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Items: 1 to 50 of 154

1.

Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research.

Rambold G, Yilmaz P, Harjes J, Klaster S, Sanz V, Link A, Glöckner FO, Triebel D.

Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz002.

2.

Decoding the ocean's microbiological secrets for marine enzyme biodiscovery.

Ferrer M, Méndez-García C, Bargiela R, Chow J, Alonso S, García-Moyano A, Bjerga GEK, Steen IH, Schwabe T, Blom C, Vester J, Weckbecker A, Shahgaldian P, de Carvalho CCCR, Meskys R, Zanaroli G, Glöckner FO, Fernández-Guerra A, Thambisetty S, de la Calle F, Golyshina OV, Yakimov MM, Jaeger KE, Yakunin AF, Streit WR, McMeel O, Calewaert JB, Tonné N, Golyshin PN; INMARE Consortium.

FEMS Microbiol Lett. 2019 Jan 1;366(1). doi: 10.1093/femsle/fny285.

3.

A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms.

Banos S, Lentendu G, Kopf A, Wubet T, Glöckner FO, Reich M.

BMC Microbiol. 2018 Nov 20;18(1):190. doi: 10.1186/s12866-018-1331-4.

4.

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K.

Nucleic Acids Res. 2019 Jan 8;47(D1):D259-D264. doi: 10.1093/nar/gky1022.

5.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
6.

The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages.

Garin-Fernandez A, Pereira-Flores E, Glöckner FO, Wichels A.

Mar Genomics. 2018 Oct;41:31-41. doi: 10.1016/j.margen.2018.05.004. Epub 2018 Jun 1.

7.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

8.

Determinants and Prediction of Esterase Substrate Promiscuity Patterns.

Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The Inmare Consortium.

ACS Chem Biol. 2018 Jan 19;13(1):225-234. doi: 10.1021/acschembio.7b00996. Epub 2017 Dec 20.

PMID:
29182315
9.

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner FO, Müller W, Marcus K, Eisenacher M.

Brief Bioinform. 2017 Oct 30. doi: 10.1093/bib/bbx140. [Epub ahead of print]

PMID:
29092005
10.

Author Correction: Surface properties of SAR11 bacteria facilitate grazing avoidance.

Dadon-Pilosof A, Conley KR, Jacobi Y, Haber M, Lombard F, Sutherland KR, Steindler L, Tikochinski Y, Richter M, Glöckner FO, Suzuki MT, West NJ, Genin A, Yahel G.

Nat Microbiol. 2017 Dec;2(12):1696. doi: 10.1038/s41564-017-0064-8.

PMID:
29057995
11.

Surface properties of SAR11 bacteria facilitate grazing avoidance.

Dadon-Pilosof A, Conley KR, Jacobi Y, Haber M, Lombard F, Sutherland KR, Steindler L, Tikochinski Y, Richter M, Glöckner FO, Suzuki MT, West NJ, Genin A, Yahel G.

Nat Microbiol. 2017 Dec;2(12):1608-1615. doi: 10.1038/s41564-017-0030-5. Epub 2017 Oct 2. Erratum in: Nat Microbiol. 2017 Dec;2(12 ):1696.

PMID:
28970475
12.

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

Beccati A, Gerken J, Quast C, Yilmaz P, Glöckner FO.

BMC Bioinformatics. 2017 Sep 30;18(1):433. doi: 10.1186/s12859-017-1841-3.

13.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893.

PMID:
28787424
14.

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 Nov 10;261:169-176. doi: 10.1016/j.jbiotec.2017.06.1198. Epub 2017 Jun 23. Review.

15.

A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences.

Yarza P, Yilmaz P, Panzer K, Glöckner FO, Reich M.

Mar Genomics. 2017 Dec;36:33-39. doi: 10.1016/j.margen.2017.05.009. Epub 2017 Jun 1.

16.

UniEuk: Time to Speak a Common Language in Protistology!

Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C.

J Eukaryot Microbiol. 2017 May;64(3):407-411. doi: 10.1111/jeu.12414. Epub 2017 Apr 21. Review.

17.

Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4.

Rast P, Glöckner I, Boedeker C, Jeske O, Wiegand S, Reinhardt R, Schumann P, Rohde M, Spring S, Glöckner FO, Jogler C, Jogler M.

Front Microbiol. 2017 Feb 13;8:202. doi: 10.3389/fmicb.2017.00202. eCollection 2017.

18.

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island.

Meyer JM, Baskaran P, Quast C, Susoy V, Rödelsperger C, Glöckner FO, Sommer RJ.

Environ Microbiol. 2017 Apr;19(4):1476-1489. doi: 10.1111/1462-2920.13697. Epub 2017 Mar 2.

PMID:
28198090
19.

Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area.

Thiele S, Richter M, Balestra C, Glöckner FO, Casotti R.

Mar Genomics. 2017 Apr;32:61-69. doi: 10.1016/j.margen.2016.12.003. Epub 2017 Jan 5.

PMID:
28063827
20.

An Information System for European culture collections: the way forward.

