107 Publikationen
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2024 | Preprint | Veröffentlicht | PUB-ID: 2993878Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource AllocationPUB | DOI
Belmann P, Osterholz B, Kleinboelting N, Pühler A, Schlüter A, Sczyrba A (2024)
bioRxiv. -
2024 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2985402Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenterPUB | DOI
Heyer R, Hellwig P, Maus I, Walke D, Schlüter A, Hassa J, Sczyrba A, Tubbesing TJ, Klocke M, Mächtig T, Schallert K, et al. (2024)
Water Research 250: 121020. -
2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2977923
Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysisPUB | PDF | DOI | WoS | PubMed | Europe PMC
Nelkner J, Huang L, Lin TW, Schulz A, Osterholz B, Henke C, Blom J, Pühler A, Sczyrba A, Schlüter A (2023)
Environmental Microbiome 18(1): 26. -
2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2983209
Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and MetaproteomicsPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, et al. (2023)
Microorganisms 11(10): 2412. -
2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984553Base4NFDI - Basic Services for NFDIPUB | DOI
Schimmler S, Altenhöner R, Bernard L, Fluck J, Klinger A, Lorenz S, Mathiak B, Miller B, Ritz R, Schörner-Sadenius T, Sczyrba A, et al. (2023)
Proceedings of the Conference on Research Data Infrastructure 1. -
2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984552Embedding the de.NBI Cloud in the National Research Data Infrastructure ActivitiesPUB | DOI
Hoffmann N, Maus I, Beier S, Belmann P, Krüger J, Tauch A, Goesmann A, Eils R, Bork P, Kohlbacher O, Kummer U, et al. (2023)
Proceedings of the Conference on Research Data Infrastructure 1. -
2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2984551NFDI4Microbiota – national research data infrastructure for microbiota researchPUB | DOI
Förstner KU, Becker A, Blom J, Bork P, Clavel T, Dieckmann M, Goesmann A, Götz B, Gübitz T, Hufsky F, Jünemann S, et al. (2023)
Research Ideas and Outcomes 9. -
2023 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2979860Advances in the clinical use of metaproteomicsPUB | DOI | WoS | PubMed | Europe PMC
Wolf M, Schallert K, Knipper L, Sickmann A, Sczyrba A, Benndorf D, Heyer R (2023)
Expert review of proteomics. -
2023 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2968667Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phagesPUB | DOI | WoS | PubMed | Europe PMC
Olo Ndela E, Roux S, Henke C, Sczyrba A, Sime Ngando T, Varsani A, Enault F (2023)
Virus Evolution 9(1): veac123. -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2969509Expansion of the global RNA virome reveals diverse clades of bacteriophagesPUB | DOI | WoS | PubMed | Europe PMC
Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Zeigler Allen L, Paez-Espino D, Bryant DA, et al. (2022)
Cell 185(21): 4023-4037.e18. -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2969511Thousands of small, novel genes predicted in global phage genomesPUB | DOI | WoS | PubMed | Europe PMC
Fremin BJ, Bhatt AS, Kyrpides NC, Sengupta A, Sczyrba A, Maria da Silva A, Buchan A, Gaudin A, Brune A, Hirsch AM, Neumann A, et al. (2022)
Cell Reports 39(12): 110984. -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2967098Adaptation of a microbial community to demand-oriented biological methanationPUB | DOI | WoS | PubMed | Europe PMC
Khesali Aghtaei H, Püttker S, Maus I, Heyer R, Huang L, Sczyrba A, Reichl U, Benndorf D (2022)
Biotechnology for Biofuels and Bioproducts 15(1): 125. -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966901
The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analysesPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Maus I, Wibberg D, Belmann P, Hahnke S, Huang L, Spröer C, Bunk B, Blom J, Sczyrba A, Pühler A, Klocke M, et al. (2022)
Frontiers in Microbiology 13: 1032515. -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2966286
Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen HabitatsPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Joshi A, Young D, Huang L, Mosberger L, Munk B, Vinzelj J, Flad V, Sczyrba A, Griffith GW, Podmirseg SM, Warthmann R, et al. (2022)
