Tag: open access pioneer award

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

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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.

——–

Open Access Pioneer Award: Bob Shafer HIV DB

Bob Shafer, an Associate Professor at Stanford, is fighting to make information about HIV freely available. He runs a database called HIVDB that aims to make information about HIV drug resistance available to the broader community. And he has been doing this for years (note – I worked with Bob when I was a PhD student and he was getting HIVDB started – we even wrote a paper together where I helped him do some phylogenetic analysis of HIV). For that alone, Bob deserves an Open Access Pioneer award. But I am giving him one here for a fight he has taken on recently.

You see, a company called Advanced Biological Laboratories, S.A has been suing Shafer and Stanford over a patent dispute. The company seems to be trying to claim to have rights over many (or maybe they think all) uses of using computers to help doctors make medical decisions. And they have been trying to get people to license their IP/software for doing this and one way they appear to be trying to get “users” is by suing them. And Bob is one of the people they have sued.

Sadly, Stanford University appears to have given in to the lawsuits even though their validity is debatable (see The Fight of His Life which provides some of the details – Hat Tip to Bill Hooker and FriendFeed for highlighting this article) and Bob has been left hanging on his own. Instead of caving to the lawsuit and shutting down HIVDB or making it less openly available or requiring people to say they will give commercial rights to Advanced Biological Laboratories for anything they develop using the DB. And rather than cave to the lawsuits Bob is fighting back – with a website called harmfulpatents.org and with a set of letters and communications. Mind you, I know little about IP/patent laws or the legal issues behind this dispute. But if this lawsuit leads to the shutting down or restriction of HIVDB that would be proof enough to me that Advanced Biological Laboratories and the legal system that supports them is doing a disservice to the progress of science.

For his efforts in keeping HIVDB open I am giving Bob Shafer a Open Access Pioneer Award.

For more on this story see
——–
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: Rick Prelinger, Image Access

Just saw an interesting article in the UC Davis “Dateline” newsletter about Rick Prelinger who is the founder of the Prelinger Library in San Francisco (and see their blog here). He gave a talk at Davis and thus they wrote an article about him here.

Some good lines from the article include

Rick Prelinger’s biggest thrill is “mainstreaming” historical documents for public consumption.

But getting history into the hands of the average citizen is no easy task, the archivist says.

Overbearing copyright issues and rampant commercialism, he argues, threaten the free exchange of information on which a knowledge society — especially its libraries — depends.

…

Rather than concern themselves with rigid lending policies or copyright protections, library systems should focus on “more product, less process” to better serve patrons, Prelinger said.

…

“If the Google book deal is approved without any changes, we could soon lose 100 million books that society doesn’t know what to do with,” said Prelinger, referring to “orphan works,” or works under copyright, but whose owner is not known.

….

On the other hand, archives are empowering, Prelinger said. “Let’s open up the past. Interesting things happen when we do so.”

In general since Prelinger has been pushing for more openness in libraries and in images, I am giving him an “Open Access Pioneer Award“.  Sorry I missed the talk but glad I read the article.  

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

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Open Access Pioneer Award #4: Carl Malamud and Public.Resource.Org

This is not about science but I think this guy deserves an award.  I just read an interesting and funny story in the S.F. Chronicle (Sebastopol man puts code manuals online) by Matthew Stannard about Carl Malamud who has been putting building codes, plumbing codes and other codes online at Public.Resource.Org.
Basically, he is doing this because many of the codes are only available for a fee.  He says

“Not everybody is going to read the building code, but everybody who wants to should be able to without putting 100 bucks in the slot,” Malamud said. “Primary legal materials are America’s operating system.”

And though his work has been questioned by some (who would like to make money off of the codes) he appears to be on solid legal ground. 

“It’s very clear in American law that you can’t get intellectual property protection for law,” said Pamela Samuelson, co-director of the UC Berkeley Center for Law and Technology. “Law belongs to everybody.”

So for this work, I am giving Malamud by Open Access Pioneer Award (#4).  Keep up the good work.

