PUB - Publikationen an der Universität Bielefeld

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• [107]
  

  2024 | Preprint | Veröffentlicht | PUB-ID: 2993878

  Belmann, P., Osterholz, B., Kleinboelting, N., Pühler, A., Schlüter, A., Sczyrba, A.: Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource Allocation. bioRxiv. (2024).

  PUB | DOI
   
• [106]
  

  2024 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985402

  Heyer, R., Hellwig, P., Maus, I., Walke, D., Schlüter, A., Hassa, J., Sczyrba, A., Tubbesing, T.J., Klocke, M., Mächtig, T., Schallert, K., Seick, I., Reichl, U., Benndorf, D.: Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter. Water Research. 250, : 121020 (2024).

  PUB | DOI
   
• [105]
  

  2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2977923

  Nelkner, J., Huang, L., Lin, T.W., Schulz, A., Osterholz, B., Henke, C., Blom, J., Pühler, A., Sczyrba, A., Schlüter, A.: Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis. Environmental Microbiome. 18, : 26 (2023).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [104]
  

  2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2983209

  Hassa, J., Tubbesing, T.J., Maus, I., Heyer, R., Benndorf, D., Effenberger, M., Henke, C., Osterholz, B., Beckstette, M., Pühler, A., Sczyrba, A., Schlüter, A.: Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms. 11, : 2412 (2023).

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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., Miller, B., Ritz, R., Schörner-Sadenius, T., Sczyrba, A., Stein, R.: Base4NFDI - Basic Services for NFDI. Proceedings of the Conference on Research Data Infrastructure. 1, (2023).

  PUB | DOI
   
• [102]
  

  2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984552

  Hoffmann, N., Maus, I., Beier, S., Belmann, P., Krüger, J., Tauch, A., Goesmann, A., Eils, R., Bork, P., Kohlbacher, O., Kummer, U., Backofen, R., Buchhalter, I., Sczyrba, A.: Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. Proceedings of the Conference on Research Data Infrastructure. 1, (2023).

  PUB | DOI
   
• [101]
  

  2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984551

  Förstner, K.U., Becker, A., Blom, J., Bork, P., Clavel, T., Dieckmann, M., Goesmann, A., Götz, B., Gübitz, T., Hufsky, F., Jünemann, S., Körner, M.-L., Marz, M., Da Rocha, U.N., Overmann, J., Pühler, A., Rebholz-Schuhmann, D., Sczyrba, A., Stoye, J., Vandendorpe, J., Van Rossum, T., McHardy, A.: NFDI4Microbiota – national research data infrastructure for microbiota research. Research Ideas and Outcomes. 9, (2023).

  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.: Advances in the clinical use of metaproteomics. Expert review of proteomics. (2023).

  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.: Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evolution . 9, : veac123 (2023).

  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., Ivanova, N., Zeigler Allen, L., Paez-Espino, D., Bryant, D.A., Bhaya, D., Krupovic, M., Dolja, V.V., Kyrpides, N.C., Koonin, E.V., Gophna, U., Narrowe, A.B., Probst, A.J., Sczyrba, A., Kohler, A., Séguin, A., Shade, A., Campbell, B.J., Lindahl, B.D., Reese, B.K., Roque, B.M., DeRito, C., Averill, C., Cullen, D., Beck, D.A.C., Walsh, D.A., Ward, D.M., Wu, D., Eloe-Fadrosh, E., Brodie, E.L., Young, E.B., Lilleskov, E.A., Castillo, F.J., Martin, F.M., LeCleir, G.R., Attwood, G.T., Cadillo-Quiroz, H., Simon, H.M., Hewson, I., Grigoriev, I.V., Tiedje, J.M., Jansson, J.K., Lee, J., VanderGheynst, J.S., Dangl, J., Bowman, J.S., Blanchard, J.L., Bowen, J.L., Xu, J., Banfield, J.F., Deming, J.W., Kostka, J.E., Gladden, J.M., Rapp, J.Z., Sharpe, J., McMahon, K.D., Treseder, K.K., Bidle, K.D., Wrighton, K.C., Thamatrakoln, K., Nusslein, K., Meredith, L.K., Ramirez, L., Buee, M., Huntemann, M., Kalyuzhnaya, M.G., Waldrop, M.P., Sullivan, M.B., Schrenk, M.O., Hess, M., Vega, M.A., O’Malley, M.A., Medina, M., Gilbert, N.E., Delherbe, N., Mason, O.U., Dijkstra, P., Chuckran, P.F., Baldrian, P., Constant, P., Stepanauskas, R., Daly, R.A., Lamendella, R., Gruninger, R.J., McKay, R.M., Hylander, S., Lebeis, S.L., Esser, S.P., Acinas, S.G., Wilhelm, S.S., Singer, S.W., Tringe, S.S., Woyke, T., Reddy, T.B.K., Bell, T.H., Mock, T., McAllister, T., Thiel, V., Denef, V.J., Liu, W.-T., Martens-Habbena, W., Allen Liu, X.-J., Cooper, Z.S., Wang, Z.: Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell. 185, 4023-4037.e18 (2022).

