Publikationen 2010/2006

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Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer KH, Glöckner FO, Rossello-Mora R (2010) Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst. Appl. Microbiol. 33:291-299 (DOI: 10.1016/j.syapm.2010.08.001)

Wecker P, Klockow C, Schüler M, Dabin J, Michel G, Glöckner FO (2010) Life cycle analysis of the model organism Rhodopirellula baltica SH1T by transcriptome studies. Microbial Biotechnology 3:583-594 (DOI:10.1111/j.1751-7915.2010.00183.x)

10.1038/ismej.2010.6Teeling H, Glöckner FO (2010) Integration von Omics-Daten in der marinen Ökosystemforschung. Laborwelt (4:6-9)

Pena A et al. (2010) Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. Isme J. 4:882-895 (DOI:10.1038/ismej.2010.6)

Meyerdierks A, Glöckner FO (2010) Metagenome Analysis. In: Cock JM, Tessmar-Raible K, Boyen C, Viard F (eds) Introduction to Marine Genomics Springer, Netherlands, pp 33-72 (DOI:10.1007/978-90-481-8639-6)

Lopez-Lopez A, Yarza PRichter M, Suarez-Suarez A, Anton J, Niemann H, Rossello-Mora R (2010) Extremely halophilic microbial communities in anaerobic sediments from a solar saltern. Environmental microbiology reports 2:258-271 (DOI:10.1111/j.1758-2229.2009.00108.x.)

Kyrpides N, Field D, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J (2010) Meeting report from the Genomic Standards Consortium (GSC) workshop 8. SIGS 3:93-96 (DOI:10.4056/sigs.1022942.)

Kottmann RKostadinov I, Duhaime MBButtigieg PL, Yilmaz P, Hankeln WWaldmann JGlöckner FO (2010) Megx.net: integrated database resource for marine ecological genomics. Nucleic Acid Res. 38:D391-D395 (DOI:10.1093/nar/gkp918)

Klockow CKlindworth AÖztürk BWecker PGlöckner FO (2010) From pure cultures to bacterial communities: knowledge generation by expression profiling. Rapp. Comm. int. Mer Médit 39:377 

Hankeln W, Buttigieg PL, Fink D, Kottmann RYilmaz PGlöckner FO (2010) MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. BMC Bioinformatics 11:358 (DOI:10.1186/1471-2105-11-358)

Glöckner J, Kube M, Shrestha PM, Weber MGlöckner FO, Reinhardt R, Liesack W (2010) Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12:1218-1229 (DOI:10.1111/j.1462-2920.2010.02164.x)

Glöckner FO, Joint I (2010) Marine microbial genomics in Europe: current status and perspectives. Microbial Biotechnology 3:523-530 (DOI:10.1111/j.1751-7915.2010.00169.x.)

Glass E, Meyer F, Gilbert JA, Field D, Hunter S, Kottmann R, Kyrpides N, Sansone S, Schriml L, Sterk P, White O, Wooley J (2010) Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10. SIGS 3:225-231 (DOI:10.1111/j.1751-7915.2010.00169.x)

Gilbert JA et al. (2010) The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. SIGS 3:249-253 (DOI:10.4056/aigs.1443528)

Gärdes A, Kaeppel E, Shehzad A, Seebah S, Teeling HYarza P, Glöckner FO, Grossart HP, Ullrich MS (2010) Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism. SIGS 3:97-107 (DOI:10.4056/sigs.922139)

Duhaime MB, Wichels A, Waldmann J, Teeling HGlöckner FO (2010) Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1. Isme J. 5:107-121 (DOI:10.1038/ismej.2010.94)

Davidsen T et al. (2010) Meeting report from the Genomic Standards Consortium (GSC) workshop 9. SIGS 3:216-224 (DOI:10.4056/sigs.1353455.)

Wooley J, Field D, Glöckner FO (2009) Extending Standards for Genomics and Metagenomics Data: A Research Coordination Network for the Genomic Standards Consortium (RCN4GSC). SIGS 1:85-90 (DOI:doi: 10.4056/sigs.26218.)

