Publications in peer-reviewed journals
We continuously collaborate with academia on scientific and infrastructure projects as documented by the following publications.
2012
Quast C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F.O. Glöckner.
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Nuc. Acids Res. 2012 (published online November 28, 2012)
doi: 10.1093/nar/gks1219
project webpage: 
http://www.arb-silva.de
Klindworth A., E. Pruesse, T. Schweer, J. Peplies, C. Quast, M. Horn, and F.O. Glöckner.
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nuc. Acids Res. 2012 (published online August 28, 2012)
doi: 10.1093/nar/gks808
Teeling H., B.M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C.M. Bennke, et al.
Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 2012, 336:608-611
doi: 10.1126/science.1218344
project webpage: http://www.mimas-project.de
Bulgarelli D., M. Rott, K. Schlaeppi, E. van Themaat, A. Ahmadinejad, F. Assenza, et al.
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 2012, 488:91-95
doi:10.1038/nature11336
Pruesse E., J. Peplies, and F.O. Glöckner.
SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012, 28:1823-1829
doi: 10.1093/bioinformatics/bts252
project webpage: http://www.arb-silva.de/aligner
Ionescu D., C. Siebert, L. Polerecky, Y.Y. Munwes, C. Lott, S. Häusler, at el.
Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea. PLoS ONE 2012, 7: e383192012
doi:10.1371/journal.pone.0038319
2011
Yilmaz P., R. Kottmann, D. Field, R. Knight, J.R. Cole, L. Amaral-Zettler, et al.
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology 2011, 29:415-420
doi:10.1038/nbt.1823
project webpage: http://gensc.org/gc_wiki/index.php/MIMARKS
Siegl A., J. Kamke, T. Hochmuth, J. Piel, M. Richter, C. Liang, T. Dandekar, and U. Hentschel.
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. The ISME Journal 2011, 5:61-70 (published online July 8, 2010)
doi:10.1038/ismej.2010.95
2009
Poitelon J.B., M. Joyeux, B. Welté, J. P. Duguet, J. Peplies, and M.S. DuBow.
Identification and phylogeny of eukaryotic 18S rDNA phylotypes detected in chlorinated finished drinking water samples from three Parisian surface water treatment plants. Letters in Applied Microbiology 2009, 49:589-95
doi:10.1111/j.1472-765X.2009.02710.x
Valenza G., S. Veihelmann, J. Peplies, D. Tichy, M. del C. Roldan-Pareja, U. Schlagenhauf, and U. Vogel.
Microbial changes in periodontitis successfully treated by mechanical plaque removal and systemic amoxicillin and metronidazole. International Journal of Medical Microbiology 2009, 299:427-38
doi:10.1016/j.ijmm.2009.03.001
2008
Amaral-Zettler L., J. Peplies, A. Ramette, B. Fuchs, W. Ludwig, and F.O. Glöckner.
Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany. Systematic and Applied Microbiology 2008, 31:258-68
doi:10.1016/j.syapm.2008.08.004
project webpage: http://www.arb-silva.de/projects/rrna-workshop/
Peplies J., R. Kottmann, W. Ludwig, and F.O. Glöckner.
A Standard Operating Procedure for Phylogenetic Inference (SOPPI) using (rRNA) marker genes. Systematic and Applied Microbiology 2008, 31:251-7
doi: 10.1016/j.syapm.2008.08.003
project webpage: http://www.arb-silva.de/projects/soppi
Yarza P., M. Richter, J. Peplies, J. Euzeby, R. Amann, K. H. Schleifer, W. Ludwig, F.O. Glöckner, and R. Rossello-Mora.
The All-Species Living Tree Project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Systematic and Applied Microbiology 2008, 31:241-50
doi: 10.1016/j.syapm.2008.07.001
project webpage: http://www.arb-silva.de/projects/living-tree
Richter M., T. Lombardot, I. Kostadinov, R. Kottmann, M. B. Duhaime, J. Peplies, and F.O. Glöckner.
JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 2008, 9:177
doi: 10.1186/1471-2105-9-177
project webpage: http://www.megx.net/jcoast
2007
Pruesse E., C. Quast, K. Knittel, B. Fuchs, W. Ludwig, J. Peplies, and F.O. Glöckner.
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nuc. Acids Res. 2007, Vol. 35:7188-96
doi: 10.1093/nar/gkm864
project webpage: http://www.arb-silva.de
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