Alexander Sczyrba

asczyrba@techfak.uni-bielefeld.de
ORCID logo https://orcid.org/0000-0002-4405-3847

PEVZ-ID
17894

107 Publikationen

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  • [107]
    2024 | Preprint | Veröffentlicht | PUB-ID: 2993878
    Belmann, P., Osterholz, B., Kleinboelting, N., Pühler, A., Schlüter, A., & Sczyrba, A. (2024). Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource Allocation. bioRxiv. https://doi.org/10.1101/2024.10.22.619569
    PUB | DOI
     
  • [106]
    2024 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985402
    Heyer, R., Hellwig, P., Maus, I., Walke, D., Schlüter, A., Hassa, J., Sczyrba, A., et al. (2024). Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter. Water Research, 250, 121020. https://doi.org/10.1016/j.watres.2023.121020
    PUB | DOI
     
  • [105]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2977923 OA
    Nelkner, J., Huang, L., Lin, T. W., Schulz, A., Osterholz, B., Henke, C., Blom, J., et al. (2023). Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis. Environmental Microbiome, 18(1), 26. https://doi.org/10.1186/s40793-023-00479-9
    PUB | PDF | DOI | WoS | PubMed | Europe PMC
     
  • [104]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2983209 OA
    Hassa, J., Tubbesing, T. J., Maus, I., Heyer, R., Benndorf, D., Effenberger, M., Henke, C., et al. (2023). Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms, 11(10), 2412. https://doi.org/10.3390/microorganisms11102412
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  • [103]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984553
    Schimmler, S., Altenhöner, R., Bernard, L., Fluck, J., Klinger, A., Lorenz, S., Mathiak, B., et al. (2023). Base4NFDI - Basic Services for NFDI. Proceedings of the Conference on Research Data Infrastructure, 1. https://doi.org/10.52825/cordi.v1i.336
    PUB | DOI
     
  • [102]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984552
    Hoffmann, N., Maus, I., Beier, S., Belmann, P., Krüger, J., Tauch, A., Goesmann, A., et al. (2023). Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. Proceedings of the Conference on Research Data Infrastructure, 1. https://doi.org/10.52825/cordi.v1i.387
    PUB | DOI
     
  • [101]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984551
    Förstner, K. U., Becker, A., Blom, J., Bork, P., Clavel, T., Dieckmann, M., Goesmann, A., et al. (2023). NFDI4Microbiota – national research data infrastructure for microbiota research. Research Ideas and Outcomes, 9. https://doi.org/10.3897/rio.9.e110501
    PUB | DOI
     
  • [100]
    2023 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2979860
    Wolf, M., Schallert, K., Knipper, L., Sickmann, A., Sczyrba, A., Benndorf, D., & Heyer, R. (2023). Advances in the clinical use of metaproteomics. Expert review of proteomics. https://doi.org/10.1080/14789450.2023.2215440
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [99]
    2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2968667
    Olo Ndela, E., Roux, S., Henke, C., Sczyrba, A., Sime Ngando, T., Varsani, A., & Enault, F. (2023). Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evolution , 9(1), veac123. https://doi.org/10.1093/ve/veac123
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [98]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2969509
    Neri, U., Wolf, Y. I., Roux, S., Camargo, A. P., Lee, B., Kazlauskas, D., Chen, I. M., et al. (2022). Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell, 185(21), 4023-4037.e18. https://doi.org/10.1016/j.cell.2022.08.023
    PUB | DOI | WoS | PubMed | Europe PMC
     
