Andreas Bremges


efficient methods and algorithms for biological sequence analysis


these techniques to study microbial communities from complex environments


Metagenomics and CAZyme discovery
Kunath, B.J., A. Bremges, A. Weimann, A.C. McHardy, P.B. Pope (2017). Methods in Molecular Biology, 1588:255-277.

Laboratory cultivation of acidophilic nanoorganisms. Physiological and bioinformatic dissection of a stable laboratory co-culture
Krause, S., A. Bremges, P.C. Münch, A.C. McHardy, J. Gescher (2017). bioRxiv, preprint.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
Sczyrba, A.*, P. Hofmann*, P. Belmann*, D. Koslicki, S. Janssen, J. Dröge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T.S. Jørgensen, N. Shapiro, P.D. Blood, A. Gurevich, Y. Bai, D. Turaev, M.Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, L.H. Hansen, S.J. Sørensen, B.K.H. Chia, B. Denis, J.L. Froula, Z. Wang, R. Egan, D.D. Kang, J.J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y. Wu, S.W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. Barton, T. Lingner, H. Lin, Y. Liao, G.G.Z. Silva, D.A. Cuevas, R.A. Edwards, S. Saha, V.C. Piro, B.Y. Renard, M. Pop, H. Klenk, M. Göker, N. Kyrpides, T. Woyke, J.A. Vorholt, P. Schulze-Lefert, E.M. Rubin, A.E. Darling, T. Rattei, A.C. McHardy (2017). bioRxiv, preprint.

From genomes to phenotypes: Traitar, the microbial trait analyzer
Weimann, A., K. Mooren, J. Frank, P.B. Pope, A. Bremges, A.C. McHardy (2016). mSystems, 1, 6:e00101-16.

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates
Maus, I., D.E. Koeck, K.G. Cibis, S. Hahnke, Y.S. Kim, T. Langer, J. Kreubel, M. Erhard, A. Bremges, S. Off, Y. Stolze, S. Jaenicke, A. Goesmann, A. Sczyrba, P. Scherer, H. König, W.H. Schwarz, V.V. Zverlov, W. Liebl, A. Pühler, A. Schlüter, M. Klocke (2016). Biotechnology for Biofuels, 9:172.

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Stolze, Y.*, A. Bremges*, M. Rumming, C. Henke, I. Maus, A. Pühler, A. Sczyrba, A. Schlüter (2016). Biotechnology for Biofuels, 9:156.

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant
Ortseifen, V., Y. Stolze, I. Maus, A. Sczyrba, A. Bremges, S.P. Albaum, S. Jaenicke, J. Fracowiak, A. Pühler, A. Schlüter (2016). Journal of Biotechnology, 231:268-279.

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., K.G. Cibis, A. Bremges, Y. Stolze, D. Wibberg, G. Tomazetto, J. Blom, A. Sczyrba, H. König, A. Pühler, A. Schlüter (2016). Journal of Biotechnology, 232:50-60.

Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing
Wibberg, D.*, A. Bremges*, T. Dammann-Kalinowski, I. Maus, I. Igeño, R. Vogelsang, C. König, A. Sczyrba, R. Blasco, A. Pühler, A. Schlüter (2016). Journal of Biotechnology, 232:61-8.

MeCorS: metagenome-enabled error correction of single cell sequencing reads
Bremges, A., E. Singer, T. Woyke, A. Sczyrba (2016). Bioinformatics, 32, 14:2199-201.

Bioboxes: standardised containers for interchangeable bioinformatics software
Belmann, P., J. Dröge, A. Bremges, A.C. McHardy, A. Sczyrba, M.D. Barton (2015). GigaScience, 4:47.

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant
Bremges, A., I. Maus, P. Belmann, F.G. Eikmeyer, A. Winkler, A. Albersmeier, A. Pühler, A. Schlüter*, A. Sczyrba* (2015). GigaScience, 4:33.

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities
Kohrs, F., S. Wolter, D. Benndorf, R. Heyer, M. Hoffmann, E. Rapp, A. Bremges, A. Sczyrba, A. Schlüter, U. Reichl (2015). Proteomics, 15, 20:3585-9.

Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344
Wibberg, D., V.M. Luque-Almagro, I. Igeño, A. Bremges, M.D. Roldán, F. Merchán, L.P. Sáez, M.I. Guijo, M.I. Manso, D. Macías, P. Cabello, G. Becerra, M.I. Ibáñez, M.I. Carmona, M.M. Escribano, F. Castillo, A. Sczyrba, C. Moreno-Vivián, R. Blasco, A. Pühler, A. Schlüter (2014). Journal of Biotechnology, 175:67-8.

A silent exonic SNP in kdm3a affects nucleic acids structure but does not regulate experimental autoimmune encephalomyelitis
Gillett, A., P. Bergman, R. Parsa, A. Bremges, R. Giegerich, M. Jagodic (2013). PLoS ONE, 8, 12:e81912.

Fine-tunig structural RNA alignments in the twilight zone
Bremges, A.*, S. Schirmer*, R. Giegerich (2010). BMC Bioinformatics, 11:222.