Casaregola S, Vasilenko A, Romano P, Robert V, Ozerskaya S, Kopf A, Glöckner FO, Smith D.

Springerplus. 2016 Jun 17;5(1):772. doi: 10.1186/s40064-016-2450-8. eCollection 2016. Review.

21.

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A.

Nucleic Acids Res. 2016 Jun 20;44(11):5022-33. doi: 10.1093/nar/gkw396. Epub 2016 May 10.

22.

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus.

Romano S, Fernàndez-Guerra A, Reen FJ, Glöckner FO, Crowley SP, O'Sullivan O, Cotter PD, Adams C, Dobson AD, O'Gara F.

Front Microbiol. 2016 Mar 30;7:387. doi: 10.3389/fmicb.2016.00387. eCollection 2016.

23.

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms.

Teeling H, Fuchs BM, Bennke CM, Krüger K, Chafee M, Kappelmann L, Reintjes G, Waldmann J, Quast C, Glöckner FO, Lucas J, Wichels A, Gerdts G, Wiltshire KH, Amann RI.

Elife. 2016 Apr 7;5:e11888. doi: 10.7554/eLife.11888.

24.

MyOSD 2014: Evaluating Oceanographic Measurements Contributed by Citizen Scientists in Support of Ocean Sampling Day.

Schnetzer J, Kopf A, Bietz MJ, Buttigieg PL, Fernandez-Guerra A, Ristov AP, Glöckner FO, Kottmann R.

J Microbiol Biol Educ. 2016 Mar 1;17(1):163-71. doi: 10.1128/jmbe.v17i1.1001. eCollection 2016 Mar.

25.

Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane.

Krukenberg V, Harding K, Richter M, Glöckner FO, Gruber-Vodicka HR, Adam B, Berg JS, Knittel K, Tegetmeyer HE, Boetius A, Wegener G.

Environ Microbiol. 2016 Sep;18(9):3073-91. doi: 10.1111/1462-2920.13283. Epub 2016 Apr 6.

PMID:
26971539
26.

Expanding the World of Marine Bacterial and Archaeal Clades.

Yilmaz P, Yarza P, Rapp JZ, Glöckner FO.

Front Microbiol. 2016 Jan 8;6:1524. doi: 10.3389/fmicb.2015.01524. eCollection 2015.

27.

Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.

28.

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data.

Panzer K, Yilmaz P, Weiß M, Reich L, Richter M, Wiese J, Schmaljohann R, Labes A, Imhoff JF, Glöckner FO, Reich M.

PLoS One. 2015 Jul 30;10(7):e0134377. doi: 10.1371/journal.pone.0134377. eCollection 2015.

29.

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.

Ten Hoopen P, Pesant S, Kottmann R, Kopf A, Bicak M, Claus S, Deneudt K, Borremans C, Thijsse P, Dekeyzer S, Schaap DM, Bowler C, Glöckner FO, Cochrane G.

Stand Genomic Sci. 2015 May 8;10:20. doi: 10.1186/s40793-015-0001-5. eCollection 2015.

30.

The ocean sampling day consortium.

Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO.

Gigascience. 2015 Jun 19;4:27. doi: 10.1186/s13742-015-0066-5. eCollection 2015.

31.

Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes.

Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D.

Environ Microbiol. 2016 Jan;18(1):21-37. doi: 10.1111/1462-2920.12907. Epub 2015 Jul 30.

PMID:
26060021
32.

Characterisation of non-autoinducing tropodithietic Acid (TDA) production from marine sponge Pseudovibrio species.

Harrington C, Reen FJ, Mooij MJ, Stewart FA, Chabot JB, Guerra AF, Glöckner FO, Nielsen KF, Gram L, Dobson AD, Adams C, O'Gara F.

Mar Drugs. 2014 Dec 10;12(12):5960-78. doi: 10.3390/md12125960.

33.

Metatranscriptome of marine bacterioplankton during winter time in the North Sea assessed by total RNA sequencing.

Kopf A, Kostadinov I, Wichels A, Quast C, Glöckner FO.

Mar Genomics. 2015 Feb;19:45-6. doi: 10.1016/j.margen.2014.11.001. Epub 2014 Nov 15.

34.

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom.

Xing P, Hahnke RL, Unfried F, Markert S, Huang S, Barbeyron T, Harder J, Becher D, Schweder T, Glöckner FO, Amann RI, Teeling H.

ISME J. 2015 Jun;9(6):1410-22. doi: 10.1038/ismej.2014.225. Epub 2014 Dec 5.

35.

Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing.

Klindworth A, Mann AJ, Huang S, Wichels A, Quast C, Waldmann J, Teeling H, Glöckner FO.

Mar Genomics. 2014 Dec;18 Pt B:185-92. doi: 10.1016/j.margen.2014.08.007. Epub 2014 Sep 6.

36.

Genomic standards consortium projects.

Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.

Stand Genomic Sci. 2014 Feb 15;9(3):599-601. doi: 10.4056/sigs.5559680. eCollection 2014 Jun 15.

37.

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.

Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R.

