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76 Publikationen
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2936223 
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| PDF | DOI | PubMed | Europe PMC
Belmann, Peter, Fischer, Björn, Krüger, Jan, Procházka, Michal, Rasche, Helena, Prinz, Manuel, Hanussek, Maximilian, et al. 2019. “de.NBI Cloud federation through ELIXIR AAI”. F1000Research 8: 842.
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
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Pankoke, Helga, Maus, Irena, Loh, Gunnar, Huser, Andrea, Seifert, Jana, Tilker, Alexandra, Hark, Sarah, Sczyrba, Alexander, Pelzer, Stefan, and Kleinbolting, Jessica. 2019. “F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota.”. FEMS microbiology letters.
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923
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Nelkner, Johanna, Henke, Christian, Lin, Timo Wentong, Pätzold, Wiebke, Hassa, Julia, Jaenicke, Sebastian, Grosch, Rita, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. 2019. “Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes”. Genes 10 (6): 424.
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933767
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Fritz, Adrian, Hofmann, Peter, Majda, Stephan, Dahms, Eik, Dröge, Johannes, Fiedler, Jessika, Lesker, Till R., et al. 2019. “CAMISIM: simulating metagenomes and microbial communities”. Microbiome 7: 17.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929
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Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. 2018. “Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants”. Microbial Biotechnology 11 (4): 667-679.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777
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Celis, Juan Sebastián, Wibberg, Daniel, Ramírez-Portilla, Catalina, Rupp, Oliver, Sczyrba, Alexander, Winkler, Anika, Kalinowski, Jörn, and Wilke, Thomas. 2018. “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts”. GigaScience 7 (7): giy075.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593
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Linden, Mikael, Prochazka, Michal, Lappalainen, Ilkka, Bucik, Dominik, Vyskocil, Pavel, Kuba, Martin, Silén, Sami, et al. 2018. “Common ELIXIR Service for Researcher Authentication and Authorisation”. F1000Research 7: 1199.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723
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Meyer, Fernando, Hofmann, Peter, Belmann, Peter, Garrido-Oter, Ruben, Fritz, Adrian, Sczyrba, Alexander, and McHardy, Alice C. 2018. “AMBER: Assessment of Metagenome BinnERs”. GigaScience: giy069.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890
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Huang, Liren, Krüger, Jan, and Sczyrba, Alexander. 2018. “Analyzing large scale genomic data on the cloud with Sparkhit”. Bioinformatics 34 (9): 1457-1465.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920750
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Maus, Irena, Rumming, Madis, Bergmann, Ingo, Heeg, Kathrin, Pohl, Marcel, Nettmann, Edith, Jaenicke, Sebastian, et al. 2018. “Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors”. Biotechnology for Biofuels 11: 167.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918275
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Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, Alexander, Littmann, S., and Emerson, D. 2018. “Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea”. Applied and Environmental Microbiology 84 (9): e02239-17.
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914959
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da Schoren Costa, Pedro, Bolzan de Campos, Samanta, Albersmeier, Andreas, Dirksen, Paul, Pereira Dresseno, André Luis, Andrade Pais dos Santos, Odair José, Lima Milani, Karina Maria, et al. 2018. “Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approach”. Plant and Soil 422 (1-2): 467-478.
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516
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Maus, Irena, Bremges, Andreas, Stolze, Yvonne, Hahnke, Sarah, Cibis, Katharina G., Koeck, Daniela E., Kim, Yong S., et al. 2017. “Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes”. Biotechnology for Biofuels 10 (1): 264.
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
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Yu, Jia, Blom, Jochen, Sczyrba, Alexander, and Goesmann, Alexander. 2017. “Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism”. Journal of Biotechnology 257: 58-60.
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
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Jünemann, Sebastian, Kleinbölting, Nils, Jaenicke, Sebastian, Henke, Christian, Hassa, Julia, Nelkner, Johanna, Stolze, Yvonne, et al. 2017. “Bioinformatics for NGS-based metagenomics and the application to biogas research”. Journal of Biotechnology 261 (SI): 10-23.
2017 | Datenpublikation | PUB-ID: 2914921
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| Dateien verfügbar | DOI
Huang, Liren, Krüger, Jan, and Sczyrba, Alexander. 2017. Sparkhit evaluation data set. Bielefeld University.