  • [97]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2969511
    Fremin, B. J., Bhatt, A. S., Kyrpides, N. C., Sengupta, A., Sczyrba, A., Maria da Silva, A., Buchan, A., et al. (2022). Thousands of small, novel genes predicted in global phage genomes. Cell Reports, 39(12), 110984. https://doi.org/10.1016/j.celrep.2022.110984
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  • [96]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967098
    Khesali Aghtaei, H., Püttker, S., Maus, I., Heyer, R., Huang, L., Sczyrba, A., Reichl, U., et al. (2022). Adaptation of a microbial community to demand-oriented biological methanation. Biotechnology for Biofuels and Bioproducts, 15(1), 125. https://doi.org/10.1186/s13068-022-02207-w
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  • [95]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966901 OA
    Maus, I., Wibberg, D., Belmann, P., Hahnke, S., Huang, L., Spröer, C., Bunk, B., et al. (2022). The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses. Frontiers in Microbiology, 13, 1032515. https://doi.org/10.3389/fmicb.2022.1032515
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  • [94]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966286 OA
    Joshi, A., Young, D., Huang, L., Mosberger, L., Munk, B., Vinzelj, J., Flad, V., et al. (2022). Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats. Microorganisms, 10(10), 1972. https://doi.org/10.3390/microorganisms10101972
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  • [93]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2965465 OA
    Young, D., Joshi, A., Huang, L., Munk, B., Wurzbacher, C., Youssef, N. H., Elshahed, M. S., et al. (2022). Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages. Microorganisms, 10(9), 1749. https://doi.org/10.3390/microorganisms10091749
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  • [92]
    2022 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2963745 OA
    Sczyrba A., & German Network for Bioinformatics Infrastructure (de.NBI) (Eds.) (2022). Development and Operation of the Federated de.NBI Cloud: Contributions of the German Network for Bioinformatics Infrastructure. Bielefeld: Center for Biotechnology, de.NBI Administration Office. https://doi.org/10.4119/unibi/2963745
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  • [91]
    2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2962388
    Meyer, F., Fritz, A., Deng, Z. - L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., et al. (2022). Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods, 19, 429-440. https://doi.org/10.1038/s41592-022-01431-4
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  • [90]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2950292 OA
    Blifernez-Klassen, O., Klassen, V., Wibberg, D., Cebeci, E., Henke, C., Rückert, C., Chaudhari, S., et al. (2021). Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia. Scientific Reports, 11(1), 1726. https://doi.org/10.1038/s41598-021-81082-1
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  • [89]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2957501 OA
    Brandt, D., Simunovic, M., Busche, T., Haak, M., Belmann, P., Jünemann, S., Schulz, T., et al. (2021). Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines. Viruses, 13(9), 1870. https://doi.org/10.3390/v13091870
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  • [88]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2956369
    Fritz, A., Bremges, A., Deng, Z. - L., Lesker, T. R., Götting, J., Ganzenmueller, T., Sczyrba, A., et al. (2021). Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biology, 22(1), 212. https://doi.org/10.1186/s13059-021-02426-8
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  • [87]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2960171
    Van Den Bossche, T., Kunath, B. J., Schallert, K., Schäpe, S. S., Abraham, P. E., Armengaud, J., Arntzen, M. Ø., et al. (2021). Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 12(1), 7305. https://doi.org/10.1038/s41467-021-27542-8
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  • [86]
    2021 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2960900
    Leitner, F., Carazo, J. M., Bischof, J., Haley, N., Audergon, P., Sorzano, C. O., del Cano, L., et al. (2021). EOSC-Life Report on the work of the initial demonstrators. Presented at the . https://doi.org/10.5281/zenodo.4817723
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  • [85]
    2021 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2955512
    Aevarsson, A., Kaczorowska, A. - K., Adalsteinsson, B. T., Ahlqvist, J., Al-Karadaghi, S., Altenbuchner, J., Arsin, H., et al. (2021). Going to extremes - a metagenomic journey into the dark matter of life. FEMS microbiology letters, fnab067. https://doi.org/10.1093/femsle/fnab067
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  • [84]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952275
    Meyer, F., Lesker, T. - R., Koslicki, D., Fritz, A., Gurevich, A., Darling, A. E., Sczyrba, A., et al. (2021). Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit. Nature Protocols, 16(4), 1785–1801. https://doi.org/10.1038/s41596-020-00480-3
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  • [83]
    2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2951537 OA
    Tabacchioni, S., Passato, S., Ambrosino, P., Huang, L., Caldara, M., Cantale, C., Hett, J., et al. (2021). Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture. Microorganisms, 9(2), 426. https://doi.org/10.3390/microorganisms9020426
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  • [82]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941645 OA
    Maus, I., Klocke, M., Derenkó, J., Stolze, Y., Beckstette, M., Jost, C., Wibberg, D., et al. (2020). Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics. Environmental Microbiome, 15(1), 7. https://doi.org/10.1186/s40793-020-00354-x
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  • [81]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2953267
    Schulte-Schrepping, J., Reusch, N., Paclik, D., Baßler, K., Schlickeiser, S., Zhang, B., Krämer, B., et al. (2020). Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell, 182(6), 1419-1440.e23. https://doi.org/10.1016/j.cell.2020.08.001
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  • [80]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2944226 OA
    Rettenmaier, R., Schneider, M., Munk, B., Lebuhn, M., Jünemann, S., Sczyrba, A., Maus, I., et al. (2020). Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum. Microorganisms, 8(6), 915. https://doi.org/10.3390/microorganisms8060915
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  • [79]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2949597 OA
