Tag: open access

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

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

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

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

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

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

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

——–

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.

——–

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.

——–

A must read for anyone interested in #OpenScience: Peter Suber’s review of 2010

Some ego surfing (i.e., searching for my own name) led me to discover a very useful resource / summary of open access advances from 2010.  The resource is a posting from Peter Suber from the SPARC Open Access newsletter from 1/2/2011.  I found out about the posting from here: BioSharing: Top 10 openness advances of 2010 – BioTorrents because they noted that something from my lab was one of the picks …

Suber, if you do not know, is one of the sages of Open Access having been promoting and discussing and working on Open Access for many many years.  In the post, he discusses what he calls “a
feast of the OA highlights from 2010″.  The whole post is worth reading are here is a summary:

Top 10 advances

  • (1) Open access policies at funding agencies
  • (2) Open access policies at universities
  • (3) Some growth numbers
  • (4) Open access archiving (green OA)
  • (5) Open access journals (gold OA)
  • (6) Data
    • I note in this section he says “The most exciting new open-data platform in 2010 was BioTorrents from Morgan Langille and Jonathan Eisen, a P2P data-sharing service for biology using BitTorrent.  Something like this will be needed in every field where researchers need to share not just megabytes or gigabytes, but terabytes and petabytes.”
    • That made my month – see our PLoS One paper on it here. 
  • (7) Books and digitization
  • (8) Copyright and licensing
  • (9) Effects of the recession
  • (10) Some highlights of the highlights

The last section is particularly entertaining as he discusses the worst and best of 2010

  • Worst includes 
    • James Murdoch objecting to the British Library opening up its archives;
    • English Heritage for claiming to own the copyright on Stonehenge,
    • Todd Platts, Republican representative from Pennsylvania for an inane copyright idea
    • Supposedly OA journals not using actual OA licenses
    • BP, for a very non open contract for research relating to the oil spill
  • Best includes
    • Biotorrents
    • Obama White House
    • UC standing up to Nature
    • many new OA mandates around the world
    • many others
He also posts links to his discussions from previous years.  Anyone interested in OA really should read his full post …
——–
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.

——–

YARFOA: Yet another reason for #OpenAccess: speeding innovation in aquaculture

Just saw this interesting paper arguing that open access to literature is critical for the field of aquaculture. The paper argues that open access to literature has accelerate innovation by promoting more partnerships with hobbyists and with others who might normally be outside the “inner circle.” Definitely worth a read and it fits under my “YARFOA” category – Yet Another Reason For Open Access.

The paper is “The importance of open access in technology transfer for marine ornamental aquaculture: The case of hobbyist-led breeding initiatives” from the Journal Aquaculture, Aquarium, Conservation & Legislation International Journal of the Bioflux Society.

It is is by Andrew Rhyne who is connected with the New England Aquarium and also at Roger Williams University.

I love the concluding paragraph by the way:

Opening the door to an open process. I would hope that others would join me in supporting the free flow of information by publishing their work in open access journals, and encouraging societies like the World Aquaculture Society, the American Fisheries Society, and European Aquaculture Society to go to an open access format. We should fully applaud blogging or posting on discussion forums in real time about efforts to rear new species or develop new live feeds. The dialog that occurs on MOFIB and other online forums can spark innovation that is not possible through traditional formats. I believe that open access is the key to faster breakthroughs, and to better translation between academia, hobbyists, and commercial industry. The Aquaculture field has an opportunity to become an exemplary model for all applied science fields: let’s seize 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.

——–

Figuring out figures in scientific papers: new search / ranking method outline in PLoS One paper

Just a quick post here.  A colleague just sent me a link to her fascinating new paper in PLoS One: PLoS ONE: Automatic Figure Ranking and User Interfacing for Intelligent Figure Search

In this paper Hong Yu from the University of Wisconsin in Milwaukee describes a system for better automated characterization of figures from scientific papers.  The system is available through their webserver “Ask Hermes“.

If you want to learn more about the system I suggest you read the paper.  Or watch their video.