  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., Gaudin, A., Brune, A., Hirsch, A.M., Neumann, A., Shade, A., Visel, A., Campbell, B., Baker, B., Hedlund, B.P., Crump, B.C., Currie, C., Kelly, C., Craft, C., Hazard, C., Francis, C., Schadt, C.W., Averill, C., Mobilian, C., Buckley, D., Hunt, D., Noguera, D., Beck, D., Valentine, D.L., Walsh, D., Sumner, D., Lymperopoulou, D., Bhaya, D., Bryant, D.A., Morrison, E., Brodie, E., Young, E., Lilleskov, E., Högfors-Rönnholm, E., Chen, F., Stewart, F., Nicol, G.W., Teeling, H., Beller, H.R., Dionisi, H., Liao, H.-L., Beman, J.M., Stegen, J., Tiedje, J., Jansson, J., VanderGheynst, J., Norton, J., Dangl, J., Blanchard, J., Bowen, J., Macalady, J., Pett-Ridge, J., Rich, J., Payet, J.P., Gladden, J.D., Raff, J.D., Klassen, J.L., Tarn, J., Neufeld, J., Gravuer, K., Hofmockel, K., Chen, K.-H., Konstantinidis, K., DeAngelis, K.M., Partida-Martinez, L.P., Meredith, L., Chistoserdova, L., Moran, M.A., Scarborough, M., Schrenk, M., Sullivan, M., David, M., O'Malley, M.A., Medina, M., Habteselassie, M., Ward, N.D., Pietrasiak, N., Mason, O.U., Sorensen, P.O., Estrada de los Santos, P., Baldrian, P., McKay, R.M., Simister, R., Stepanauskas, R., Neumann, R., Malmstrom, R., Cavicchioli, R., Kelly, R., Hatzenpichler, R., Stocker, R., Cattolico, R.A., Ziels, R., Vilgalys, R., Blumer-Schuette, S., Crowe, S., Roux, S., Hallam, S., Lindow, S., Brawley, S.H., Tringe, S., Woyke, T., Whitman, T., Bianchi, T., Mock, T., Donohue, T., James, T.Y., Kalluri, U.C., Karaoz, U., Denef, V., Liu, W.-T., Whitman, W., Ouyang, Y.: Thousands of small, novel genes predicted in global phage genomes. Cell Reports. 39, : 110984 (2022).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [96]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967098

  Khesali Aghtaei, H., Püttker, S., Maus, I., Heyer, R., Huang, L., Sczyrba, A., Reichl, U., Benndorf, D.: Adaptation of a microbial community to demand-oriented biological methanation. Biotechnology for Biofuels and Bioproducts. 15, : 125 (2022).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [95]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966901

  Maus, I., Wibberg, D., Belmann, P., Hahnke, S., Huang, L., Spröer, C., Bunk, B., Blom, J., Sczyrba, A., Pühler, A., Klocke, M., Schlüter, A.: 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 (2022).

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• [94]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966286

  Joshi, A., Young, D., Huang, L., Mosberger, L., Munk, B., Vinzelj, J., Flad, V., Sczyrba, A., Griffith, G.W., Podmirseg, S.M., Warthmann, R., Lebuhn, M., Insam, H.: Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats. Microorganisms. 10, : 1972 (2022).

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• [93]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2965465

  Young, D., Joshi, A., Huang, L., Munk, B., Wurzbacher, C., Youssef, N.H., Elshahed, M.S., Moon, C.D., Ochsenreither, K., Griffith, G.W., Callaghan, T.M., Sczyrba, A., Lebuhn, M., Flad, V.: Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages. Microorganisms. 10, : 1749 (2022).

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• [92]
  

  2022 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2963745

  Sczyrba, A., German Network for Bioinformatics Infrastructure (de.NBI) eds: Development and Operation of the Federated de.NBI Cloud: Contributions of the German Network for Bioinformatics Infrastructure. Center for Biotechnology, de.NBI Administration Office, Bielefeld (2022).

  PUB | PDF | DOI
   
• [91]
  

  2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2962388

  Meyer, F., Fritz, A., Deng, Z.-L., Koslicki, D., Lesker, T.R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J.J., Brown, C.T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P.T.L.C., Cristian, A., Dabrowski, P.W., Darling, A.E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M.A., Hansen, L.H., Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T.S., Kieser, S.D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V.R., Marchet, C., Marijon, P., Meleshko, D., Mende, D.R., Milanese, A., Nagarajan, N., Nissen, J., Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V.C., Porter, J.S., Rasmussen, S., Rees, E.R., Reinert, K., Renard, B., Robertsen, E.M., Rosen, G.L., Ruscheweyh, H.-J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, S.J., Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N.P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A., McHardy, A.C.: Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods. 19, 429-440 (2022).

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• [90]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2950292

  Blifernez-Klassen, O., Klassen, V., Wibberg, D., Cebeci, E., Henke, C., Rückert, C., Chaudhari, S., Rupp, O., Blom, J., Winkler, A., Al-Dilaimi, A., Goesmann, A., Sczyrba, A., Kalinowski, J., Bräutigam, A., Kruse, O.: Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia. Scientific Reports. 11, : 1726 (2021).

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• [89]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2957501

  Brandt, D., Simunovic, M., Busche, T., Haak, M., Belmann, P., Jünemann, S., Schulz, T., Klages, L.J., Vinke, S., Beckstette, M., Pohl, E., Scherer, C., Sczyrba, A., Kalinowski, J.: Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines. Viruses. 13, : 1870 (2021).

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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., Dilthey, A., Klawonn, F., McHardy, A.C.: Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biology. 22, : 212 (2021).

