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Items: 1 to 20 of 120

1.

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.

Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO.

Nucleic Acids Res. 2007;35(21):7188-96. Epub 2007 Oct 18.

2.

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO.

Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. doi: 10.1093/nar/gks1219. Epub 2012 Nov 28.

3.

The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.

Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R.

Syst Appl Microbiol. 2008 Sep;31(4):241-50. doi: 10.1016/j.syapm.2008.07.001. Epub 2008 Aug 9.

PMID:
18692976
4.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO.

Nucleic Acids Res. 2014 Jan;42(Database issue):D643-8. doi: 10.1093/nar/gkt1209. Epub 2013 Nov 28.

5.

25 years of serving the community with ribosomal RNA gene reference databases and tools.

Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, Bruns G, Yarza P, Peplies J, Westram R, Ludwig W.

J Biotechnol. 2017 Jun 23. pii: S0168-1656(17)31494-3. doi: 10.1016/j.jbiotec.2017.06.1198. [Epub ahead of print]

6.

probeBase: an online resource for rRNA-targeted oligonucleotide probes.

Loy A, Horn M, Wagner M.

Nucleic Acids Res. 2003 Jan 1;31(1):514-6.

7.
8.

Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.

Amaral-Zettler L, Peplies J, Ramette A, Fuchs B, Ludwig W, Glöckner FO.

Syst Appl Microbiol. 2008 Sep;31(4):258-68. doi: 10.1016/j.syapm.2008.08.004.

PMID:
18922366
9.

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.

10.

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.

Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D294-6.

11.

A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes.

Peplies J, Kottmann R, Ludwig W, Glöckner FO.

Syst Appl Microbiol. 2008 Sep;31(4):251-7. doi: 10.1016/j.syapm.2008.08.003. Epub 2008 Sep 10.

PMID:
18786793
12.

An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).

Wu D, Hartman A, Ward N, Eisen JA.

PLoS One. 2008 Jul 2;3(7):e2566. doi: 10.1371/journal.pone.0002566. Erratum in: PLoS ONE. 2008;3(7). doi: 10.1371/annotation/c1aa88dd-4360-4902-8599-4d7edca79817.

13.

V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets.

Hartmann M, Howes CG, Veldre V, Schneider S, Vaishampayan PA, Yannarell AC, Quince C, Johansson P, Björkroth KJ, Abarenkov K, Hallam SJ, Mohn WW, Nilsson RH.

FEMS Microbiol Lett. 2011 Jun;319(2):140-5. doi: 10.1111/j.1574-6968.2011.02274.x. Epub 2011 Apr 27.

14.

SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

Pruesse E, Peplies J, Glöckner FO.

Bioinformatics. 2012 Jul 15;28(14):1823-9. doi: 10.1093/bioinformatics/bts252. Epub 2012 May 3.

15.

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.

Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM; Ribosomal Database Project.

Nucleic Acids Res. 2003 Jan 1;31(1):442-3.

16.

Automatic identification of large collections of protein-coding or rRNA sequences.

Arigon AM, Perrière G, Gouy M.

Biochimie. 2008 Apr;90(4):609-14. Epub 2007 Sep 2.

PMID:
17920750
17.

A new version of the RDP (Ribosomal Database Project).

Maidak BL, Cole JR, Parker CT Jr, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR.

Nucleic Acids Res. 1999 Jan 1;27(1):171-3.

18.

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA.

BMC Bioinformatics. 2010 Jun 12;11:317. doi: 10.1186/1471-2105-11-317.

19.

The RDP-II (Ribosomal Database Project).

Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM.

Nucleic Acids Res. 2001 Jan 1;29(1):173-4.

20.

ARB: a software environment for sequence data.

Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH.

Nucleic Acids Res. 2004 Feb 25;32(4):1363-71. Print 2004.

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