    Maus, I., Tubbesing, T. J., Wibberg, D., Heyer, R., Hassa, J., Tomazetto, G., Huang, L., et al. (2020). The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms, 8(12), 2024. doi:10.3390/microorganisms8122024
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  • [78]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2948401 OA
    Moore, M., Wesemann, C., Gossmann, N., Sahm, A., Krüger, J., Sczyrba, A., & Dietz, K. - J. (2020). ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom. BMC Bioinformatics, 21(1), 490. doi:10.1186/s12859-020-03749-2
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  • [77]
    2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941704
    Lesker, T. R., Durairaj, A. C., Galvez, E. J. C., Lagkouvardos, I., Baines, J. F., Clavel, T., Sczyrba, A., et al. (2020). An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. Cell reports, 30(9), 2909-2922.e6. doi:10.1016/j.celrep.2020.02.036
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  • [76]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923 OA
    Nelkner, J., Henke, C., Lin, T. W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., et al. (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. https://doi.org/10.3390/genes10060424
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  • [75]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933767
    Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., Lesker, T. R., et al. (2019). CAMISIM: simulating metagenomes and microbial communities. Microbiome, 7(1), 17. https://doi.org/10.1186/s40168-019-0633-6
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  • [74]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
    Pankoke, H., Maus, I., Loh, G., Huser, A., Seifert, J., Tilker, A., Hark, S., et al. (2019). Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota. FEMS microbiology letters. https://doi.org/10.1093/femsle/fnz033
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  • [73]
    2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2936223 OA
    Belmann, P., Fischer, B., Krüger, J., Procházka, M., Rasche, H., Prinz, M., Hanussek, M., et al. (2019). de.NBI Cloud federation through ELIXIR AAI. F1000Research, 8, 842. doi:10.12688/f1000research.19013.1
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  • [72]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593
    Linden, M., Prochazka, M., Lappalainen, I., Bucik, D., Vyskocil, P., Kuba, M., Silén, S., et al. (2018). Common ELIXIR Service for Researcher Authentication and Authorisation. F1000Research, 7, 1199. https://doi.org/10.12688/f1000research.15161.1
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  • [71]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723
    Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A., & McHardy, A. C. (2018). AMBER: Assessment of Metagenome BinnERs. GigaScience, 7(6), giy069. https://doi.org/10.1093/gigascience/giy069
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  • [70]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777
    Celis, J. S., Wibberg, D., Ramírez-Portilla, C., Rupp, O., Sczyrba, A., Winkler, A., Kalinowski, J., et al. (2018). Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience, 7(7), giy075. doi:10.1093/gigascience/giy075
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  • [69]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920750
    Maus, I., Rumming, M., Bergmann, I., Heeg, K., Pohl, M., Nettmann, E., Jaenicke, S., et al. (2018). Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnology for Biofuels, 11(1), 167. doi:10.1186/s13068-018-1162-4
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  • [68]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890
    Huang, L., Krüger, J., & Sczyrba, A. (2018). Analyzing large scale genomic data on the cloud with Sparkhit. Bioinformatics, 34(9), 1457-1465. doi:10.1093/bioinformatics/btx808
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  • [67]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929
    Stolze, Y., Bremges, A., Maus, I., Pühler, A., Sczyrba, A., & Schlüter, A. (2018). Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants. Microbial Biotechnology, 11(4), 667-679. doi:10.1111/1751-7915.12982
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  • [66]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914959
    da Schoren Costa, P., Bolzan de Campos, S., Albersmeier, A., Dirksen, P., Pereira Dresseno, A. L., Andrade Pais dos Santos, O. J., Lima Milani, K. M., 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. doi:10.1007/s11104-017-3492-6
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  • [65]
    2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918275
    Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, A., Littmann, S., & Emerson, D. (2018). Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology, 84(9), e02239-17. doi:10.1128/aem.02239-17
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  • [64]
    2017 | Zeitschriftenaufsatz | PUB-ID: 2913876
    Sczyrba, A., Hofman, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., et al. (2017). Benchmark data sets, software results and reference data for the first CAMI challenge. GigaScience Database. https://doi.org/10.5524/100344
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  • [63]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367
    Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., et al. (2017). Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods, 14(11), 1063-1071. https://doi.org/10.1038/nmeth.4458
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  • [62]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153 OA
    Yu, J., Blom, J., Sczyrba, A., & Goesmann, A. (2017). Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Journal of Biotechnology, 257, 58-60. https://doi.org/10.1016/j.jbiotec.2017.02.020
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  • [61]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516 OA
    Maus, I., Bremges, A., Stolze, Y., Hahnke, S., Cibis, K. G., Koeck, D. E., Kim, Y. S., et al. (2017). Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels, 10(1), 264. doi:10.1186/s13068-017-0947-1
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  • [60]
    2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
    Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., et al. (2017). Bioinformatics for NGS-based metagenomics and the application to biogas research. Journal of Biotechnology, 261(SI), 10-23. doi:10.1016/j.jbiotec.2017.08.012
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  • [59]
    2017 | Datenpublikation | PUB-ID: 2914921 OA
    Huang, L., Krüger, J., & Sczyrba, A. (2017). Sparkhit evaluation data set. Bielefeld University. doi:10.4119/unibi/2914921
    PUB | Dateien verfügbar | DOI
     