  PUB | DOI | WoS | PubMed | Europe PMC | Preprint
   
• [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., Bassignani, A., Benndorf, D., Fuchs, S., Giannone, R.J., Griffin, T.J., Hagen, L.H., Halder, R., Henry, C., Hettich, R.L., Heyer, R., Jagtap, P., Jehmlich, N., Jensen, M., Juste, C., Kleiner, M., Langella, O., Lehmann, T., Leith, E., May, P., Mesuere, B., Miotello, G., Peters, S.L., Pible, O., Queiros, P.T., Reichl, U., Renard, B.Y., Schiebenhoefer, H., Sczyrba, A., Tanca, A., Trappe, K., Trezzi, J.-P., Uzzau, S., Verschaffelt, P., von Bergen, M., Wilmes, P., Wolf, M., Martens, L., Muth, T.: Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications. 12, : 7305 (2021).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [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., Conesa, P., Cox, C.J., De Moro, G., Erwan, C., Exter, K., Le Corguillé, G., Dallet, R., Gueguen, L., Heriche, J.-K., Serrano, B., Sun, Y., Burel, J.-M., Zullino, S., Longo, D.L., Pommier, C., Hallab, A., Eiteneuer, C., David, R., Usadel, B., Owen, S., Gruden, K., Pieruschka, R., Sczyrba, A., Pühler, A., Beracochea, M., Finn, R., Gribbon, P., Zaliani, A., Skyner, R., von Delft, F., Skuta, C., Leach, A., Tang, J., Capella, S., Fernández, J.M., Rambla, J., Beltran, S.: EOSC-Life Report on the work of the initial demonstrators. (2021).

  PUB | DOI
   
• [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., Atlasson, U.A., Brandt, D., Cichowicz-Cieslak, M., Cornish, K.A.S., Courtin, J., Dabrowski, S., Dahle, H., Djeffane, S., Dorawa, S., Dusaucy, J., Enault, F., Fedoy, A.-E., Freitag-Pohl, S., Fridjonsson, O.H., Galiez, C., Glomsaker, E., Guerin, M., Gundeso, S.E., Gudmundsdottir, E.E., Gudmundsson, H., Hakansson, M., Henke, C., Helleux, A., Henriksen, J.R., Hjorleifdottir, S., Hreggvidsson, G.O., Jasilionis, A., Jochheim, A., Jonsdottir, I., Jonsdottir, L.B., Jurczak-Kurek, A., Kaczorowski, T., Kalinowski, J., Kozlowski, L.P., Krupovic, M., Kwiatkowska-Semrau, K., Lanes, O., Lange, J., Lebrat, J., Linares-Pasten, J., Liu, Y., Lorentsen, S.A., Luttermann, T., Mas, T., Merre, W., Mirdita, M., Morzywolek, A., Ndela, E.O., Karlsson, E.N., Olgudottir, E., Pedersen, C., Perler, F., Petursdottir, S.K., Plotka, M., Pohl, E., Prangishvili, D., Ray, J.L., Reynisson, B., Robertsdottir, T., Sandaa, R.-A., Sczyrba, A., Skirnisdottir, S., Soding, J., Solstad, T., Steen, I.H., Stefansson, S.K., Steinegger, M., Overa, K.S., Striberny, B., Svensson, A., Szadkowska, M., Tarrant, E.J., Terzian, P., Tourigny, M., van den Bergh, T., Vanhalst, J., Vincent, J., Vroling, B., Walse, B., Wang, L., Watzlawick, H., Welin, M., Werbowy, O., Wons, E., Zhang, R.: Going to extremes - a metagenomic journey into the dark matter of life. FEMS microbiology letters. : fnab067 (2021).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [84]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952275

  Meyer, F., Lesker, T.-R., Koslicki, D., Fritz, A., Gurevich, A., Darling, A.E., Sczyrba, A., Bremges, A., McHardy, A.C.: Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit. Nature Protocols. 16, 1785–1801 (2021).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [83]
  

  2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2951537

  Tabacchioni, S., Passato, S., Ambrosino, P., Huang, L., Caldara, M., Cantale, C., Hett, J., Del Fiore, A., Fiore, A., Schlüter, A., Sczyrba, A., Maestri, E., Marmiroli, N., Neuhoff, D., Nesme, J., Sørensen, S.J., Aprea, G., Nobili, C., Presenti, O., Giovannetti, G., Giovannetti, C., Pihlanto, A., Brunori, A., Bevivino, A.: Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture. Microorganisms. 9, : 426 (2021).

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• [82]
  

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941645

  Maus, I., Klocke, M., Derenkó, J., Stolze, Y., Beckstette, M., Jost, C., Wibberg, D., Blom, J., Henke, C., Willenbücher, K., Rumming, M., Rademacher, A., Pühler, A., Sczyrba, A., Schlüter, A.: 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, : 7 (2020).

  PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [81]
  

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2953267

  Schulte-Schrepping, J., Reusch, N., Paclik, D., Baßler, K., Schlickeiser, S., Zhang, B., Krämer, B., Krammer, T., Brumhard, S., Bonaguro, L., De Domenico, E., Wendisch, D., Grasshoff, M., Kapellos, T.S., Beckstette, M., Pecht, T., Saglam, A., Dietrich, O., Mei, H.E., Schulz, A.R., Conrad, C., Kunkel, D., Vafadarnejad, E., Xu, C.-J., Horne, A., Herbert, M., Drews, A., Thibeault, C., Pfeiffer, M., Hippenstiel, S., Hocke, A., Müller-Redetzky, H., Heim, K.-M., Machleidt, F., Uhrig, A., Bosquillon de Jarcy, L., Jürgens, L., Stegemann, M., Glösenkamp, C.R., Volk, H.-D., Goffinet, C., Landthaler, M., Wyler, E., Georg, P., Schneider, M., Dang-Heine, C., Neuwinger, N., Kappert, K., Tauber, R., Corman, V., Raabe, J., Kaiser, K.M., Vinh, M.T., Rieke, G., Meisel, C., Ulas, T., Becker, M., Geffers, R., Witzenrath, M., Drosten, C., Suttorp, N., von Kalle, C., Kurth, F., Händler, K., Schultze, J.L., Aschenbrenner, A.C., Li, Y., Nattermann, J., Sawitzki, B., Saliba, A.-E., Sander, L.E., Angelov, A., Bals, R., Bartholomäus, A., Becker, A., Bezdan, D., Bonifacio, E., Bork, P., Clavel, T., Colome-Tatche, M., Diefenbach, A., Dilthey, A., Fischer, N., Förstner, K., Frick, J.-S., Gagneur, J., Goesmann, A., Hain, T., Hummel, M., Janssen, S., Kalinowski, J., Kallies, R., Kehr, B., Keller, A., Kim-Hellmuth, S., Klein, C., Kohlbacher, O., Korbel, J.O., Kurth, I., Landthaler, M., Li, Y., Ludwig, K., Makarewicz, O., Marz, M., McHardy, A., Mertes, C., Nöthen, M., Nürnberg, P., Ohler, U., Ossowski, S., Overmann, J., Peter, S., Pfeffer, K., Poetsch, A.R., Pühler, A., Rajewsky, N., Ralser, M., Rieß, O., Ripke, S., Nunes da Rocha, U., Rosenstiel, P., Saliba, A.-E., Sander, L.E., Sawitzki, B., Schiffer, P., Schulte, E.-C., Schultze, J.L., Sczyrba, A., Stegle, O., Stoye, J., Theis, F., Vehreschild, J., Vogel, J., von Kleist, M., Walker, A., Walter, J., Wieczorek, D., Ziebuhr, J.: Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell. 182, 1419-1440.e23 (2020).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [80]
  

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2944226

  Rettenmaier, R., Schneider, M., Munk, B., Lebuhn, M., Jünemann, S., Sczyrba, A., Maus, I., Zverlov, V., Liebl, W.: Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum. Microorganisms. 8, : 915 (2020).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [79]
  

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2949597

  Maus, I., Tubbesing, T.J., Wibberg, D., Heyer, R., Hassa, J., Tomazetto, G., Huang, L., Bunk, B., Spröer, C., Benndorf, D., Zverlov, V., Pühler, A., Klocke, M., Sczyrba, A., Schlüter, A.: The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms. 8, : 2024 (2020).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [78]
  

  2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2948401

  Moore, M., Wesemann, C., Gossmann, N., Sahm, A., Krüger, J., Sczyrba, A., Dietz, K.-J.: ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom. BMC Bioinformatics. 21, : 490 (2020).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [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., McHardy, A.C., Strowig, T.: An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. Cell reports. 30, 2909-2922.e6 (2020).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [76]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923

  Nelkner, J., Henke, C., Lin, T.W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., Pühler, A., Sczyrba, A., Schlüter, A.: 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, : 424 (2019).

  PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [75]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933767

  Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., Lesker, T.R., Belmann, P., DeMaere, M.Z., Darling, A.E., Sczyrba, A., Bremges, A., McHardy, A.C.: CAMISIM: simulating metagenomes and microbial communities. Microbiome. 7, : 17 (2019).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [74]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798

  Pankoke, H., Maus, I., Loh, G., Huser, A., Seifert, J., Tilker, A., Hark, S., Sczyrba, A., Pelzer, S., Kleinbolting, J.: Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota. FEMS microbiology letters. (2019).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [73]
  

  2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2936223

  Belmann, P., Fischer, B., Krüger, J., Procházka, M., Rasche, H., Prinz, M., Hanussek, M., Lang, M., Bartusch, F., Gläßle, B., Krüger, J., Pühler, A., Sczyrba, A.: de.NBI Cloud federation through ELIXIR AAI. F1000Research. 8, : 842 (2019).

  PUB | PDF | DOI | Download (ext.) | PubMed | Europe PMC
   
• [72]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593

  Linden, M., Prochazka, M., Lappalainen, I., Bucik, D., Vyskocil, P., Kuba, M., Silén, S., Belmann, P., Sczyrba, A., Newhouse, S., Matyska, L., Nyrönen, T.: Common ELIXIR Service for Researcher Authentication and Authorisation. F1000Research. 7, : 1199 (2018).