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367
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Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, et al. 2017. “Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software”. Nature Methods 14 (11): 1063-1071.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815
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Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. 2016. “Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants”. Biotechnology for Biofuels 9: 156.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633
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Lux, Markus, Krüger, Jan, Rinke, Christian, Maus, Irena, Schlüter, Andreas, Woyke, Tanja, Sczyrba, Alexander, and Hammer, Barbara. 2016. “acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data”. BMC Bioinformatics 17: 543.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904836
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Heyer, R., Benndorf, D., Kohrs, F., De Vrieze, J., Boon, N., Hoffmann, M., Rapp, E., Schlüter, Andreas, Sczyrba, Alexander, and Reichl, U. 2016. “Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type”. Biotechnology for Biofuels 9 (1): 155.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489
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Maus, Irena, Cibis, Katharina Gabriela, Bremges, Andreas, Stolze, Yvonne, Wibberg, Daniel, Tomazetto, Geizecler, Blom, Jochen, et al. 2016. “Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment”. Journal of Biotechnology 232: 50-60.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302
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Wibberg, Daniel, Bremges, Andreas, Dammann-Kalinowski, Tanja, Maus, Irena, Igeño, Maria Isabel, Vogelsang, Ralph, König, Christoph, et al. 2016. “Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing”. Journal of Biotechnology 232: 61-68.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901418
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Campos, Samanta B., Lisboa, Bruno B., Camargo, Flavio A.O., Bayer, Cimelio, Sczyrba, Alexander, Dirksen, Paul, Albersmeier, Andreas, et al. 2016. “Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systems”. Soil Biology and Biochemistry 96: 191-197.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190
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Stiefel, Fabian, Fischer, Simon, Sczyrba, Alexander, Otte, Kerstin, and Hesse, Friedemann. 2016. “miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering”. Journal of Biotechnology 225: 31-43.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729
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Bremges, Andreas, Singer, Esther, Woyke, Tanja, and Sczyrba, Alexander. 2016. “MeCorS: Metagenome-enabled error correction of single cell sequencing reads”. Bioinformatics 32 (14): 2199-2201.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900928
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Nesme, Joseph, Achouak, Wafa, Agathos, Spiros, Bailey, Mark, Baldrian, Petr, Brunel, Dominique, Frostegard, Asa, et al. 2016. “Back to the future of soil metagenomics”. Frontiers in Microbiology 7: 73.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901675
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Krahn, Thomas, Wibberg, Daniel, Maus, Irena, Winkler, Anika, Bontron, Séverine, Sczyrba, Alexander, Nordmann, Patrice, Pühler, Alfred, Poirel, Laurent, and Schlüter, Andreas. 2016. “Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene.”. Antimicrobial Agents and Chemotherapy 60 (5): 3032-3040.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905260
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Maus, Irena, Koeck, Daniela E., Cibis, Katharina G., Hahnke, Sarah, Kim, Yong S., Langer, Thomas, Kreubel, Jana, et al. 2016. “Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates”. Biotechnology for Biofuels 9 (1): 171.
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234
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Ortseifen, Vera, Stolze, Yvonne, Maus, Irena, Sczyrba, Alexander, Bremges, Andreas, Albaum, Stefan, Jaenicke, Sebastian, Fracowiak, Jochen, Pühler, Alfred, and Schlüter, Andreas. 2016. “An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant”. Journal of Biotechnology 231: 268-279.
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906
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Bremges, Andreas, Maus, Irena, Belmann, Peter, Eikmeyer, Felix Gregor, Winkler, Anika, Albersmeier, Andreas, Pühler, Alfred, Schlüter, Andreas, and Sczyrba, Alexander. 2015. “Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant”. GigaScience 4 (1): 33.
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833
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Kohrs, Fabian, Wolter, Sophie, Benndorf, Dirk, Heyer, Robert, Hoffmann, Marcus, Rapp, Erdmann, Bremges, Andreas, Sczyrba, Alexander, Schlüter, Andreas, and Reichl, Udo. 2015. “Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities”. Proteomics 15 (20): 3585-3589.
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183
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Field, Erin K., Sczyrba, Alexander, Lyman, Audrey E., Harris, Christopher C., Woyke, Tanja, Stepanauskas, Ramunas, and Emerson, David. 2015. “Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount”. The ISME journal 9: 857-870.
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501
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Belmann, Peter, Dröge, Johannes, Bremges, Andreas, McHardy, Alice C, Sczyrba, Alexander, and Barton, Michael D. 2015. “Bioboxes: standardised containers for interchangeable bioinformatics software”. GigaScience 4: 47.
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156
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Paul, Blair G., Bagby, Sarah C., Czornyj, Elizabeth, Arambula, Diego, Handa, Sumit, Sczyrba, Alexander, Ghosh, Partho, Miller, Jeff F., and Valentine, David L. 2015. “Targeted diversity generation by intraterrestrial archaea and archaeal viruses”. Nature Communications 6: 6585.
