

Well, it is now formal so I guess I can post about it here.  UC Davis is officially developing a genomics partnership with the Beijing Genomics Institute (BGI).

For more on this breaking news see

Not much detail there I know – but in essence the plan is to build a partnership between UC Davis and BGI with BGI provided genomics and informatics expertise and capabilities and Davis providing biological expertise and diversity (of course, Davis has some genomics chops too and BGI does some biology but you probably get the point). 
For those who do not know, BGI is a relative newcomer on the block in terms of large scale genomics research institutes.  But by being new they have had a massive advantage in a way in that they are really the first to be developed as a “Second-generation Genome Center” having been built / developed with the new second generation sequencing systems at its core.  Thus while other large centers around the world have tried to adapt to the new second generation sequencing systems, BGI started from scratch and could build it’s enterprise around the new systems.  
I am excited about the possible connections with BGI though I confess I do not know a whole lot about the plans.  There have been lots of whisperings here at Davis about building a partnership with BGI and people have been a bit nervous about word getting out too early.  So, though I have heard some details I have not been an active part of the discussions.  However, whatever the plans are I am looking forward to interactions with BGI.  They are really pushing the frontiers of genome sequencing in many ways.  And despite the moans and groans from many people, I do not think genome sequencing is on a downward slope in any way.  For example, as a tool in studying microbes, genome sequencing still has many many years of use – after all there are hundreds of millions of microbial species that have yet to be studied and each one has lots of intraspecific diversity (e.g., across geography) to be characterized.  
And as a UC Davis faculty member I think BGI picked a great place to work with.  Davis has an almost unprecedented diversity of faculty working on some area in the life sciences – and these faculty come from across campus from the College of Biological Sciences, School of Medicine, Viticulture and Enology, School of Veterinary Medicine, College of Agriculture and Environmental Sciences, College of Engineering, School of Nursing, and College of Letters and Sciences.  In fact, you could say – in a way – UC Davis is a campus more dedicated to Life Sciences than almost any other place in the world.  
This development is just one of many that make me impressed with the new UC Davis Administration.    Ever since Chancellor Katehi came on board I have been pleased with almost every major initiative and development and administrative hire on campus.  Sure – the budget cuts from the California government hurt.  But in challenging times, you need great leadership.  And we certainly have it at UC Davis these days.  And if you think I am just sucking up, you should read some of the things I wrote about our previous administration.  I really am impressed here.  
I do not know what will happen with the BGI – UC Davis partnership.  Right now it is just a plan.  But I will do what I can to help it succeed and I am looking forward to interactions with BGI and the bright future at UC Davis. 
——–
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.

——–

Alternative Real Time Twitter Feed for #AGBT #Experiment

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#AGBT’, interval: 6000, title: ‘Marco Island AGBT Meeting tweets’, subject: ‘Genomics Live’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: true, loop: false, live: false, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘all’ } }).render().start();

——–
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.

——–

Tracking Advances in Genome Biology & Technology meeting w/ Twitter Widget: #AGBT

Just a little experiment here seeing if this twitter widget tracks #AGBT tweets in real time …

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#AGBT’, interval: 6000, title: ‘AGBT Meeting’, subject: ‘Genomics Live’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: false, loop: true, live: true, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘default’ } }).render().start();

——–
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.

——–

IQ Test for bacteria

ResearchBlogging.org

Social IQ of bacteria

Another quick one here.  Interesting paper out in BMC Genomics: Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

The paper is from Eshel-Ben Jacob and colleagues from many institutions around the world.

Here is a summary of the article (from the paper)

Background

The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium.

Results

The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes.

Conclusions

These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.

The organism is certainly interesting.  See http://en.wikipedia.org/wiki/Paenibacillus_vortex for more detail (Eshel-Ben Jacob told me he updated the site).

