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Items: 1 to 20 of 27

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.

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
5.

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
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.

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD.

Nucleic Acids Res. 2008 Jan;36(Database issue):D623-31. Epub 2007 Oct 27.

9.

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.

10.

Effects of differing temperature management on development of Actinobacteria populations during composting.

Steger K, Jarvis A, Vasara T, Romantschuk M, Sundh I.

Res Microbiol. 2007 Sep;158(7):617-24. Epub 2007 Jun 9.

PMID:
17683913
11.

RNAmmer: consistent and rapid annotation of ribosomal RNA genes.

Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW.

Nucleic Acids Res. 2007;35(9):3100-8. Epub 2007 Apr 22.

12.

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahrén D, Tsoka S, Darzentas N, Kunin V, López-Bigas N.

Nucleic Acids Res. 2005 Oct 24;33(19):6083-9. Print 2005.

13.

Farmer's lung disease and microbiological composition of hay: a case-control study.

Roussel S, Reboux G, Dalphin JC, Pernet D, Laplante JJ, Millon L, Piarroux R.

Mycopathologia. 2005 Nov;160(4):273-9.

PMID:
16244894
14.

Rfam: annotating non-coding RNAs in complete genomes.

Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4.

15.

Environmental genome shotgun sequencing of the Sargasso Sea.

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO.

Science. 2004 Apr 2;304(5667):66-74. Epub 2004 Mar 4.

16.

Studies on peat and peat microorganism. I. Taxonomic studies on thermophilic Actinomycetes isolated from peat.

KUSTER E, LOCCI R.

Arch Mikrobiol. 1963;45:188-97. No abstract available.

PMID:
13927630
17.

Production and isolation of thermoviridin, an antibiotic produced by Thermoactinomyces viridis n. sp.

SCHUURMANS DM, OLSON BH, SAN CLEMENTE CL.

Appl Microbiol. 1956 Mar;4(2):61-6. No abstract available.

18.

The Pathway Tools software.

Karp PD, Paley S, Romero P.

Bioinformatics. 2002;18 Suppl 1:S225-32.

PMID:
12169551
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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