Haploflow: Strain-resolved de novo assembly of viral genomes.

Fritz, Bremges, et al. (2021). bioRxiv, preprint.

CAMITAX: Taxon labels for microbial genomes.

Bremges et al. (2020). GigaScience, 9, 1:1–7.

Assessing taxonomic metagenome profilers with OPAL.

Meyer, Bremges, et al. (2019). Genome Biology, 20, 1:51.

CAMISIM: Simulating metagenomes and microbial communities.

Fritz*, Hofmann*, et al. (2019). Microbiome, 7, 1:17.

Critical Assessment of Metagenome Interpretation enters the second round.

Bremges et al. (2018). mSystems, 3, 4:e00103–18.

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

Stolze, Bremges, et al. (2018). Microbial Biotechnology, 11, 4:667–679.

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

Maus*, Bremges*, et al. (2017). Biotechnology for Biofuels, 10:264.

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

Sczyrba*, Hofmann*, Belmann*, et al. (2017). Nature Methods, 14, 11:1063–1071.

Fast and memory-efficient noisy read overlapping with KD-trees.

Parkhomchuk*, Bremges*, et al. (2017). bioRxiv, preprint.

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

Krause, Bremges, et al. (2017). Scientific Reports, 7, 1:3289.

Metagenomics and CAZyme discovery.

Kunath, Bremges, et al. (2017). Methods in Molecular Biology, 1588:255–277.

From genomes to phenotypes: Traitar, the microbial trait analyzer.

Weimann et al. (2016). mSystems, 1, 6:e00101–16.

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

Bremges et al. (2016). Bioinformatics, 32, 14:2199–201.

Fine-tuning structural RNA alignments in the twilight zone.

Bremges*, Schirmer*, et al. (2010). BMC Bioinformatics, 11:222.