Assessing taxonomic metagenome profilers with OPAL

by Meyer, Fernando, Bremges, Andreas, Belmann, Peter, Janssen, Stefan, McHardy, Alice C, Koslicki, David
Published in Genome Biology

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

by Weimann, Aaron, Mooren, Kyra, Frank, Jeremy, Pope, Phillip B, Bremges, Andreas, McHardy, Alice C
Published in mSystems

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

by Khaledi, Ariane, Weimann, Aaron, Schniederjans, Monika, Asgari, Ehsaneddin, Kuo, Tzu‐Hao, Oliver, Antonio, Cabot, Gabriel, Kola, Axel, Gastmeier, Petra, Hogardt, Michael, Jonas, Daniel, Mofrad, Mohammad RK, Bremges, Andreas, McHardy, Alice C, Häussler, Susanne
Published in EMBO molecular medicine

Haploflow: strain-resolved de novo assembly of viral genomes

by Fritz, Adrian, Bremges, Andreas, Deng, Zhi-Luo, Lesker, Till Robin, Götting, Jasper, Ganzenmueller, Tina, Sczyrba, Alexander, Dilthey, Alexander, Klawonn, Frank, McHardy, Alice Carolyn
Published in Genome Biology

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

by Bremges, Andreas, Singer, Esther, Woyke, Tanja, Sczyrba, Alexander
Published in Bioinformatics (Oxford, England)

Critical Assessment of Metagenome Interpretation Enters the Second Round

by Bremges, Andreas, McHardy, Alice C
Published in mSystems

CAMISIM: simulating metagenomes and microbial communities

by Fritz, Adrian, Hofmann, Peter, Majda, Stephan, Dahms, Eik, Dröge, Johannes, Fiedler, Jessika, Lesker, Till R, Belmann, Peter, DeMaere, Matthew Z, Darling, Aaron E, Sczyrba, Alexander, Bremges, Andreas, McHardy, Alice C
Published in Microbiome

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

by Krause, Susanne, Bremges, Andreas, Münch, Philipp C, McHardy, Alice C, Gescher, Johannes
Published in Scientific reports

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

by Gillett, Alan, Bergman, Petra, Parsa, Roham, Bremges, Andreas, Giegerich, Robert, Jagodic, Maja
Published in PloS one

Fine-tuning structural RNA alignments in the twilight zone

by Bremges, Andreas, Schirmer, Stefanie, Giegerich, Robert
Published in BMC bioinformatics

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

by Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, Schlüter, Andreas
Published in Biotechnology for biofuels

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

by Maus, Irena, Koeck, Daniela E, Cibis, Katharina G, Hahnke, Sarah, Kim, Yong S, Langer, Thomas, Kreubel, Jana, Erhard, Marcel, Bremges, Andreas, Off, Sandra, Stolze, Yvonne, Jaenicke, Sebastian, Goesmann, Alexander, Sczyrba, Alexander, Scherer, Paul, König, Helmut, Schwarz, Wolfgang H, Zverlov, Vladimir V, Liebl, Wolfgang, Pühler, Alfred, Schlüter, Andreas, Klocke, Michael
Published in Biotechnology for biofuels

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

by Grießmeier, Victoria, Bremges, Andreas, McHardy, Alice C, Gescher, Johannes
Published in Scientific reports