Basically the general idea is summarized in their background section of the abstract:

Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.

I particularly like that they also allow searching just for open access figures, which may be of significant value to people who want to do things like make a slide presentation with no copyrighted/protected material in it.  For example see the results of a search for open access figures using the keyword phylogenomics.

Anyway – definitely worth checking this out.

Yu, H., Liu, F., & Ramesh, B. (2010). Automatic Figure Ranking and User Interfacing for Intelligent Figure Search PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0012983

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

——–

Interesting take on peer review & openness from outside the sciences in @nytimes

I assume many supporters of open science may have seen this already but if not it is worth a look.  The New York Times had an interesting article on Monday by Patricia Cohen: For Scholars, Web Changes Sacred Rite of Peer Review.

The article starts off with a familiar refrain

For professors, publishing in elite journals is an unavoidable part of university life. The grueling process of subjecting work to the up-or-down judgment of credentialed scholarly peers has been a cornerstone of academic culture since at least the mid-20th century.

It follows with a very important discussion focusing on how the web can transform scholarly publishing.  For example:

… scholars have begun to challenge the monopoly that peer review has on admission to career-making journals and, as a consequence, to the charmed circle of tenured academe. They argue that in an era of digital media there is a better way to assess the quality of work. Instead of relying on a few experts selected by leading publications, they advocate using the Internet to expose scholarly thinking to the swift collective judgment of a much broader interested audience.

This likely will sound very familiar to those who have read my blog, those who follow the discussions on peer review, or those with a pulse in the scientific community.  But there is a catch that caught me off guard here and might surprise many of you.  This catch is highlighted by the fact that the article was in the Arts section of the Times.  You see, the article was about transformation in the humanities.  Seems as though there is an almost completely parallel universe there where peer review and publishing and sharing are all getting re-evaluated.

This is yet another case of why we need more cross talk between the arts/humanities and the sciences.  For example, the article discusses how the journal Shakespeare Quarterly is becoming the first humanities journal to “open its reviewing to the World Wide Web.” They even recently conducted an experiment in fully open review where four preprints were posted on the web and feedback was solicited.  The feedback was then used by editors to guide the revision of the preprints to become published articles.  Sounds a lot like Biology Direct.  Note however, that they are not talking about publishing the final articles in an open access manner (see discussion of this on BigThink here) – but more about engaging the broader audience in commentary before an article is published.

The article does suggest that perhaps the humanities are lagging a bit behind the sciences in experimenting with new forms of peer review but I think that is OK.  We desperately need new experiments and ideas in this arena.  Peer review, at least the way it operates right now, has many problems.  I think there must be many better ways to go about things.  And thus cross pollination across fields from arts and humanities to economics to physics to life sciences is a good thing.

Interestingly Cohen identifies what she considers to be the most daunting obstacle to opening up review:

peer-review publishing is the path to a job and tenure, and no would-be professor wants to be the academic canary in the coal mine.

I think this is the same main obstacle in the sciences.  That is, it is our system of promotion and tenure and hiring that is the main roadblock.

Finally, I note that though the article was focusing mostly on opening up peer review, it does have some interesting bits on openness in general. In particular, there is a great line at the end from Dan Cohen from George Mason

“There is an ethical imperative to share information,” said Mr. Cohen, who regularly posts his work online, where he said thousands read it. Engaging people in different disciplines and from outside academia has made his scholarship better, he said.

I could not agree more.  Seems like the arts and humanities and sciences actually have much much more in common that many might think.

For some related posts from the web see

Some recent web stuff on peer review in the sciences
——–
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.

——–

Scooped in a good way by my own brother re Nature-UC dispute

Well, I so wanted to write a piece about the Nature-UC dispute going on right now. In summary, a group from the University of California (University Committee on Library and Scholarly Communication (UCOLASC) including librarians and scientists and various others circulated a letter a few days ago to UC faculty suggesting a possible boycott of Nature journals due in large part to impending price increases. The letter became public (see for example here). Some News stories were written. Some blogs and many tweets were posted (including mine, wondering why I had not heard anything about the whole issue before). Nature responded. UC responded back. More news stories were written (e.g., SJ Mercury news here) and more blogs and tweets came out.
But something was missing in the whole thing from my point of view. What was missing was a discussion of how this whole discussion should not really be about UC vs. Nature.  It should be about how the publishing systems right now is broken – about how we should expect commercial publishers to want to make money and how what we need to do as scientists is to take control of publishing to make it more open and to save taxpayer’s money because we do not really need many of the broken parts of the publishing system.