2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466
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Osterholz, Benedikt, Wiebke, Pätzold, Fust, Annika, Rumming, Madis, Schlüter, Andreas, and Sczyrba, Alexander. 2015. “A Bioinformatics Pipeline for the Detection of β-lactamase Genes in Metagenome Sequence Data and its Application to Production-Scale Biogas Plants”. Presented at the 3rd International Symposium on the environmental Dimension of Antibiotic Resistance, Wernigerode , ed. Julius Kühn-Institut, Bundesforschungsinstitut für Kulturpflanzen Institut für Epidemiologie und Pathogendiagnostik.
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992
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Piao, Hailan, Lachman, Medora, Malfatti, Stephanie, Sczyrba, Alexander, Knierim, Bernhard, Auer, Manfred, Tringe, Susannah Green, Mackie, Roderick Ian, Yeoman, Carl James, and Hess, Matthias. 2014. “Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling”. Frontiers in Microbiology 5 (307).
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433
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Kamke, Janine, Rinke, Christian, Schwientek, Patrick, Mavromatis, Kostas, Ivanova, Natalia, Sczyrba, Alexander, Woyke, Tanja, and Hentschel, Ute. 2014. “The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features”. PLoS ONE 9 (1): e87353.
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689051
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Ghylin, Trevor W., Garcia, Sarahi L., Moya, Francisco, Oyserman, Ben O., Schwientek, Patrick, Forest, Katrina T., Mutschler, James, et al. 2014. “Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage”. The ISME Journal 8 (12): 2503-2516.
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2698163
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Heins, Richard A, Cheng, Xiaoliang, Nath, Sangeeta, Deng, Kai, Bowen, Benjamin P, Chivian, Dylan C, Datta, Supratim, et al. 2014. “Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry”. ACS chemical biology 9 (9): 2082-2091.
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2672695
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Swan, Brandon K., Chaffin, Mark D., Martinez-Garcia, Manuel, Morrison, Hilary G., Field, Erin K., Poulton, Nicole J., Masland, E. Dashiell P., et al. 2014. “Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres”. PloS one 9 (4): 95380.
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
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Henrich, Birgit, Rumming, Madis, Sczyrba, Alexander, Velleuer, Eunike, Dietrich, Ralf, Gerlach, Wolfgang, Gombert, Michael, et al. 2014. “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”. PLoS ONE 9 (3): e92297.
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2662055
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Wibberg, Daniel, Luque-Almagro, Víctor M., Igeño, M. Isabel, Bremges, Andreas, Roldán, M. Dolores, Merchán, Faustino, Sáez, Lara P., et al. 2014. “Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344”. Journal of biotechnology 175: 67-68.
2013 | Konferenzbeitrag | PUB-ID: 2909357
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Gisbrecht, Andrej, Hammer, Barbara, Mokbel, Bassam, and Sczyrba, Alexander. 2013. “Nonlinear dimensionality reduction for cluster identification in metagenomic samples”. In IV, 174-179.
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500
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Gisbrecht, Andrej, Hammer, Barbara, Mokbel, Bassam, and Sczyrba, Alexander. 2013. “Nonlinear dimensionality reduction for cluster identification in metagenomic samples”. In 17th International Conference on Information Visualisation IV 2013, ed. Ebad Banissi, 174-179.
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613567
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Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N, Anderson, Iain J, Cheng, Jan-Fang, Darling, Aaron, et al. 2013. “Insights into the phylogeny and coding potential of microbial dark matter”. Nature 499 (7459): 431-437.
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424
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Campbell, James H., O'Donoghue, Patrick, Campbell, Alisha G., Schwientek, Patrick, Sczyrba, Alexander, Woyke, Tanja, Söll, Dieter, and Podar, Mircea. 2013. “UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota”. Proceedings of the National Academy of Sciences of the United States of America 110 (14): 5540-5545.
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352
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Kamke, Janine, Sczyrba, Alexander, Ivanova, Natalia, Schwientek, Patrick, Rinke, Christian, Mavromatis, Kostas, Woyke, Tanja, and Hentschel, Ute. 2013. “Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges”. The ISME journal 7 (12): 2287-2300.
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234
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Zaremba-Niedzwiedzka, Katarzyna, Viklund, Johan, Zhao, Weizhou, Ast, Jennifer, Sczyrba, Alexander, Woyke, Tanja, McMahon, Katherina, Bertilsson, Stefan, Stepanauskas, Ramunas, and Andersson, Siv Ge. 2013. “Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade”. Genome biology 14 (11): R130.