Critical Assessment of Metagenome Interpretation: the second round of challenges

by Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo, Koslicki, David, Lesker, Till Robin, Gurevich, Alexey, Robertson, Gary, Alser, Mohammed, Antipov, Dmitry, Beghini, Francesco, Bertrand, Denis, Brito, Jaqueline J, Brown, C. Titus, Buchmann, Jan, Buluç, Aydin, Chen, Bo, Chikhi, Rayan, Cristian, Alexandru, Dabrowski, Piotr Wojciech, Darling, Aaron E, Egan, Rob, Eskin, Eleazar, Georganas, Evangelos, Goltsman, Eugene, Gray, Melissa A, Hansen, Lars Hestbjerg, Hofmeyr, Steven, Huang, Pingqin, Irber, Luiz, Jia, Huijue, Jørgensen, Tue Sparholt, Kieser, Silas D, Klemetsen, Terje, Kola, Axel, Kolmogorov, Mikhail, Korobeynikov, Anton, Kwan, Jason, LaPierre, Nathan, Lemaitre, Claire, Li, Chenhao, Limasset, Antoine, Malcher-Miranda, Fabio, Mangul, Serghei, Marijon, Pierre, Meleshko, Dmitry, Mende, Daniel R, Milanese, Alessio, Nagarajan, Niranjan, Nissen, Jakob, Nurk, Sergey, Oliker, Leonid, Paoli, Lucas, Peterlongo, Pierre, Piro, Vitor C, Porter, Jacob S, Rasmussen, Simon, Rees, Evan R, Reinert, Knut, Renard, Bernhard, Robertsen, Espen Mikal, Rosen, Gail L, Ruscheweyh, Hans-Joachim, Sarwal, Varuni, Segata, Nicola, Seiler, Enrico, Shi, Lizhen, Sun, Fengzhu, Sunagawa, Shinichi, Sørensen, Søren Johannes, Thomas, Ashleigh, Tong, Chengxuan, Trajkovski, Mirko, Tremblay, Julien, Uritskiy, Gherman, Vicedomini, Riccardo, Wang, Zhengyang, Wang, Ziye, Wang, Zhong, Warren, Andrew, Willassen, Nils Peder, Yelick, Katherine, You, Ronghui, Zeller, Georg, Zhao, Zhengqiao, Zhu, Shanfeng, Zhu, Jie, Garrido-Oter, Ruben, Gastmeier, Petra, Hacquard, Stephane, Häußler, Susanne, Khaledi, Ariane, Maechler, Friederike, Mesny, Fantin, Radutoiu, Simona, Schulze-Lefert, Paul, Smit, Nathiana, Strowig, Till, Bremges, Andreas, Sczyrba, Alexander, McHardy, Alice Carolyn
Published in Nature methods

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

by Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, Schlüter, Andreas
Published in Microbial biotechnology

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

by Maus, Irena, Bremges, Andreas, Stolze, Yvonne, Hahnke, Sarah, Cibis, Katharina G, Koeck, Daniela E, Kim, Yong S, Kreubel, Jana, Hassa, Julia, Wibberg, Daniel, Weimann, Aaron, Off, Sandra, Stantscheff, Robbin, Zverlov, Vladimir V, Schwarz, Wolfgang H, König, Helmut, Liebl, Wolfgang, Scherer, Paul, McHardy, Alice C, Sczyrba, Alexander, Klocke, Michael, Pühler, Alfred, Schlüter, Andreas
Published in Biotechnology for biofuels

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

by Maus, Irena, Cibis, Katharina Gabriela, Bremges, Andreas, Stolze, Yvonne, Wibberg, Daniel, Tomazetto, Geizecler, Blom, Jochen, Sczyrba, Alexander, König, Helmut, Pühler, Alfred, Schlüter, Andreas
Published in Journal of biotechnology

CAMITAX: Taxon labels for microbial genomes

by Bremges, Andreas, Fritz, Adrian, McHardy, Alice C
Published in Gigascience

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

by Ortseifen, Vera, Stolze, Yvonne, Maus, Irena, Sczyrba, Alexander, Bremges, Andreas, Albaum, Stefan P., Jaenicke, Sebastian, Fracowiak, Jochen, Pühler, Alfred, Schlüter, Andreas
Published in Journal of biotechnology

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

by Verwaaijen, Bart, Wibberg, Daniel, Nelkner, Johanna, Gordin, Miriam, Rupp, Oliver, Winkler, Anika, Bremges, Andreas, Blom, Jochen, Grosch, Rita, Pühler, Alfred, Schlüter, Andreas
Published in Journal of biotechnology