Wecker P, Klockow C, Ellrott A, Quast C, Langhammer P, Harder J, Glöckner FO (2009) Transcriptional response of the model planctomycete Rhodopirellula baltica SH1T to changing environmental conditions. BMC Genomics 10:410 (DOI:10.1186/1471-2164-10-410)

Strittmatter AW et al. (2009) Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ. Microbiol. 11:1038-1055 (DOI:10.1111/j.1462-2920.2008.01825.x.)

Meyerdierks A, Kube M, Kostadinov I, Teeling H, Glöckner FO, Reinhardt R, Amann R (2009) Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ. Microbiol. 12:422-439 (DOI:10.1111/j.1462-2920.2009.02083.x.)

Field D, Sterk P, Kyrpides N, Kottmann R, Glöckner FO, Hirschman L, Garrity G, Wooley J, Gilna P (2009) Meeting reports from the Genomic Standards Consortium (GSC) workshops 6 and 7. SIGS 1:68-71 (DOI:10.4056/sigs.25165.)

Yarza P, Richter MPeplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rossello-Mora R (2008) The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst. Appl. Microbiol. 31:241-250 (DOI:10.1016/j.syapm.2008.07.001.)

Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P, Genomic Stand C (2008) Laying the foundation for a genomic rosetta stone: Creating information hubs through the use of consensus identifiers. Omics 12:123-127 (DOI:10.1089/omi.2008.0020.)

Richter M, Lombardot TKostadinov I, Kottmann RDuhaime MB, Peplies JGlöckner FO (2008) JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta) genomes. BMC Bioinformatics 9:177 (DOI:10.1186/1471-2105-9-177)

Peplies J, Kottmann R, Ludwig W, Glöckner FO (2008) A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst. Appl. Microbiol. 31:251-257 (DOI:10.1016/j.syapm.2008.08.003)

Kottmann R, Gray T, Murphy S, Kagan L, Kravitz S, Lombardot T, Field D, Glöckner FO, Consortium tGS (2008) A standard MIGS/MIMS compliant XML schema: Toward the development of the Genomic Contextual Data Markup Language (GCDML). Omics 12:115-121 (DOI:10.1089/omi.2008.0A10.)

Hieu CX, Voigt B, Albrecht D, Becher D, Lombardot T, Glöckner FO, Amann R, Hecker M, Schweder T (2008) Detailed proteome analysis of growing cells of the planctomycete Rhodopirellula baltica SH1T. Proteomics 8:1608-1623 (DOI:10.1002/pmic.200701017.)

Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O (2008) Toward a standards-compliant genomic and metagenomic publication record. Omics 12:157-160 (DOI:10.1089/omi.2008.A2B2.)

Field D et al. (2008) Working together to put molecules on the map. Nature 453:978-978 (DOI:10.1038/453978b)

Field D et al. (2008) Meeting report: the fourth Genomic Standards Consortium (GSC) workshop. Omics 12:101-108 (DOI:10.1089/omi.2008.0014.)

Field D et al. (2008) Meeting report: the fifth Genomic Standards Consortium (GSC) workshop. Omics 12:109-113 (DOI:10.1089/omi.2008.A3B3.)

Field D et al. (2008) The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol. 26:541-547 (DOI:10.1038/nbt1360.)

Bohnebeck ULombardot TKottmann RGlöckner FO (2008) MetaMine - A tool to detect and analyse gene patterns in their environmental context. BMC Bioinformatics 9:459 (DOI:10.1186/1471-2105-9-459)

Amaral-Zettler L, Peplies J, Ramette A, Fuchs B, Ludwig W, Glöckner FO (2008) Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany. Syst Appl Microbiol 31:258-268 (DOI:10.1016/j.syapm.2008.08.004.)

