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Items: 1 to 20 of 33

1.

The DNA bank network: the start from a german initiative.

Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW.

Biopreserv Biobank. 2011 Mar;9(1):51-5. doi: 10.1089/bio.2010.0029.

PMID:
24850206
2.

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.

Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC.

Nucleic Acids Res. 2012 Jan;40(Database issue):D571-9. doi: 10.1093/nar/gkr1100. Epub 2011 Dec 1.

3.

Complete genome sequence of Mahella australiensis type strain (50-1 BON).

Sikorski J, Teshima H, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Ngatchou-Djao OD, Rohde M, Pukall R, Spring S, Abt B, Göker M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP, Lapidus A.

Stand Genomic Sci. 2011 Jul 1;4(3):331-41. doi: 10.4056/sigs.1864526. Epub 2011 Jun 30.

4.

Bacterial Catabolism of Dimethylsulfoniopropionate (DMSP).

Reisch CR, Moran MA, Whitman WB.

Front Microbiol. 2011 Aug 12;2:172. doi: 10.3389/fmicb.2011.00172. eCollection 2011.

5.

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti.

Maclean AM, Haerty W, Golding GB, Finan TM.

Microbiology. 2011 Sep;157(Pt 9):2522-33. doi: 10.1099/mic.0.050542-0. Epub 2011 Jun 23.

PMID:
21700663
6.

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
7.

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
8.

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
9.

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.

10.

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.

11.

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR.

Appl Environ Microbiol. 2009 Apr;75(7):2046-56. doi: 10.1128/AEM.02294-08. Epub 2009 Feb 5.

12.

The ether-cleaving methyltransferase system of the strict anaerobe Acetobacterium dehalogenans: analysis and expression of the encoding genes.

Schilhabel A, Studenik S, Vödisch M, Kreher S, Schlott B, Pierik AJ, Diekert G.

J Bacteriol. 2009 Jan;191(2):588-99. doi: 10.1128/JB.01104-08. Epub 2008 Nov 14. Erratum in: J Bacteriol. 2009 Mar;191(6):1994. Pierik, Antonio Y [corrected to Pierik, Antonio J].

14.

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
15.

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.

16.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Zerbino DR, Birney E.

Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.

17.

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.

18.

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.

19.

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.

PMID:
15223320
20.

Rfam: an RNA family database.

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

Nucleic Acids Res. 2003 Jan 1;31(1):439-41.

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