  PUB | DOI | Download (ext.) | PubMed | Europe PMC
   
• [71]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723

  Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A., McHardy, A.C.: AMBER: Assessment of Metagenome BinnERs. GigaScience. 7, : giy069 (2018).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [70]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777

  Celis, J.S., Wibberg, D., Ramírez-Portilla, C., Rupp, O., Sczyrba, A., Winkler, A., Kalinowski, J., Wilke, T.: Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience. 7, : giy075 (2018).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [69]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920750

  Maus, I., Rumming, M., Bergmann, I., Heeg, K., Pohl, M., Nettmann, E., Jaenicke, S., Blom, J., Pühler, A., Schlüter, A., Sczyrba, A., Klocke, M.: Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnology for Biofuels. 11, : 167 (2018).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [68]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890

  Huang, L., Krüger, J., Sczyrba, A.: Analyzing large scale genomic data on the cloud with Sparkhit. Bioinformatics. 34, 1457-1465 (2018).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [67]
  

  2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929

  Stolze, Y., Bremges, A., Maus, I., Pühler, A., Sczyrba, A., Schlüter, A.: Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants. Microbial Biotechnology. 11, 667-679 (2018).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [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., Etto, R.M., Battistus, A.G., Peres Rodrigues da Costa, A.C., Martinez de Oliveira, A.L., Weigert Galvão, C., Guimarães, V.F., Sczyrba, A., Wendisch, V.F., Passaglia, L.: Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approach. Plant and Soil. 422, 467-478 (2018).

  PUB | DOI | WoS
   
• [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.: Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology. 84, : e02239-17 (2018).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [64]
  

  2017 | Zeitschriftenaufsatz | PUB-ID: 2913876

  Sczyrba, A., Hofman, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T.S., Shapiro, N., Blood, P.D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M.Z., Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvočiūtė, M., Hestbjerg Hansen, L., Sørensen, S.J., Chia, B.K.H., Denis, B., Froula, J.L., Wang, Z., Egan, R., Don Kang, D., Cook, J.J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y.-W., Singer, S.W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M., Lingner, T., Lin, H.-H., Liao, Y.-C., Gueiros Z. Silva, G., Cuevas, D.A., Edwards, R.A., Saha, S., Piro, V.C., Renard, B.Y., Pop, M., Klenk, H.-P., Göker, M., Kyrpides, N.C., Woyke, T., Vorholt, J.A., Schulze-Lefert, P., Rubin, E.M., Darling, A.E., Rattei, T., McHardy, A.C.: Benchmark data sets, software results and reference data for the first CAMI challenge. GigaScience Database. (2017).

  PUB | DOI
   
• [63]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367

  Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T.S., Shapiro, N., Blood, P.D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M.Z., Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvočiūtė, M., Hansen, L.H., Sørensen, S.J., Chia, B.K.H., Denis, B., Froula, J.L., Wang, Z., Egan, R., Don Kang, D., Cook, J.J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y.-W., Singer, S.W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M.D., Lingner, T., Lin, H.-H., Liao, Y.-C., Silva, G.G.Z., Cuevas, D.A., Edwards, R.A., Saha, S., Piro, V.C., Renard, B.Y., Pop, M., Klenk, H.-P., Göker, M., Kyrpides, N.C., Woyke, T., Vorholt, J.A., Schulze-Lefert, P., Rubin, E.M., Darling, A.E., Rattei, T., McHardy, A.C.: Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods. 14, 1063-1071 (2017).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [62]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153

  Yu, J., Blom, J., Sczyrba, A., Goesmann, A.: Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Journal of Biotechnology. 257, 58-60 (2017).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [61]
  

  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516

  Maus, I., Bremges, A., Stolze, Y., Hahnke, S., Cibis, K.G., Koeck, D.E., Kim, Y.S., Kreubel, J., Hassa, J., Wibberg, D., Weimann, A., Off, S., Stantscheff, R., Zverlov, V.V., Schwarz, W.H., König, H., Liebl, W., Scherer, P., McHardy, A.C., Sczyrba, A., Klocke, M., Pühler, A., Schlüter, A.: Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels. 10, : 264 (2017).

  PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
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  2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556

  Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., Albaum, S., Schlüter, A., Goesmann, A., Sczyrba, A., Stoye, J.: Bioinformatics for NGS-based metagenomics and the application to biogas research. Journal of Biotechnology. 261, 10-23 (2017).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [59]
  

  2017 | Datenpublikation | PUB-ID: 2914921

  Huang, L., Krüger, J., Sczyrba, A.: Sparkhit evaluation data set. Bielefeld University (2017).

  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., Schlüter, A., Sczyrba, A., Reichl, U.: Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnology for Biofuels. 9, : 155 (2016).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [57]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905260

  Maus, I., Koeck, D.E., Cibis, K.G., Hahnke, S., Kim, Y.S., Langer, T., Kreubel, J., Erhard, M., Bremges, A., Off, S., Stolze, Y., Jaenicke, S., Goesmann, A., Sczyrba, A., Scherer, P., König, H., Schwarz, W.H., Zverlov, V.V., Liebl, W., Pühler, A., Schlüter, A., Klocke, M.: 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, : 171 (2016).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [56]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729

  Bremges, A., Singer, E., Woyke, T., Sczyrba, A.: MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics. 32, 2199-2201 (2016).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [55]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900928

  Nesme, J., Achouak, W., Agathos, S., Bailey, M., Baldrian, P., Brunel, D., Frostegard, A., Heulin, T., Jansson, J.K., Jurkevitch, E., Kowalchuk, G.A., Kruus, K.L., Lagares, A., Lapin-Scott, H.M., Le Paslier, D., ic-Mulec, I., Murrell, C., Myrold, D.D., Nalin, R., Nannipieri, P., Neufeld, J.D., O'Gara, F., Parnell, J.J., Pühler, A., Pylro, V., Ramos, J.L., Roesch, L., Schleper, C., Schloter, M., Sczyrba, A., Sessitsch, A., Sjöling, S., Sørensen, J., Sørensen, S.J., Tebbe, C.C., Topp, E., Tsiamis, G., Van Elsas, J.D., Van Keulen, G., Wagner, M., Widmer, F., Zhang, T., Zhang, X., Zhao, L., Zhu, Y.-G., Vogel, T.M., Simonet, P.: Back to the future of soil metagenomics. Frontiers in Microbiology. 7, : 73 (2016).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [54]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815