But perhaps more interesting is the concept that Eshel-Ben Jacob has been pushing on bacterial social intelligence.  See for more detail:

The main idea behind this is to look at social communication strategies as a measure of intelligence.  And from a genomics point of view one can measure the genetic diversity of genes likely involved in these processes.  Such counting of genes is not the most useful thing in the world but more important, these organisms really have some fascinating behaviors and in the end we should measure behavior diversity not genomic diversity of putative social genes to measure “bacterial IQ”. 

Sirota-Madi, A., Olender, T., Helman, Y., Ingham, C., Brainis, I., Roth, D., Hagi, E., Brodsky, L., Leshkowitz, D., Galatenko, V., Nikolaev, V., Mugasimangalam, R., Bransburg-Zabary, S., Gutnick, D., Lancet, D., & Ben-Jacob, E. (2010). Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments BMC Genomics, 11 (1) DOI: 10.1186/1471-2164-11-710

——–
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.

——–

Nature’s publishing machine really wants you to pay for stuff, even if it is supposed to be free #OA #fb

Well, this is annoying. I recently published a paper in Nature for which I was senior and corresponding author on “A phylogeny driven genomic encyclopedia of bacteria and archaea.” Though I did not want to submit it to Nature, the project involved a large large large number of other people and in fairness to their contribution to the project I agreed to submit it to Nature. However, the reason I agreed in the end was that Nature said they would use their Genome Paper open license for it. For papers reporting genome sequence data, Nature claims to make the papers available at no charge and supposedly uses a Creative Commons license for publishing the paper. In addition, I note, that as the work was done my many US Government employees, we did not sign over Copyright to Nature.

On the html version of the paper, this “semi-openness” of the paper is described:

“This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.”

Other than the strange spelling of license, this seems good. However, Nature’s machine seems to not be set up to make the copyright/license issues clear in every place/way. For example: if you go to the Nature site for my paper, it seems Nature is now claiming Copyright for the paper. For example see the PDF here.

And then if you click on the “Rights” link from the paper you get this which makes no mention of the Creative Commons license:
But wait. It gets better. If you go through the rights page and fill out the form asking to use the paper in an academic setting, you find out it will cost hundreds of dollars to use, according to this:

I suppose you could say that this all could be part of the Nature publishing machine just making a mistake here or there.  In fact, I would bet that this is in essence what has happened.  The system is designed for articles for which Nature holds the Copyright and has the rights to sell.  And the papers that do not follow that model get caught up in the machinery.  Nevertheless, it is annoying.  And it  makes me worry a bit about what is going to happen with Nature’s new supposedly “open access” journal “Scientific Reports” which actually is not quite as open as it might seem. (The journal uses a somewhat restrictive Creative Commons license which does not fit the standard definition of “Open Access”).

This seems to be YARFOA – Yet another reason for (full) open access.  If you set something free, even if someone claimed they had rights to it, it would seem more obvious to everyone out there that such a claim would be inappropriate.

I note – I am not saying Nature is trying to steal rights here.  In fact, in the past Nature has done a decent job at making sure that papers that were supposed to be available at no cost were.  For example, I looked into papers I published in Nature that Nature told us would be freely available for ever more?  This is what we were told for papers reporting genome sequence data years ago.  It was a very nice policy of Nature’s that helped spread knowledge about genome papers and also helped convince me publishing in Nature was not so bad in terms of openness while I was starting to become a more openaccess advocate.  So I decided to take a look at some of the papers that I was an author on that were supposedly made freely available forever.  Here is a sampling:

Every once in a while, I had noticed in the past some of these papers were not freely available and Nature quickly corrected this so I do think they are trying not to violate their commitments.  But again, in their system, buying access is a key component and alas if the switch is going to be set wrong, it seems that it is set on “you have to pay for this” as a default.  I hope they use a different default setting for their new semi-open journal ….  
Meanwhile, if you want to do something non -commercial with our paper, feel free to do so, regardless of what the Nature website says.  
——–
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.

——–