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Items: 1 to 20 of 23

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.

En route to a genome-based classification of Archaea and Bacteria?

Klenk HP, Göker M.

Syst Appl Microbiol. 2010 Jun;33(4):175-82. doi: 10.1016/j.syapm.2010.03.003. Epub 2010 Apr 20. Review.

PMID:
20409658
4.

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.

PMID:
20377449
5.

Prodigal: prokaryotic gene recognition and translation initiation site identification.

Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ.

BMC Bioinformatics. 2010 Mar 8;11:119. doi: 10.1186/1471-2105-11-119.

6.

Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1.

Takaki Y, Shimamura S, Nakagawa S, Fukuhara Y, Horikawa H, Ankai A, Harada T, Hosoyama A, Oguchi A, Fukui S, Fujita N, Takami H, Takai K.

DNA Res. 2010 Jun;17(3):123-37. doi: 10.1093/dnares/dsq005. Epub 2010 Feb 26.

7.

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.

8.

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.

9.

IMG ER: a system for microbial genome annotation expert review and curation.

Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC.

Bioinformatics. 2009 Sep 1;25(17):2271-8. doi: 10.1093/bioinformatics/btp393. Epub 2009 Jun 27.

PMID:
19561336
10.

Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'.

Jumas-Bilak E, Roudière L, Marchandin H.

Int J Syst Evol Microbiol. 2009 May;59(Pt 5):1028-35. doi: 10.1099/ijs.0.006718-0. Erratum in: Int J Syst Evol Microbiol. 2009 Jul;59(Pt 7):1851.

PMID:
19406787
11.

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
12.

Calditerrivibrio nitroreducens gen. nov., sp. nov., a thermophilic, nitrate-reducing bacterium isolated from a terrestrial hot spring in Japan.

Iino T, Nakagawa T, Mori K, Harayama S, Suzuki K.

Int J Syst Evol Microbiol. 2008 Jul;58(Pt 7):1675-9. doi: 10.1099/ijs.0.65714-0.

PMID:
18599715
13.

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.

14.

EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences.

Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW.

Int J Syst Evol Microbiol. 2007 Oct;57(Pt 10):2259-61.

PMID:
17911292
15.
16.

Enzymology and bioenergetics of respiratory nitrite ammonification.

Simon J.

FEMS Microbiol Rev. 2002 Aug;26(3):285-309. Review.

17.
18.

Inhibition of microbial H2S production in an oil reservoir model column by nitrate injection.

Myhr S, Lillebø BL, Sunde E, Beeder J, Torsvik T.

Appl Microbiol Biotechnol. 2002 Mar;58(3):400-8. Epub 2001 Dec 8.

PMID:
11935194
19.

Multiple sequence alignment using partial order graphs.

Lee C, Grasso C, Sharlow MF.

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

PMID:
11934745
20.

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