Sort by
Items per page

Send to

Choose Destination

Search results

Items: 23


Assessing taxonomic metagenome profilers with OPAL.

Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D.

Genome Biol. 2019 Mar 4;20(1):51. doi: 10.1186/s13059-019-1646-y.


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.


Critical Assessment of Metagenome Interpretation Enters the Second Round.

Bremges A, McHardy AC.

mSystems. 2018 Jul 10;3(4). pii: e00103-18. doi: 10.1128/mSystems.00103-18. eCollection 2018 Jul-Aug. No abstract available.


Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

Verwaaijen B, Wibberg D, Nelkner J, Gordin M, Rupp O, Winkler A, Bremges A, Blom J, Grosch R, Pühler A, Schlüter A.

J Biotechnol. 2018 Feb 10;267:12-18. doi: 10.1016/j.jbiotec.2017.12.021. Epub 2017 Dec 24.


Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds.

Grießmeier V, Bremges A, McHardy AC, Gescher J.

Sci Rep. 2017 Dec 5;7(1):17028. doi: 10.1038/s41598-017-17312-2.


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.


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.


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.


Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms.

Krause S, Bremges A, Münch PC, McHardy AC, Gescher J.

Sci Rep. 2017 Jun 12;7(1):3289. doi: 10.1038/s41598-017-03315-6.


Metagenomics and CAZyme Discovery.

Kunath BJ, Bremges A, Weimann A, McHardy AC, Pope PB.

Methods Mol Biol. 2017;1588:255-277. doi: 10.1007/978-1-4939-6899-2_20.


From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.

Weimann A, Mooren K, Frank J, Pope PB, Bremges A, McHardy AC.

mSystems. 2016 Dec 27;1(6). pii: e00101-16. doi: 10.1128/mSystems.00101-16. eCollection 2016 Nov-Dec.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis.

Gillett A, Bergman P, Parsa R, Bremges A, Giegerich R, Jagodic M.

PLoS One. 2013 Dec 3;8(12):e81912. doi: 10.1371/journal.pone.0081912. eCollection 2013.


Fine-tuning structural RNA alignments in the twilight zone.

Bremges A, Schirmer S, Giegerich R.

BMC Bioinformatics. 2010 Apr 30;11:222. doi: 10.1186/1471-2105-11-222.

Supplemental Content

Loading ...
Support Center