  • [58]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904836
    Heyer, R., Benndorf, D., Kohrs, F., De Vrieze, J., Boon, N., Hoffmann, M., Rapp, E., et al. (2016). Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnology for Biofuels, 9(1), 155. doi:10.1186/s13068-016-0572-4
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  • [57]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905260
    Maus, I., Koeck, D. E., Cibis, K. G., Hahnke, S., Kim, Y. S., Langer, T., Kreubel, J., 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. doi:10.1186/s13068-016-0581-3
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  • [56]
    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729
    Bremges, A., Singer, E., Woyke, T., & Sczyrba, A. (2016). MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics, 32(14), 2199-2201. doi:10.1093/bioinformatics/btw144
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900928
    Nesme, J., Achouak, W., Agathos, S., Bailey, M., Baldrian, P., Brunel, D., Frostegard, A., et al. (2016). Back to the future of soil metagenomics. Frontiers in Microbiology, 7, 73. doi:10.3389/fmicb.2016.00073
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    Stolze, Y., Bremges, A., Rumming, M., Henke, C., Maus, I., Pühler, A., Sczyrba, A., et al. (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(1), 156. doi:10.1186/s13068-016-0565-3
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633 OA
    Lux, M., Krüger, J., Rinke, C., Maus, I., Schlüter, A., Woyke, T., Sczyrba, A., et al. (2016). acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data. BMC Bioinformatics, 17(1), 543. doi:10.1186/s12859-016-1397-7
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489
    Maus, I., Cibis, K. G., Bremges, A., Stolze, Y., Wibberg, D., Tomazetto, G., Blom, J., 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. doi:10.1016/j.jbiotec.2016.05.001
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302
    Wibberg, D., Bremges, A., Dammann-Kalinowski, T., Maus, I., Igeño, M. I., Vogelsang, R., König, C., 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. doi:10.1016/j.jbiotec.2016.04.008
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901418
    Campos, S. B., Lisboa, B. B., Camargo, F. A. O., Bayer, C., Sczyrba, A., Dirksen, P., Albersmeier, A., 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. doi:10.1016/j.soilbio.2016.02.010
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190
    Stiefel, F., Fischer, S., Sczyrba, A., Otte, K., & Hesse, F. (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. doi:10.1016/j.jbiotec.2016.03.028
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901675
    Krahn, T., Wibberg, D., Maus, I., Winkler, A., Bontron, S., Sczyrba, A., Nordmann, P., et al. (2016). Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene. Antimicrobial Agents and Chemotherapy, 60(5), 3032-3040. doi:10.1128/AAC.00124-16
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    2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234
    Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S., Jaenicke, S., et al. (2016). An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology, 231, 268-279. doi:10.1016/j.jbiotec.2016.06.014
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    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906 OA
    Bremges, A., Maus, I., Belmann, P., Eikmeyer, F. G., Winkler, A., Albersmeier, A., Pühler, A., et al. (2015). Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. GigaScience, 4(1), 33. https://doi.org/10.1186/s13742-015-0073-6
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    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501
    Belmann, P., Dröge, J., Bremges, A., McHardy, A. C., Sczyrba, A., & Barton, M. D. (2015). Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience, 4(1), 47. https://doi.org/10.1186/s13742-015-0087-0
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    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156
    Paul, B. G., Bagby, S. C., Czornyj, E., Arambula, D., Handa, S., Sczyrba, A., Ghosh, P., et al. (2015). Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nature Communications, 6(1), 6585. doi:10.1038/ncomms7585
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    2015 | Preprint | Veröffentlicht | PUB-ID: 2901613
    Lux, M., Hammer, B., & Sczyrba, A. (2015). Automated Contamination Detection in Single-Cell Sequencing. bioRxiv
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    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833
    Kohrs, F., Wolter, S., Benndorf, D., Heyer, R., Hoffmann, M., Rapp, E., Bremges, A., et al. (2015). Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics, 15(20), 3585-3589. doi:10.1002/pmic.201400557
