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Items: 1 to 50 of 64

1.

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes.

Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A.

Genes (Basel). 2019 Jun 3;10(6). pii: E424. doi: 10.3390/genes10060424.

2.

F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota.

Pankoke H, Maus I, Loh G, Hüser A, Seifert J, Tilker A, Hark S, Sczyrba A, Pelzer S, Kleinbölting J.

FEMS Microbiol Lett. 2019 Mar 27. pii: fnz033. doi: 10.1093/femsle/fnz033. [Epub ahead of print]

PMID:
30915459
3.

CAMISIM: simulating metagenomes and microbial communities.

Fritz A, Hofmann P, Majda S, Dahms E, Dröge J, Fiedler J, Lesker TR, Belmann P, DeMaere MZ, Darling AE, Sczyrba A, Bremges A, McHardy AC.

Microbiome. 2019 Feb 8;7(1):17. doi: 10.1186/s40168-019-0633-6.

4.

Common ELIXIR Service for Researcher Authentication and Authorisation.

Linden M, Prochazka M, Lappalainen I, Bucik D, Vyskocil P, Kuba M, Silén S, Belmann P, Sczyrba A, Newhouse S, Matyska L, Nyrönen T.

F1000Res. 2018 Aug 6;7. pii: ELIXIR-1199. doi: 10.12688/f1000research.15161.1. eCollection 2018.

5.

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors.

Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M.

Biotechnol Biofuels. 2018 Jun 19;11:167. doi: 10.1186/s13068-018-1162-4. eCollection 2018.

6.

Binning enables efficient host genome reconstruction in cnidarian holobionts.

Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy075.

7.

AMBER: Assessment of Metagenome BinnERs.

Meyer F, Hofmann P, Belmann P, Garrido-Oter R, Fritz A, Sczyrba A, McHardy AC.

Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy069.

8.

Insights into the Fundamental Physiology of the Uncultured Fe-Oxidizing Bacterium Leptothrix ochracea.

Fleming EJ, Woyke T, Donatello RA, Kuypers MMM, Sczyrba A, Littmann S, Emerson D.

Appl Environ Microbiol. 2018 Apr 16;84(9). pii: e02239-17. doi: 10.1128/AEM.02239-17. Print 2018 May 1.

9.

Analyzing large scale genomic data on the cloud with Sparkhit.

Huang L, Krüger J, Sczyrba A.

Bioinformatics. 2018 May 1;34(9):1457-1465. doi: 10.1093/bioinformatics/btx808.

10.

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.

Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A.

Microb Biotechnol. 2018 Jul;11(4):667-679. doi: 10.1111/1751-7915.12982. Epub 2017 Dec 4.

11.

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.

Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A.

Biotechnol Biofuels. 2017 Nov 13;10:264. doi: 10.1186/s13068-017-0947-1. eCollection 2017.

12.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

13.

Bioinformatics for NGS-based metagenomics and the application to biogas research.

Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J.

J Biotechnol. 2017 Nov 10;261:10-23. doi: 10.1016/j.jbiotec.2017.08.012. Epub 2017 Aug 18. Review.

14.

Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

Yu J, Blom J, Sczyrba A, Goesmann A.

J Biotechnol. 2017 Sep 10;257:58-60. doi: 10.1016/j.jbiotec.2017.02.020. Epub 2017 Feb 21.

15.

acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.

Lux M, Krüger J, Rinke C, Maus I, Schlüter A, Woyke T, Sczyrba A, Hammer B.

BMC Bioinformatics. 2016 Dec 20;17(1):543. doi: 10.1186/s12859-016-1397-7.

16.

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.

Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M.

Biotechnol Biofuels. 2016 Aug 11;9:171. doi: 10.1186/s13068-016-0581-3. eCollection 2016.

17.

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants.

Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A.

Biotechnol Biofuels. 2016 Jul 26;9:156. doi: 10.1186/s13068-016-0565-3. eCollection 2016.

18.

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type.

Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U.

Biotechnol Biofuels. 2016 Jul 26;9:155. doi: 10.1186/s13068-016-0572-4. eCollection 2016.

19.

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.

Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum SP, Jaenicke S, Fracowiak J, Pühler A, Schlüter A.

J Biotechnol. 2016 Aug 10;231:268-279. doi: 10.1016/j.jbiotec.2016.06.014. Epub 2016 Jun 14.

PMID:
27312700
20.

Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment.

Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, Schlüter A.

J Biotechnol. 2016 Aug 20;232:50-60. doi: 10.1016/j.jbiotec.2016.05.001. Epub 2016 May 7.

PMID:
27165504
21.

MeCorS: Metagenome-enabled error correction of single cell sequencing reads.

Bremges A, Singer E, Woyke T, Sczyrba A.

Bioinformatics. 2016 Jul 15;32(14):2199-201. doi: 10.1093/bioinformatics/btw144. Epub 2016 Mar 15.

22.

Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing.

Wibberg D, Bremges A, Dammann-Kalinowski T, Maus I, Igeño MI, Vogelsang R, König C, Luque-Almagro VM, Roldán MD, Sczyrba A, Moreno-Vivián C, Blasco R, Pühler A, Schlüter A.

J Biotechnol. 2016 Aug 20;232:61-8. doi: 10.1016/j.jbiotec.2016.04.008. Epub 2016 Apr 6.

PMID:
27060556
23.

miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering.

Stiefel F, Fischer S, Sczyrba A, Otte K, Hesse F.

J Biotechnol. 2016 May 10;225:31-43. doi: 10.1016/j.jbiotec.2016.03.028. Epub 2016 Mar 19.

PMID:
27002234
24.

Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene.

Krahn T, Wibberg D, Maus I, Winkler A, Bontron S, Sczyrba A, Nordmann P, Pühler A, Poirel L, Schlüter A.

Antimicrob Agents Chemother. 2016 Apr 22;60(5):3032-40. doi: 10.1128/AAC.00124-16. Print 2016 May.

25.

Back to the Future of Soil Metagenomics.

Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P.

Front Microbiol. 2016 Feb 10;7:73. doi: 10.3389/fmicb.2016.00073. eCollection 2016. No abstract available.

26.

Bioboxes: standardised containers for interchangeable bioinformatics software.

Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD.

Gigascience. 2015 Oct 15;4:47. doi: 10.1186/s13742-015-0087-0. eCollection 2015.

27.

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant.

Bremges A, Maus I, Belmann P, Eikmeyer F, Winkler A, Albersmeier A, Pühler A, Schlüter A, Sczyrba A.

Gigascience. 2015 Jul 30;4:33. doi: 10.1186/s13742-015-0073-6. eCollection 2015.

28.

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities.

Kohrs F, Wolter S, Benndorf D, Heyer R, Hoffmann M, Rapp E, Bremges A, Sczyrba A, Schlüter A, Reichl U.

Proteomics. 2015 Oct;15(20):3585-9. doi: 10.1002/pmic.201400557. Epub 2015 Aug 12.

PMID:
26152594
29.

Targeted diversity generation by intraterrestrial archaea and archaeal viruses.

Paul BG, Bagby SC, Czornyj E, Arambula D, Handa S, Sczyrba A, Ghosh P, Miller JF, Valentine DL.

Nat Commun. 2015 Mar 23;6:6585. doi: 10.1038/ncomms7585.

30.

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount.

Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D.

ISME J. 2015 Mar 17;9(4):857-70. doi: 10.1038/ismej.2014.183.

31.

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling.

Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe SG, Mackie RI, Yeoman CJ, Hess M.

Front Microbiol. 2014 Jul 22;5:307. doi: 10.3389/fmicb.2014.00307. eCollection 2014.

32.

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage.

Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan LK, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F, Malmstrom R, Bertilsson S, McMahon KD.

ISME J. 2014 Dec;8(12):2503-16. doi: 10.1038/ismej.2014.135. Epub 2014 Aug 5.

33.

Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.

Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S.

ACS Chem Biol. 2014 Sep 19;9(9):2082-91. doi: 10.1021/cb500244v. Epub 2014 Jul 17.

34.

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.

Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland ED, Harris CC, Sczyrba A, Chain PS, Koren S, Woyke T, Stepanauskas R.

