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Items: 16

1.

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.

2.

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.

Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC.

Nat Methods. 2010 Jun;7(6):455-7. doi: 10.1038/nmeth.1457. Epub 2010 May 2.

PMID:
20436475
3.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA.

Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

4.

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.

PMID:
18853362
5.

Catenulispora subtropica sp. nov. and Catenulispora yoronensis sp. nov.

Tamura T, Ishida Y, Otoguro M, Suzuki K.

Int J Syst Evol Microbiol. 2008 Jul;58(Pt 7):1552-5. doi: 10.1099/ijs.0.65561-0.

PMID:
18599693
6.

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.

7.

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.

Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC.

Nucleic Acids Res. 2008 Jan;36(Database issue):D475-9. Epub 2007 Nov 2.

8.

Catenulispora rubra sp. nov., an acidophilic actinomycete isolated from forest soil.

Tamura T, Ishida Y, Sakane T, Suzuki K.

Int J Syst Evol Microbiol. 2007 Oct;57(Pt 10):2272-4. Erratum in: Int J Syst Evol Microbiol. 2007 Dec;57(Pt 12):2979.

PMID:
17911295
9.

Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales.

Cavaletti L, Monciardini P, Schumann P, Rohde M, Bamonte R, Busti E, Sosio M, Donadio S.

Int J Syst Evol Microbiol. 2006 Aug;56(Pt 8):1747-53.

PMID:
16902002
10.

Catenulispora acidiphila gen. nov., sp. nov., a novel, mycelium-forming actinomycete, and proposal of Catenulisporaceae fam. nov.

Busti E, Cavaletti L, Monciardini P, Schumann P, Rohde M, Sosio M, Donadio S.

Int J Syst Evol Microbiol. 2006 Aug;56(Pt 8):1741-6.

PMID:
16902001
11.

Antibiotic-producing ability by representatives of a newly discovered lineage of actinomycetes.

Busti E, Monciardini P, Cavaletti L, Bamonte R, Lazzarini A, Sosio M, Donadio S.

Microbiology. 2006 Mar;152(Pt 3):675-83.

PMID:
16514148
12.

Laboratory cultivation of widespread and previously uncultured soil bacteria.

Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH.

Appl Environ Microbiol. 2003 Dec;69(12):7210-5.

13.

Multiple sequence alignment using partial order graphs.

Lee C, Grasso C, Sharlow MF.

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

PMID:
11934745
14.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G.

Nat Genet. 2000 May;25(1):25-9. No abstract available.

15.
16.

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

Woese CR, Kandler O, Wheelis ML.

Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9.

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