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    2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466
    Osterholz, B., Wiebke, P., Fust, A., Rumming, M., Schlüter, A., & Sczyrba, A. (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.
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    2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183
    Field, E. K., Sczyrba, A., Lyman, A. E., Harris, C. C., Woyke, T., Stepanauskas, R., & Emerson, D. (2015). Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. The ISME journal, 9(4), 857-870. doi:10.1038/ismej.2014.183
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    2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901612
    Lux, M., Sczyrba, A., & Hammer, B. (2015). Automatic discovery of metagenomic structure. 2015 International Joint Conference on Neural Networks (IJCNN) Institute of Electrical & Electronics Engineers (IEEE). doi:10.1109/ijcnn.2015.7280500
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    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992
    Piao, H., Lachman, M., Malfatti, S., Sczyrba, A., Knierim, B., Auer, M., Tringe, S. G., et al. (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), 307. doi:10.3389/fmicb.2014.00307
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    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2698163
    Heins, R. A., Cheng, X., Nath, S., Deng, K., Bowen, B. P., Chivian, D. C., Datta, S., 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. doi:10.1021/cb500244v
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    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433
    Kamke, J., Rinke, C., Schwientek, P., Mavromatis, K., Ivanova, N., Sczyrba, A., Woyke, T., et al. (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. doi:10.1371/journal.pone.0087353
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    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689051
    Ghylin, T. W., Garcia, S. L., Moya, F., Oyserman, B. O., Schwientek, P., Forest, K. T., Mutschler, J., et al. (2014). Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal, 8(12), 2503-2516. doi:10.1038/ismej.2014.135
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    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2672695
    Swan, B. K., Chaffin, M. D., Martinez-Garcia, M., Morrison, H. G., Field, E. K., Poulton, N. J., Masland, E. D. P., et al. (2014). Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres. PloS one, 9(4), e95380. doi:10.1371/journal.pone.0095380
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    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
    Henrich, B., Rumming, M., Sczyrba, A., Velleuer, E., Dietrich, R., Gerlach, W., Gombert, M., et al. (2014). Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma. PLoS ONE, 9(3), e92297. doi:10.1371/journal.pone.0092297
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    2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2662055
    Wibberg, D., Luque-Almagro, V. M., Igeño, M. I., Bremges, A., Roldán, M. D., Merchán, F., Sáez, L. P., et al. (2014). Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Journal of biotechnology, 175, 67-68. doi:10.1016/j.jbiotec.2014.02.004
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    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234
    Zaremba-Niedzwiedzka, K., Viklund, J., Zhao, W., Ast, J., Sczyrba, A., Woyke, T., McMahon, K., et al. (2013). Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology, 14(11), R130. doi:10.1186/gb-2013-14-11-r130
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    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613567
    Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J. - F., Darling, A., et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499(7459), 431-437. doi:10.1038/nature12352
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    2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500
    Gisbrecht, A., Hammer, B., Mokbel, B., & Sczyrba, A. (2013). Nonlinear dimensionality reduction for cluster identification in metagenomic samples. In E. Banissi (Ed.), 17th International Conference on Information Visualisation IV 2013 (pp. 174-179). Piscataway, NJ: IEEE. doi:10.1109/IV.2013.22
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    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563543
    Campbell, A. G., Campbell, J. H., Schwientek, P., Woyke, T., Sczyrba, A., Allman, S., Beall, C. J., et al. (2013). Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity. PLoS ONE, 8(3), e59361. doi:10.1371/journal.pone.0059361
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    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424