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

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Open Access Pioneer Award #3: Joe Derisi

So I was reading the web page of WTOP radio, which I used to listen to all the time in DC and somehow still have their page near the top of my bookmarks. And there was a headline I could not resist. It said: “Malaria Researcher Wins Heinz Award.” As I know a few people studying malaria here and there I had to check it out. And indeed, one of the winners of the award is Joe Derisi, from UCSF, who I know reasonably well and like very much. I am very pleased to see him win one of these Heinz Awards

The Heinz Site says “Joseph DeRisi receives the Heinz Award in Technology, the Economy and Employment for his extraordinary breakthroughs in detecting both new and existing viruses.”

In addition to his science they say

“Joseph DeRisi has made breakthrough discoveries in the laboratory that have provided clarity and insight into the detection of some of the world’s most threatening viruses as well as distinguished himself as a generous and tireless advocate for the free and open sharing of scientific research. With a brilliant mind and expansive heart, he has ennobled the field of science.”

Here here. Derisi is one of the true pioneers of Open Science, not only promoting Open Access publishing but also promoting open sharing of methods, equipment, data, and everything. And, not that he needs another award (to go with his Heinz, his HHMI position, and his Macarthur among many things), but I am giving him my Open Access Pioneer Award #3 for his firm commitment to open science.

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

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Open Access Pioneer Award #2: R. Preston McAfee

Great article in the LA Times on August 18 by Gale Holland about “Free digital textbooks.” (see Free digital texts begin to challenge costly college textbooks in California)

The article discussed some issues in open source textbook publishing including in particular R. Preston McAfee’s work on creating a free online economics textbook. McAfee is a professor at Caltech and is a self described right winger.

“I’m a right-wing economist, so they can’t call me a communist,” McAfee said.

And he goes on to say

“What makes us rich as a society is what we know and what we can do,” he said. “Anything that stands in the way of the dissemination of knowledge is a real problem.”

The article discussed other open source educational materials including:

  • Merlot, from Cal. St. Universities which is a “a searchable collection of peer-reviewed, online multimedia materials.”
  • Connexions, from Rice University , which “stores free, open-licensed educational materials in fields such as music, electrical engineering and psychology.
  • OpenCourseWare from MIT which includes “virtually its entire curricula online — video lectures, problems sets and exams for more than 1,800 courses in 33 disciplines.”
  • Wikibooks, a collection of editable textbooks
  • The Digital Marketplace, from Cal. St. U. which is a “website for selecting, comparing, sharing, approving and distributing both open-source and commercial online educational materials.”
Now, I am not saying here there is not a place for textbooks in the normal model (I have one).  Unlike basic science papers, for which the cost of making a presentable paper is relatively low, the cost of producing a textbook can be very very high.  Thus I think publishers are welcome to work with authors to come up with their own models for how to publish the texts.  But nevertheless, the more we can get good open source textbooks out there, the better off we will be.  And thus, for his role in promoting the release of what seems to be a high quality open source textbook, I am giving R. Preston McAfee my second “Open Access Pioneer Award.

Hat tip to Jeremy Peterson and Eilleen Hamilton for pointing this out.

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

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An Open Access pioneer – Trent Reznor

Normally, everything I write about here is at least indirectly connected to science in some way. However, today I am drifting into the world of music. The New York Times had an article a few days ago about Trent Reznor (Trent Reznor’s Frustration and Fury – Take It. It’s Free). Trent, the brains behind the band Nine Inch Nails (full disclosure – I am a fan of his music), has been railing against the constraints of the music industry for year.

And now he is going even further and in essence putting his music into the public domain as much as possible (see his web site NIN.com for more detail). For example

“Mr. Reznor even posts online all the raw digital tracks from Nine Inch Nails albums for anyone to remix. “I’m done with them,” he said. “Why not?”

And he is doing this even though the $$$ for producing his music does not come from the government. He does it in part because he wants his ideas and music to spread and he wants to contribute to musical development. There are obvious parallels between what he (and others) are doing in music and those who develop Open Source software and those who release their data and publications to be as free as possible. I know I am not the first to discuss this, but just thought I would put it out there.

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

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