  Stolze, Y., Bremges, A., Rumming, M., Henke, C., Maus, I., Pühler, A., Sczyrba, A., Schlüter, A.: 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).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [53]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633

  Lux, M., Krüger, J., Rinke, C., Maus, I., Schlüter, A., Woyke, T., Sczyrba, A., Hammer, B.: acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data. BMC Bioinformatics. 17, : 543 (2016).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [52]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489

  Maus, I., Cibis, K.G., Bremges, A., Stolze, Y., Wibberg, D., Tomazetto, G., Blom, J., Sczyrba, A., König, H., Pühler, A., Schlüter, A.: 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).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [51]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302

  Wibberg, D., Bremges, A., Dammann-Kalinowski, T., Maus, I., Igeño, M.I., Vogelsang, R., König, C., Luque-Almagro, V.M., Roldán, M.D., Sczyrba, A., Moreno-Vivián, C., Blasco, R., Pühler, A., Schlüter, A.: 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).

  PUB | DOI | WoS | PubMed | Europe PMC
   
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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., Kalinowski, J., Beneduzi, A., Costa, P.B., Passaglia, L.M.P., Vargas, L.K., Wendisch, V.F.: 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).

  PUB | DOI | WoS
   
• [49]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190

  Stiefel, F., Fischer, S., Sczyrba, A., Otte, K., Hesse, F.: 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).

  PUB | DOI | WoS | PubMed | Europe PMC
   
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  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901675

  Krahn, T., Wibberg, D., Maus, I., Winkler, A., Bontron, S., Sczyrba, A., Nordmann, P., Pühler, A., Poirel, L., Schlüter, A.: Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene. Antimicrobial Agents and Chemotherapy. 60, 3032-3040 (2016).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [47]
  

  2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234

  Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S., Jaenicke, S., Fracowiak, J., Pühler, A., Schlüter, A.: An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology. 231, 268-279 (2016).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [46]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906

  Bremges, A., Maus, I., Belmann, P., Eikmeyer, F.G., Winkler, A., Albersmeier, A., Pühler, A., Schlüter, A., Sczyrba, A.: Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. GigaScience. 4, : 33 (2015).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
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  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501

  Belmann, P., Dröge, J., Bremges, A., McHardy, A.C., Sczyrba, A., Barton, M.D.: Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience. 4, : 47 (2015).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [44]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156

  Paul, B.G., Bagby, S.C., Czornyj, E., Arambula, D., Handa, S., Sczyrba, A., Ghosh, P., Miller, J.F., Valentine, D.L.: Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nature Communications. 6, : 6585 (2015).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [43]
  

  2015 | Preprint | Veröffentlicht | PUB-ID: 2901613

  Lux, M., Hammer, B., Sczyrba, A.: Automated Contamination Detection in Single-Cell Sequencing. bioRxiv. (2015).

  PUB
   
• [42]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833

  Kohrs, F., Wolter, S., Benndorf, D., Heyer, R., Hoffmann, M., Rapp, E., Bremges, A., Sczyrba, A., Schlüter, A., Reichl, U.: Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics. 15, 3585-3589 (2015).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [41]
  

  2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466

  Osterholz, B., Wiebke, P., Fust, A., Rumming, M., Schlüter, A., Sczyrba, A.: 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 (2015).

  PUB
   
• [40]
  

  2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183

  Field, E.K., Sczyrba, A., Lyman, A.E., Harris, C.C., Woyke, T., Stepanauskas, R., Emerson, D.: Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. The ISME journal. 9, 857-870 (2015).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [39]
  

  2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901612

  Lux, M., Sczyrba, A., Hammer, B.: Automatic discovery of metagenomic structure. 2015 International Joint Conference on Neural Networks (IJCNN). Institute of Electrical & Electronics Engineers (IEEE) (2015).

  PUB | DOI
   
• [38]
  

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992

  Piao, H., Lachman, M., Malfatti, S., Sczyrba, A., Knierim, B., Auer, M., Tringe, S.G., Mackie, R.I., Yeoman, C.J., Hess, M.: 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).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
   
• [37]
  

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2698163

  Heins, R.A., Cheng, X., Nath, S., Deng, K., Bowen, B.P., Chivian, D.C., Datta, S., Friedland, G.D., D'Haeseleer, P., Wu, D., Tran-Gyamfi, M., Scullin, C.S., Singh, S., Shi, W., Hamilton, M.G., Bendall, M.L., Sczyrba, A., Thompson, J., Feldman, T., Guenther, J.M., Gladden, J.M., Cheng, J.-F., Adams, P.D., Rubin, E.M., Simmons, B.A., Sale, K.L., Northen, T.R., Deutsch, S.: Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS chemical biology. 9, 2082-2091 (2014).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [36]
  

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433

  Kamke, J., Rinke, C., Schwientek, P., Mavromatis, K., Ivanova, N., Sczyrba, A., Woyke, T., Hentschel, U.: 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, : e87353 (2014).