    Campbell, J. H., O'Donoghue, P., Campbell, A. G., Schwientek, P., Sczyrba, A., Woyke, T., Söll, D., et al. (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. doi:10.1073/pnas.1303090110
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    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352
    Kamke, J., Sczyrba, A., Ivanova, N., Schwientek, P., Rinke, C., Mavromatis, K., Woyke, T., et al. (2013). Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. The ISME journal, 7(12), 2287-2300. https://doi.org/10.1038/ismej.2013.111
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    2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613623
    Swan, B. K., Tupper, B., Sczyrba, A., Lauro, F. M., Martinez-Garcia, M., González, J. M., Luo, H., et al. (2013). Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America, 110(28), 11463-11468. doi:10.1073/pnas.1304246110
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    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2518330
    Garcia, S. L., McMahon, K. D., Martinez-Garcia, M., Srivastava, A., Sczyrba, A., Stepanauskas, R., Grossart, H. - P., et al. (2012). Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME journal, 7(1), 137-147. doi:10.1038/ismej.2012.86
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    2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2547307
    El-Kalioby, M., Abouelhoda, M., Krüger, J., Giegerich, R., Sczyrba, A., Wall, D. P., & Tonellato, P. (2012). Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics, 13(Suppl 17), S22. doi:10.1186/1471-2105-13-S17-S22
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    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410148
    Woyke, T., Sczyrba, A., Lee, J., Rinke, C., Tighe, D., Clingenpeel, S., Malmstrom, R., et al. (2011). Decontamination of MDA Reagents for Single Cell Whole Genome Amplification. PLoS ONE, 6(10), e26161. https://doi.org/10.1371/journal.pone.0026161
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    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2351462
    Kim, T. - W., Chokhawala, H. A., Hess, M., Dana, C. M., Baer, Z., Sczyrba, A., Rubin, E. M., et al. (2011). High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery. Angewandte Chemie, 123(47), 11411-11414. https://doi.org/10.1002/ange.201104685
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    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2329885
    Swan, B. K., Martinez-Garcia, M., Preston, C. M., Sczyrba, A., Woyke, T., Lamy, D., Reinthaler, T., et al. (2011). Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean. Science, 333(6047), 1296-1300. https://doi.org/10.1126/science.1203690
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    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2789582
    Sales, C. M., Mahendra, S., Grostern, A., Parales, R. E., Goodwin, L. A., Woyke, T., Nolan, M., et al. (2011). Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190. Journal of Bacteriology, 193(17), 4549-4550. doi:10.1128/JB.00415-11
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    2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991643
    Hess, M., Sczyrba, A., Egan, R., Kim, T. W., Chokhawala, H., Schroth, G., Luo, S., et al. (2011). Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 331(6016), 463-467. https://doi.org/10.1126/science.1200387
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    2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991615
    Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Desai, N., Eisen, J. A., et al. (2010). Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci, 3(3), 243-248. https://doi.org/10.4056/sigs.1433550
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    2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020 OA
    Lamprecht, A. - L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., & Giegerich, R. (2008). GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics, 9(Suppl 4), S13. https://doi.org/10.1186/1471-2105-9-S4-S13
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    2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588303
    Sczyrba, A., Konermann, S., & Giegerich, R. (2008). Two interactive bioinformatics courses at the bielefeld university bioinformatics server. BRIEFINGS IN BIOINFORMATICS, 9(3), 243-249. https://doi.org/10.1093/bib/bbm063
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    2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756 OA
    Spitzer, M., Lorkowski, S., Cullen, P., Sczyrba, A., & Fuellen, G. (2006). IsoSVM - Distinguishing isoforms and paralogs on the protein level. BMC Bioinformatics, 7(1), 110. https://doi.org/10.1186/1471-2105-7-110
