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Complete genome sequence of Kytococcus sedentarius type strain (541).

Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Mavrommatis K, Chen A, Palaniappan K, D'haeseleer P, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Schneider S, Göker M, Pukall R, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2009 Jul 20;1(1):12-20. doi: 10.4056/sigs.761.


Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses.

Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R.

Syst Appl Microbiol. 2010 Oct;33(6):291-9. doi: 10.1016/j.syapm.2010.08.001.


Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum.

Lu YK, Marden J, Han M, Swingley WD, Mastrian SD, Chowdhury SR, Hao J, Helmy T, Kim S, Kurdoglu AA, Matthies HJ, Rollo D, Stothard P, Blankenship RE, Bauer CE, Touchman JW.

BMC Genomics. 2010 May 25;11:325. doi: 10.1186/1471-2164-11-325.


How many bootstrap replicates are necessary?

Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A.

J Comput Biol. 2010 Mar;17(3):337-54. doi: 10.1089/cmb.2009.0179.


The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC.

Nucleic Acids Res. 2010 Jan;38(Database issue):D346-54. doi: 10.1093/nar/gkp848. Epub 2009 Nov 13.


A rapid bootstrap algorithm for the RAxML Web servers.

Stamatakis A, Hoover P, Rougemont J.

Syst Biol. 2008 Oct;57(5):758-71. doi: 10.1080/10635150802429642.


Interaction of the signal transduction protein GlnJ with the cellular targets AmtB1, GlnE and GlnD in Rhodospirillum rubrum: dependence on manganese, 2-oxoglutarate and the ADP/ATP ratio.

Teixeira PF, Jonsson A, Frank M, Wang H, Nordlund S.

Microbiology. 2008 Aug;154(Pt 8):2336-47. doi: 10.1099/mic.0.2008/017533-0.


Comparative proteomic studies in Rhodospirillum rubrum grown under different nitrogen conditions.

Selao TT, Nordlund S, Norén A.

J Proteome Res. 2008 Aug;7(8):3267-75. doi: 10.1021/pr700771u. Epub 2008 Jun 21.


The minimum information about a genome sequence (MIGS) specification.

Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.

Nat Biotechnol. 2008 May;26(5):541-7. doi: 10.1038/nbt1360.


The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.

Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. Epub 2007 Oct 12.


Specificity and regulation of interaction between the PII and AmtB1 proteins in Rhodospirillum rubrum.

Wolfe DM, Zhang Y, Roberts GP.

J Bacteriol. 2007 Oct;189(19):6861-9. Epub 2007 Jul 20.


Identifying bacterial genes and endosymbiont DNA with Glimmer.

Delcher AL, Bratke KA, Powers EC, Salzberg SL.

Bioinformatics. 2007 Mar 15;23(6):673-9. Epub 2007 Jan 19.


Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL.

Appl Environ Microbiol. 2006 Jul;72(7):5069-72.


List of new names and new combinations previously effectively, but not validly, published.

[No authors listed]

Int J Syst Evol Microbiol. 2006 Jan;56(Pt 1):1-6. Erratum in: Int J Syst Evol Microbiol. 2006 Mar;56(Pt 3):677.


CooA, a paradigm for gas sensing regulatory proteins.

Roberts GP, Kerby RL, Youn H, Conrad M.

J Inorg Biochem. 2005 Jan;99(1):280-92. Review.


Improved prediction of signal peptides: SignalP 3.0.

Bendtsen JD, Nielsen H, von Heijne G, Brunak S.

J Mol Biol. 2004 Jul 16;340(4):783-95.


Multiple sequence alignment using partial order graphs.

Lee C, Grasso C, Sharlow MF.

Bioinformatics. 2002 Mar;18(3):452-64.


Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Krogh A, Larsson B, von Heijne G, Sonnhammer EL.

J Mol Biol. 2001 Jan 19;305(3):567-80.


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