And it should not have really been about Nature vs. UC – Nature to me is not the issue here.  I personally would not have gone after Nature in the way the UC library group did.  Nature does some good things and some bad things.  As do many, if not all publishers, even, God forbid, PLoS.  Nature in fact has been doing some useful experimenting with some nice web/open science features.  We should neither expect them to do good things or bad things.  What we need to do is think about the whole system of publishing, not just go after one publisher.

Fortunately, before I wrote this up, I found a blog post that covers many of my feelings on the issue. And it just happens to be by my brother, Michael (CoFounder of PLoS), who is traveling on the East Coast and who I have not had a chance to talk to at all about the Nature-UC issue. So I recommend people go to his post: The Nature kerfuffle: boycott the business model not the price

I am not saying I agree with every sentiment in his post but the key part to me is:

“It’s time for UC to follow suit. Rather than haggling over prices, the faculty, students, staff and administration of all ten UC campuses should unite to end the business practices that empower NPG and other publishes to regularly attempt to extort money from our chronically cash-strapped library system.”

I have little to add to this so will leave it there.   Read his post for more.
——————————————–
Here are some links about the UC-Nature dust up

——–
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: getting more & more support incl. from #UCDavis

Everyone interested in science should take a look at the press release from the “Alliance for Taxpayer Access.” The release discusses how “Major research institution leaders support legislation to ensure public access to publicly funded research”. I am quoting much of the release here because I think it is very valuable:

The provosts and presidents of 27 major private and public research institutions have voiced their support for the Federal Research Public Access Act in an “Open Letter to the Higher Education Community,” released Friday by the Harvard University Provost. The Act, first introduced in the Senate last year, was introduced in the House of Representatives on April 15. The letter signals expanded support for public access to publicly funded research among the largest research institutions in the U.S.

The letter reads, in part:

“As scholars and university administrators, we are acutely aware that the present system of scholarly communication does not always serve the best interests of our institutions or the general public. Scholarly publishers, academic libraries, university leaders, and scholars themselves must engage in an ongoing dialogue about the means of scholarly production and distribution. This dialogue must acknowledge both our competing interests and our common goals. The passage of FRPAA will be an important step in catalyzing that dialogue, but it is not the last one that we will need to take.

For the full letter see “The Open Letter to the Higher Education Community” is available at http://osc.hul.harvard.edu/docs/FRPAA-open-letter-2010.php.

I am very very happy to note that UC Davis is one of the signatories (represented by Provost Enrique Lavernia).  This is a good change of pace as one of our previous vice-provosts Barbara Horwitz was an extreme anti-open access advocate.

And if you want your institution to be added to the list of supporters, talk to your administrators and get them to register their support here.  Seems to me that many should want to get on board.

Hat tip to Michael Rogawski from the UC Davis Department of Neurology for pointing this out.

——–
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.

——–

ISI – late to index #PLoS One but now marketing that they do so

Well, just a mini post here. In case you did not know – PLoS One is now being indexed by ISI (see their announcement: PLoS ONE and see the PLOS blog post here
and see Erik Svensson’s blog post for an interesting take) and will get an impact factor and be in their Citation Index and all such things. Now mind you, I think “Impact Factor” is a silly thing overall in that we should evaluate papers not journals per se.

So why am I writing this – because I find it pretty funny that despite being slow to recognize PLoS One ISI is now promoting the fact that they are indexing PLoS One on their home page. See the screen capture above.

http://friendfeed.com/treeoflife/fa0c4b0b/isi-late-to-index-plos-one-but-now-marketing-that?embed=1

——–
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.

——–