PLoS One. 2014 Apr 17;9(4):e95380. doi: 10.1371/journal.pone.0095380. eCollection 2014.

35.

Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma.

Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gerlach W, Gombert M, Rahn S, Stoye J, Borkhardt A, Fischer U.

PLoS One. 2014 Mar 18;9(3):e92297. doi: 10.1371/journal.pone.0092297. eCollection 2014.

36.

Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.

Wibberg D, Luque-Almagro VM, Igeño MI, Bremges A, Roldán MD, Merchán F, Sáez LP, Guijo MI, Manso MI, Macías D, Cabello P, Becerra G, Ibáñez MI, Carmona MI, Escribano MM, Castillo F, Sczyrba A, Moreno-Vivián C, Blasco R, Pühler A, Schlüter A.

J Biotechnol. 2014 Apr 10;175:67-8. doi: 10.1016/j.jbiotec.2014.02.004. Epub 2014 Feb 16.

PMID:
24553071
37.

The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features.

Kamke J, Rinke C, Schwientek P, Mavromatis K, Ivanova N, Sczyrba A, Woyke T, Hentschel U.

PLoS One. 2014 Jan 31;9(1):e87353. doi: 10.1371/journal.pone.0087353. eCollection 2014.

38.

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade.

Zaremba-Niedzwiedzka K, Viklund J, Zhao W, Ast J, Sczyrba A, Woyke T, McMahon K, Bertilsson S, Stepanauskas R, Andersson SG.

Genome Biol. 2013 Nov 28;14(11):R130. doi: 10.1186/gb-2013-14-11-r130.

39.

Insights into the phylogeny and coding potential of microbial dark matter.

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T.

Nature. 2013 Jul 25;499(7459):431-7. doi: 10.1038/nature12352. Epub 2013 Jul 14.

PMID:
23851394
40.

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges.

Kamke J, Sczyrba A, Ivanova N, Schwientek P, Rinke C, Mavromatis K, Woyke T, Hentschel U.

ISME J. 2013 Dec;7(12):2287-300. doi: 10.1038/ismej.2013.111. Epub 2013 Jul 11.

41.

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.

Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas R.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11463-8. doi: 10.1073/pnas.1304246110. Epub 2013 Jun 25.

42.

Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity.

Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M.

PLoS One. 2013;8(3):e59361. doi: 10.1371/journal.pone.0059361. Epub 2013 Mar 26.

43.

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.

Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5540-5. doi: 10.1073/pnas.1303090110. Epub 2013 Mar 18.

44.

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.

El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P.

BMC Bioinformatics. 2012;13 Suppl 17:S22. doi: 10.1186/1471-2105-13-S17-S22. Epub 2012 Dec 13.

45.

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton.

Garcia SL, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F.

ISME J. 2013 Jan;7(1):137-47. doi: 10.1038/ismej.2012.86. Epub 2012 Jul 19.

46.

Decontamination of MDA reagents for single cell whole genome amplification.

Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng JF.

PLoS One. 2011;6(10):e26161. doi: 10.1371/journal.pone.0026161. Epub 2011 Oct 20.

47.

High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery.

Kim TW, Chokhawala HA, Hess M, Dana CM, Baer Z, Sczyrba A, Rubin EM, Blanch HW, Clark DS.

Angew Chem Int Ed Engl. 2011 Nov 18;50(47):11215-8. doi: 10.1002/anie.201104685. Epub 2011 Sep 16. No abstract available.

PMID:
21922616
48.

Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean.

Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland ED, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R.

Science. 2011 Sep 2;333(6047):1296-300. doi: 10.1126/science.1203690.

49.

Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190.

Sales CM, Mahendra S, Grostern A, Parales RE, Goodwin LA, Woyke T, Nolan M, Lapidus A, Chertkov O, Ovchinnikova G, Sczyrba A, Alvarez-Cohen L.

J Bacteriol. 2011 Sep;193(17):4549-50. doi: 10.1128/JB.00415-11. Epub 2011 Jul 1.

50.

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project.

Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R.

Stand Genomic Sci. 2010 Dec 25;3(3):243-8. doi: 10.4056/sigs.1433550.

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