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    2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773613 OA
    Sczyrba, A., Beckstette, M., Brivanlou, A. H., Giegerich, R., & Altmann, C. R. (2005). XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics, 6(1), 123. https://doi.org/10.1186/1471-2164-6-123
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    2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383529 OA
    Beckstette, M., Mailänder, J. T., Marhöfer, R. J., Sczyrba, A., Ohlebusch, E., Giegerich, R., & Selzer, P. M. (2004). Genlight: Interactive high-throughput sequence analysis and comparative genomics. Journal of Integrative Bioinformatics, 1(1), 90-107. https://doi.org/10.2390/biecoll-jib-2004-8
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    2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383536
    Beckstette, M., Sczyrba, A., & Selzer, P. M. (2004). Genlight: Interactive high-throughput sequence analysis and comparative genomics. In R. Giegerich (Ed.), GI-Edition / Proceedings: Vol. 53. German Conference on Bioinformatics. GCB 2004 ; October 4 - 6, 2004, Bielefeld, Germany (pp. 179-186). Bonn: Gesellschaft für Informatik.
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    2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383561
    Sczyrba, A., Beckstette, M., Giegerich, R., & Altman, C. (2004). Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis. In R. Giegerich & J. Stoye (Eds.), GI-Edition / Proceedings: Vol. 53. German Conference on Bioinformatics 2004 : GCB 2004, October 4 - 6, 2004, Bielefeld, Germany (pp. 6-7). Bonn: Gesellschaft für Informatik.
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    2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607400 OA
    Taher, L., Rinner, O., Garg, S., Sczyrba, A., & Morgenstern, B. (2004). AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research, 32(Web Server), W305-W308. https://doi.org/10.1093/nar/gkh386
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    2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607394 OA
    Krüger, J., Sczyrba, A., Kurtz, S., & Giegerich, R. (2004). e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. NUCLEIC ACIDS RESEARCH, 32(Web Server), W301-W304. https://doi.org/10.1093/nar/gkh478
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    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610494
    Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., & Morgenstern, B. (2003). AGenDA: homology-based gene prediction. BIOINFORMATICS, 19(12), 1575-1577. https://doi.org/10.1093/bioinformatics/btg181
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    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773844 OA
    Sczyrba, A., Krüger, J., Mersch, H., Kurtz, S., & Giegerich, R. (2003). RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Research, 31(13), 3767-3770. https://doi.org/10.1093/nar/gkg576
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    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612470
    Morgenstern, B., Goel, S., Sczyrba, A., & Dress, A. (2003). AltAVisT: Comparing alternative multiple sequence alignments. BIOINFORMATICS, 19(3), 425-426. https://doi.org/10.1093/bioinformatics/btf882
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    2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609260
    Dondrup, M., Goesmann, A., Bartels, D., Kalinowski, J., Krause, L., Linke, B., Rupp, O., et al. (2003). EMMA: a platform for consistent storage and efficient analysis of microarray data. JOURNAL OF BIOTECHNOLOGY, 106(2-3), 135-146. https://doi.org/10.1016/j.jbiotec.2003.08.010
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    2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897716
    Gopal, S., Schroeder, M., Pieper, U., Sczyrba, A., Aytekin-Kurban, G., Bekiranov, S., Fajardo, J. E., et al. (2001). Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet, 27(3), 337-340.
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    2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1616752
    Altmann, C. R., Bell, E., Sczyrba, A., Pun, J., Bekiranov, S., Gaasterland, T., & Brivanlou, A. H. (2001). Microarray-based analysis of early development in Xenopus laevis. DEVELOPMENTAL BIOLOGY, 236(1), 64-75. https://doi.org/10.1006/dbio.2001.0298
    PUB | DOI | WoS | PubMed | Europe PMC
     
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    2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897767
    Gaasterland, T., Sczyrba, A., Thomas, E., & Kurban, G. (2000). MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region. Genome Res, 10(4), 502-510.
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