Woebken D, Teeling HWecker P, Dumitriu A, Kostadinov I, DeLong EF, Amann R, Glöckner FO (2007) Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-compairison with planctomycete genomes. ISME J.(5):419-35 (DOI:10.1038/ismej.2007.63)

Richter M, Kube M, Bazylinski DA, Lombardot T, Glöckner FO, Reinhardt R, Schüler D (2007) Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. J. Bacteriol. 189:4899-4910 (DOI:10.1128/JB.00119-07)

Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies JGlöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res. 35:7188-7196 (DOI:10.1093/nar/gkm864)

Mussmann M et al. (2007) Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS. Biol. 5:1923-1937 (DOI:10.1371/journal.pbio.0050230)

Lombardot T, Kottmann R, Giuliani G, de Bono A, Addor N, Glöckner FO (2007) MetaLook: a 3D visualisation software for marine ecological genomics. BMC Bioinformatics 8:406 (DOI:10.1186/1471-2105-8-406)

Fuchs BM, Spring S, Teeling H, Quast C, Wulf J, Schattenhofer M, Yan S, Ferriera S, Johnson J, Glöckner FO, Amann R (2007) Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc. Natl. Acad. Sci. USA 104:2891-2896 (DOI:10.1073/pnas.0608046104)

Field D, Garrity G, Gray T, Selengut J, Sterk P, Thomson N, Tatusova T, Cochrane G, Glöckner FOKottmann R, Lister AL, Tateno Y, Vaughan R (2007) eGenomics: Cataloguing our complete genome collection III. Comp. and Funct. Genomics 2007:1-7 (DOI:10.1155/2007/47304)

Borriss M, Lombardot T, Glöckner FO, Becher D, Albrecht D, Schweder T (2007) Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b. Extremophiles 11:95-104 (DOI:10.1007/s00792-006-0014-5)

Zaunmüller T, Kelly DJ, Glöckner FO, Unden G (2006) Succinate dehydrogenase functioning by a reverse redox loop mechanism and fumarate reductase in sulphate-reducing bacteria. Microbiol. 152:2443-2453 (DOI:10.1099/mic.0.28849-0)

Würdemann C, Peplies J, Schübbe S, Ellrott A, Schuler D, Glöckner FO (2006) Evaluation of gene expression analysis using RNA-targeted partial genome arrays. Syst. Appl. Microbiol. 29:349-357 (DOI:10.1016/j.syapm.2006.03.005)

Woyke T et al. (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950-955 (DOI:10.1038/nature05192)

Teeling H, Glöckner FO (2006) RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. BMC Bioinformatics 7:1-6 (DOI:10.1186/1471-2105-7-66)

Schübbe S, Würdemann C, Peplies J, Heyen U, Wawer C, Glöckner FO, Schüler D (2006) Transcriptional organization and regulation of magnetosome operons in Magnetospirillum gryphiswaldense. Appl. Environ. Microbiol. 72:5757-5765 (DOI:10.1128/AEM.00201-06)

Peplies J, Lachmund C, Glöckner FO, Manz W (2006) A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities. Appl. Environ. Microbiol. 72:4829-4838 (DOI:10.1128/AEM.02949-05)

Lombardot TKottmann R, Pfeffer H, Richter MTeeling HQuast CGlöckner FO (2006) Megx.net - database resource for marine ecological genomics. Nucleic Acid Res. 34:D390-D393 (DOI:10.1093/nar/gkp918.)

Glöckner FO, Meyerdierks A (2006) Metagenome Analysis. In: Stackebrandt E (ed) Molecular Identification, Systematics, and Population Structure of Prokaryotes. Springer-Verlag, Heidelberg (ISBN 978-3-540-31292-5)

Glöckner FO (2006) Umweltgenomik: Schlüssel zum Verständnis mariner mikrobieller Diversität und Funktion. Jahrbuch der Max Planck Gesellschaft 

Bauer M et al. (2006) Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8:2201-2213 (DOI:10.1111/j.1462-2920.2006.01152.x)

Anton J, Pena A, Santos MVF, Glöckner FO, Bauer M, Dopazo J, Herrero J, Rossello-Mora R, Amann R (2006) Salinibacter ruber: Genomics and Biogeography. In: Gunde-Cimerman N, Plemenitas A, Oren A (eds) Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya. Cellular Origins, Life in Extreme Habitats and Astrobiology (COLE). Kluwer Academic Publishers, Dordrecht, Netherlands, pp 257-266 (ISBN 978-1-4020-3633-0)

 

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