Publications

Critical Assessment of Metagenome Interpretation: the second round of challenges.

Meyer*, Fritz*, et al. (2022). Nature Methods, 19, 4:429–440.

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

Fritz, Bremges, et al. (2021). Genome Biology, 22, 1:212.

Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit.

Meyer et al. (2021). Nature Protocols, 16, 4:1785–1801.

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning‐enabled molecular diagnostics.

Khaledi*, Weimann*, et al. (2020). EMBO Molecular Medicine, 12, 3:e10264.

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.

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

Verwaaijen et al. (2018). Journal of Biotechnology, 267:12–18.

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

Grießmeier, Bremges, et al. (2017). Scientific Reports, 7, 1:17028.

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.

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 et al. (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*, Bremges*, et al. (2016). Journal of Biotechnology, 232:61–8.

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

Maus et al. (2016). Biotechnology for Biofuels, 9:171.

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

Ortseifen et al. (2016). Journal of Biotechnology, 231:268–279.

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

Stolze*, Bremges*, et al. (2016). Biotechnology for Biofuels, 9:156.

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

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

Bioboxes: standardised containers for interchangeable bioinformatics software.

Belmann et al. (2015). GigaScience, 4:47.

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

Kohrs et al. (2015). Proteomics, 15, 20:3585–9.

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

Bremges et al. (2015). GigaScience, 4:33.

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

Wibberg et al. (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 et al. (2013). PLOS ONE, 8, 12:e81912.

Fine-tuning structural RNA alignments in the twilight zone.

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