  PUB | DOI | WoS | PubMed | Europe PMC
   
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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., Dwulit-Smith, J., Chan, L.-K., Martinez-Garcia, M., Sczyrba, A., Stepanauskas, R., Grossart, H.-P., Woyke, T., Warnecke, F., Malmstrom, R., Bertilsson, S., McMahon, K.D.: Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal. 8, 2503-2516 (2014).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [34]
  

  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., Harris, C.C., Sczyrba, A., Chain, P.S.G., Koren, S., Woyke, T., Stepanauskas, R.: Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres. PloS one. 9, : e95380 (2014).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [33]
  

  2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333

  Henrich, B., Rumming, M., Sczyrba, A., Velleuer, E., Dietrich, R., Gerlach, W., Gombert, M., Rahn, S., Stoye, J., Borkhardt, A., Fischer, U.: Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma. PLoS ONE. 9, : e92297 (2014).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [32]
  

  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., Guijo, M.I., Manso, M.I., Macías, D., Cabello, P., Becerra, G., Ibáñez, M.I., Carmona, M.I., Escribano, M.P., Castillo, F., Sczyrba, A., Moreno-Vivián, C., Blasco, R., Pühler, A., Schlüter, A.: Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Journal of biotechnology. 175, 67-68 (2014).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [31]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234

  Zaremba-Niedzwiedzka, K., Viklund, J., Zhao, W., Ast, J., Sczyrba, A., Woyke, T., McMahon, K., Bertilsson, S., Stepanauskas, R., Andersson, S.G.: Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology. 14, : R130 (2013).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [30]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613567

  Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B.K., Gies, E.A., Dodsworth, J.A., Hedlund, B.P., Tsiamis, G., Sievert, S.M., Liu, W.-T., Eisen, J.A., Hallam, S.J., Kyrpides, N.C., Stepanauskas, R., Rubin, E.M., Hugenholtz, P., Woyke, T.: Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499, 431-437 (2013).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [29]
  

  2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500

  Gisbrecht, A., Hammer, B., Mokbel, B., Sczyrba, A.: Nonlinear dimensionality reduction for cluster identification in metagenomic samples. In: Banissi, E. (ed.) 17th International Conference on Information Visualisation IV 2013. p. 174-179. IEEE, Piscataway, NJ (2013).

  PUB | DOI
   
• [28]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563543

  Campbell, A.G., Campbell, J.H., Schwientek, P., Woyke, T., Sczyrba, A., Allman, S., Beall, C.J., Griffen, A., Leys, E., Podar, M.: Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity. PLoS ONE. 8, : e59361 (2013).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [27]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424

  Campbell, J.H., O'Donoghue, P., Campbell, A.G., Schwientek, P., Sczyrba, A., Woyke, T., Söll, D., Podar, M.: 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, 5540-5545 (2013).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [26]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352

  Kamke, J., Sczyrba, A., Ivanova, N., Schwientek, P., Rinke, C., Mavromatis, K., Woyke, T., Hentschel, U.: Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. The ISME journal. 7, 2287-2300 (2013).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [25]
  

  2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613623

  Swan, B.K., Tupper, B., Sczyrba, A., Lauro, F.M., Martinez-Garcia, M., González, J.M., Luo, H., Wright, J.J., Landry, Z.C., Hanson, N.W., Thompson, B.P., Poulton, N.J., Schwientek, P., Acinas, S.G., Giovannoni, S.J., Moran, M.A., Hallam, S.J., Cavicchioli, R., Woyke, T., Stepanauskas, R.: 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, 11463-11468 (2013).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [24]
  

  2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2518330

  Garcia, S.L., McMahon, K.D., Martinez-Garcia, M., Srivastava, A., Sczyrba, A., Stepanauskas, R., Grossart, H.-P., Woyke, T., Warnecke, F.: Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME journal. 7, 137-147 (2012).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [23]
  

  2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2547307

  El-Kalioby, M., Abouelhoda, M., Krüger, J., Giegerich, R., Sczyrba, A., Wall, D.P., Tonellato, P.: Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics. 13, : S22 (2012).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [22]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410148

  Woyke, T., Sczyrba, A., Lee, J., Rinke, C., Tighe, D., Clingenpeel, S., Malmstrom, R., Stepanauskas, R., Cheng, J.-F.: Decontamination of MDA Reagents for Single Cell Whole Genome Amplification. PLoS ONE. 6, : e26161 (2011).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [21]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2351462

  Kim, T.-W., Chokhawala, H.A., Hess, M., Dana, C.M., Baer, Z., Sczyrba, A., Rubin, E.M., Blanch, H.W., Clark, D.S.: High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery. Angewandte Chemie. 123, 11411-11414 (2011).

  PUB | DOI | PubMed | Europe PMC
   
• [20]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2329885

  Swan, B.K., Martinez-Garcia, M., Preston, C.M., Sczyrba, A., Woyke, T., Lamy, D., Reinthaler, T., Poulton, N.J., Masland, E.D.P., Gomez, M.L., Sieracki, M.E., DeLong, E.F., Herndl, G.J., Stepanauskas, R.: Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean. Science. 333, 1296-1300 (2011).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [19]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2789582

  Sales, C.M., Mahendra, S., Grostern, A., Parales, R.E., Goodwin, L.A., Woyke, T., Nolan, M., Lapidus, A., Chertkov, O., Ovchinnikova, G., Sczyrba, A., Alvarez-Cohen, L.: Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190. Journal of Bacteriology. 193, 4549-4550 (2011).

  PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC | GenBank
   
• [18]
  

  2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991643

  Hess, M., Sczyrba, A., Egan, R., Kim, T.W., Chokhawala, H., Schroth, G., Luo, S., Clark, D.S., Chen, F., Zhang, T., Mackie, R.I., Pennacchio, L.A., Tringe, S.G., Visel, A., Woyke, T., Wang, Z., Rubin, E.M.: Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 331, 463-467 (2011).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [17]
  

  2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991615

  Gilbert, J.A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C.T., Desai, N., Eisen, J.A., Evers, D., Field, D., Feng, W., Huson, D., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantindis, K., Kostka, J., Kyrpides, N., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, A., Shade, A., Stevens, R.: Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 3, 243-248 (2010).

  PUB | DOI | PubMed | Europe PMC
   
• [16]
  

  2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020

  Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics. 9, : S13 (2008).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [15]
  

  2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588303

  Sczyrba, A., Konermann, S., Giegerich, R.: Two interactive bioinformatics courses at the bielefeld university bioinformatics server. BRIEFINGS IN BIOINFORMATICS. 9, 243-249 (2008).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [14]
  

  2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756

  Spitzer, M., Lorkowski, S., Cullen, P., Sczyrba, A., Fuellen, G.: IsoSVM - Distinguishing isoforms and paralogs on the protein level. BMC Bioinformatics. 7, 110 (2006).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [13]
  

  2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773613

  Sczyrba, A., Beckstette, M., Brivanlou, A.H., Giegerich, R., Altmann, C.R.: XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics. 6, : 123 (2005).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [12]
  

  2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383529

  Beckstette, M., Mailänder, J.T., Marhöfer, R.J., Sczyrba, A., Ohlebusch, E., Giegerich, R., Selzer, P.M.: Genlight: Interactive high-throughput sequence analysis and comparative genomics. Journal of Integrative Bioinformatics. 1, 90-107 (2004).

  PUB | PDF | DOI
   
• [11]
  

  2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383536

  Beckstette, M., Sczyrba, A., Selzer, P.M.: Genlight: Interactive high-throughput sequence analysis and comparative genomics. In: Giegerich, R. (ed.) German Conference on Bioinformatics. GCB 2004 ; October 4 - 6, 2004, Bielefeld, Germany . GI-Edition / Proceedings. 53, p. 179-186. Gesellschaft für Informatik, Bonn (2004).

  PUB
   
• [10]
  

  2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383561

  Sczyrba, A., Beckstette, M., Giegerich, R., Altman, C.: Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis. In: Giegerich, R. and Stoye, J. (eds.) German Conference on Bioinformatics 2004 : GCB 2004, October 4 - 6, 2004, Bielefeld, Germany . GI-Edition / Proceedings. 53, p. 6-7. Gesellschaft für Informatik, Bonn (2004).

  PUB
   
• [9]
  

  2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607400

  Taher, L., Rinner, O., Garg, S., Sczyrba, A., Morgenstern, B.: AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research. 32, W305-W308 (2004).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [8]
  

  2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607394

  Krüger, J., Sczyrba, A., Kurtz, S., Giegerich, R.: e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. NUCLEIC ACIDS RESEARCH. 32, W301-W304 (2004).

  PUB | PDF | DOI | WoS | PubMed | Europe PMC
   
• [7]
  

  2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610494

  Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., Morgenstern, B.: AGenDA: homology-based gene prediction. BIOINFORMATICS. 19, 1575-1577 (2003).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [6]
  

  2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773844

  Sczyrba, A., Krüger, J., Mersch, H., Kurtz, S., Giegerich, R.: RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Research. 31, 3767-3770 (2003).

  PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
   
• [5]
  

  2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612470

  Morgenstern, B., Goel, S., Sczyrba, A., Dress, A.: AltAVisT: Comparing alternative multiple sequence alignments. BIOINFORMATICS. 19, 425-426 (2003).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [4]
  

  2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609260

  Dondrup, M., Goesmann, A., Bartels, D., Kalinowski, J., Krause, L., Linke, B., Rupp, O., Sczyrba, A., Pühler, A., Meyer, F.: EMMA: a platform for consistent storage and efficient analysis of microarray data. JOURNAL OF BIOTECHNOLOGY. 106, 135-146 (2003).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [3]
  

  2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897716

  Gopal, S., Schroeder, M., Pieper, U., Sczyrba, A., Aytekin-Kurban, G., Bekiranov, S., Fajardo, J.E., Eswar, N., Sanchez, R., Sali, A., Gaasterland, T.: Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet. 27, 337-340 (2001).

  PUB
   
• [2]
  

  2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1616752

  Altmann, C.R., Bell, E., Sczyrba, A., Pun, J., Bekiranov, S., Gaasterland, T., Brivanlou, A.H.: Microarray-based analysis of early development in Xenopus laevis. DEVELOPMENTAL BIOLOGY. 236, 64-75 (2001).

  PUB | DOI | WoS | PubMed | Europe PMC
   
• [1]
  

  2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897767

  Gaasterland, T., Sczyrba, A., Thomas, E., Kurban, G.: MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region. Genome Res. 10, 502-510 (2000).

  PUB