Nat Rev Microbiol. 2014 Sep;12(9):635-45. doi: 10.1038/nrmicro3330. Review.

PMID:
25118885
38.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP.

PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014 Aug.

39.

Single-cell genomics reveals potential for magnetite and greigite biomineralization in an uncultivated multicellular magnetotactic prokaryote.

Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D.

Environ Microbiol Rep. 2014 Oct;6(5):524-31. doi: 10.1111/1758-2229.12198. Epub 2014 Aug 28.

PMID:
25079475
40.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

Waldmann J, Gerken J, Hankeln W, Schweer T, Glöckner FO.

BMC Res Notes. 2014 Jun 14;7:365. doi: 10.1186/1756-0500-7-365.

41.

The founding charter of the Genomic Observatories Network.

Davies N, Field D, Amaral-Zettler L, Clark MS, Deck J, Drummond A, Faith DP, Geller J, Gilbert J, Glöckner FO, Hirsch PR, Leong JA, Meyer C, Obst M, Planes S, Scholin C, Vogler AP, Gates RD, Toonen R, Berteaux-Lecellier V, Barbier M, Barker K, Bertilsson S, Bicak M, Bietz MJ, Bobe J, Bodrossy L, Borja A, Coddington J, Fuhrman J, Gerdts G, Gillespie R, Goodwin K, Hanson PC, Hero JM, Hoekman D, Jansson J, Jeanthon C, Kao R, Klindworth A, Knight R, Kottmann R, Koo MS, Kotoulas G, Lowe AJ, Marteinsson VT, Meyer F, Morrison N, Myrold DD, Pafilis E, Parker S, Parnell JJ, Polymenakou PN, Ratnasingham S, Roderick GK, Rodriguez-Ezpeleta N, Schonrogge K, Simon N, Valette-Silver NJ, Springer YP, Stone GN, Stones-Havas S, Sansone SA, Thibault KM, Wecker P, Wichels A, Wooley JC, Yahara T, Zingone A; GOs-COS.

Gigascience. 2014 Mar 7;3(1):2. doi: 10.1186/2047-217X-3-2.

42.

The gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata: an in-depth metagenomic investigation and discovery of Zetaproteobacteria.

Jan C, Petersen JM, Werner J, Teeling H, Huang S, Glöckner FO, Golyshina OV, Dubilier N, Golyshin PN, Jebbar M, Cambon-Bonavita MA.

Environ Microbiol. 2014 Sep;16(9):2723-38. doi: 10.1111/1462-2920.12406. Epub 2014 Mar 4.

PMID:
24447589
43.

Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.

Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glöckner FO, Golyshina OV, Golyshin PN, Teeling H; MAMBA Consortium.

Environ Microbiol. 2014 Aug;16(8):2525-37. doi: 10.1111/1462-2920.12393. Epub 2014 Feb 27.

44.

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.

45.

Permanent draft genome of Rhodopirellula rubra SWK7.

Klindworth A, Richter M, Richter-Heitmann T, Wegner CE, Frank CS, Harder J, Glöckner FO.

Mar Genomics. 2014 Feb;13:11-2. doi: 10.1016/j.margen.2013.11.005. Epub 2013 Nov 26.

PMID:
24291061
46.

Permanent draft genomes of the two Rhodopirellula europaea strains 6C and SH398.

Richter-Heitmann T, Richter M, Klindworth A, Wegner CE, Frank CS, Glöckner FO, Harder J.

Mar Genomics. 2014 Feb;13:15-6. doi: 10.1016/j.margen.2013.11.003. Epub 2013 Nov 25.

PMID:
24286834
47.

Permanent draft genomes of the Rhodopirellula maiorica strain SM1.

Richter M, Richter-Heitmann T, Klindworth A, Wegner CE, Frank CS, Harder J, Glöckner FO.

Mar Genomics. 2014 Feb;13:19-20. doi: 10.1016/j.margen.2013.11.001. Epub 2013 Nov 25.

PMID:
24286833
48.

Permanent draft genome of Rhodopirellula sallentina SM41.

Wegner CE, Richter M, Richter-Heitmann T, Klindworth A, Frank CS, Glöckner FO, Harder J.

Mar Genomics. 2014 Feb;13:17-8. doi: 10.1016/j.margen.2013.11.002. Epub 2013 Nov 25.

PMID:
24286832
49.

Permanent draft genomes of the three Rhodopirellula baltica strains SH28, SWK14 and WH47.

Richter M, Richter-Heitmann T, Klindworth A, Wegner CE, Frank CS, Harder J, Glöckner FO.

Mar Genomics. 2014 Feb;13:13-4. doi: 10.1016/j.margen.2013.11.004. Epub 2013 Nov 25.

PMID:
24286831
50.

The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides.

Mann AJ, Hahnke RL, Huang S, Werner J, Xing P, Barbeyron T, Huettel B, Stüber K, Reinhardt R, Harder J, Glöckner FO, Amann RI, Teeling H.

Appl Environ Microbiol. 2013 Nov;79(21):6813-22. doi: 10.1128/AEM.01937-13. Epub 2013 Aug 30.

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