Microorganisms 10(10): 1972. -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2965465
Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel LineagesPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Young D, Joshi A, Huang L, Munk B, Wurzbacher C, Youssef NH, Elshahed MS, Moon CD, Ochsenreither K, Griffith GW, Callaghan TM, et al. (2022)
Microorganisms 10(9): 1749. -
2022 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2963745
Development and Operation of the Federated de.NBI Cloud: Contributions of the German Network for Bioinformatics InfrastructurePUB | PDF | DOI
Sczyrba A, German Network for Bioinformatics Infrastructure (de.NBI) (Eds) (2022)
Bielefeld: Center for Biotechnology, de.NBI Administration Office. -
2022 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2962388Critical Assessment of Metagenome Interpretation: the second round of challengesPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC | Preprint
Meyer F, Fritz A, Deng Z-L, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, et al. (2022)
Nature Methods 19: 429-440. -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2950292
Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortiaPUB | PDF | DOI | WoS | PubMed | Europe PMC | Preprint
Blifernez-Klassen O, Klassen V, Wibberg D, Cebeci E, Henke C, Rückert C, Chaudhari S, Rupp O, Blom J, Winkler A, Al-Dilaimi A, et al. (2021)
Scientific Reports 11(1): 1726. -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2957501
Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling PipelinesPUB | PDF | DOI | WoS | PubMed | Europe PMC
Brandt D, Simunovic M, Busche T, Haak M, Belmann P, Jünemann S, Schulz T, Klages LJ, Vinke S, Beckstette M, Pohl E, et al. (2021)
Viruses 13(9): 1870. -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2956369Haploflow: strain-resolved de novo assembly of viral genomesPUB | DOI | WoS | PubMed | Europe PMC | Preprint
Fritz A, Bremges A, Deng Z-L, Lesker TR, Götting J, Ganzenmueller T, Sczyrba A, Dilthey A, Klawonn F, McHardy AC (2021)
Genome Biology 22(1): 212. -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2960171Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflowsPUB | DOI | WoS | PubMed | Europe PMC
Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, et al. (2021)
Nature Communications 12(1): 7305. -
2021 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2960900EOSC-Life Report on the work of the initial demonstratorsPUB | DOI
Leitner F, Carazo JM, Bischof J, Haley N, Audergon P, Sorzano CO, del Cano L, Conesa P, Cox CJ, De Moro G, Erwan C, et al. (2021) . -
2021 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2955512Going to extremes - a metagenomic journey into the dark matter of lifePUB | DOI | WoS | PubMed | Europe PMC
Aevarsson A, Kaczorowska A-K, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, Arsin H, Atlasson UA, Brandt D, Cichowicz-Cieslak M, Cornish KAS, et al. (2021)
FEMS microbiology letters: fnab067. -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2952275Tutorial: assessing metagenomics software with the CAMI benchmarking toolkitPUB | DOI | WoS | PubMed | Europe PMC
Meyer F, Lesker T-R, Koslicki D, Fritz A, Gurevich A, Darling AE, Sczyrba A, Bremges A, McHardy AC (2021)
Nature Protocols 16(4): 1785–1801. -
2021 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2951537
Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable AgriculturePUB | PDF | DOI | WoS | PubMed | Europe PMC
Tabacchioni S, Passato S, Ambrosino P, Huang L, Caldara M, Cantale C, Hett J, Del Fiore A, Fiore A, Schlüter A, Sczyrba A, et al. (2021)
Microorganisms 9(2): 426. -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941645
Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomicsPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Maus I, Klocke M, Derenkó J, Stolze Y, Beckstette M, Jost C, Wibberg D, Blom J, Henke C, Willenbücher K, Rumming M, et al. (2020)
Environmental Microbiome 15(1): 7. -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2953267Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell CompartmentPUB | DOI | WoS | PubMed | Europe PMC
Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, et al. (2020)
Cell 182(6): 1419-1440.e23. -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2944226
Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellumPUB | PDF | DOI | WoS | PubMed | Europe PMC
Rettenmaier R, Schneider M, Munk B, Lebuhn M, Jünemann S, Sczyrba A, Maus I, Zverlov V, Liebl W (2020)
Microorganisms 8(6): 915. -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2949597
The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics AnalysesPUB | PDF | DOI | WoS | PubMed | Europe PMC
Maus I, Tubbesing TJ, Wibberg D, Heyer R, Hassa J, Tomazetto G, Huang L, Bunk B, Spröer C, Benndorf D, Zverlov V, et al. (2020)
Microorganisms 8(12): 2024. -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2948401
ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdomPUB | PDF | DOI | WoS | PubMed | Europe PMC
Moore M, Wesemann C, Gossmann N, Sahm A, Krüger J, Sczyrba A, Dietz K-J (2020)
BMC Bioinformatics 21(1): 490. -
2020 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941704An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome.PUB | DOI | WoS | PubMed | Europe PMC
Lesker TR, Durairaj AC, Galvez EJC, Lagkouvardos I, Baines JF, Clavel T, Sczyrba A, McHardy AC, Strowig T (2020)
Cell reports 30(9): 2909-2922.e6. -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923
Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial GenesPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A (2019)
Genes 10(6): 424. -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933767CAMISIM: simulating metagenomes and microbial communitiesPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Fritz A, Hofmann P, Majda S, Dahms E, Dröge J, Fiedler J, Lesker TR, Belmann P, DeMaere MZ, Darling AE, Sczyrba A, et al. (2019)
Microbiome 7(1): 17. -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota.PUB | DOI | WoS | PubMed | Europe PMC
Pankoke H, Maus I, Loh G, Huser A, Seifert J, Tilker A, Hark S, Sczyrba A, Pelzer S, Kleinbolting J (2019)
FEMS microbiology letters. -
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2936223
de.NBI Cloud federation through ELIXIR AAIPUB | PDF | DOI | Download (ext.) | PubMed | Europe PMC
Belmann P, Fischer B, Krüger J, Procházka M, Rasche H, Prinz M, Hanussek M, Lang M, Bartusch F, Gläßle B, Krüger J, et al. (2019)
F1000Research 8: 842. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593Common ELIXIR Service for Researcher Authentication and AuthorisationPUB | DOI | Download (ext.) | PubMed | Europe PMC
Linden M, Prochazka M, Lappalainen I, Bucik D, Vyskocil P, Kuba M, Silén S, Belmann P, Sczyrba A, Newhouse S, Matyska L, et al. (2018)
F1000Research 7: 1199. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723AMBER: Assessment of Metagenome BinnERsPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Meyer F, Hofmann P, Belmann P, Garrido-Oter R, Fritz A, Sczyrba A, McHardy AC (2018)
GigaScience 7(6): giy069. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777Binning Enables Efficient Host Genome Reconstruction in Cnidarian HolobiontsPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T (2018)
GigaScience 7(7): giy075. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920750Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactorsPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, et al. (2018)
Biotechnology for Biofuels 11(1): 167. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890Analyzing large scale genomic data on the cloud with SparkhitPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Huang L, Krüger J, Sczyrba A (2018)
Bioinformatics 34(9): 1457-1465. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plantsPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A (2018)
Microbial Biotechnology 11(4): 667-679. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914959Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approachPUB | DOI | WoS
da Schoren Costa P, Bolzan de Campos S, Albersmeier A, Dirksen P, Pereira Dresseno AL, Andrade Pais dos Santos OJ, Lima Milani KM, Etto RM, Battistus AG, Peres Rodrigues da Costa AC, Martinez de Oliveira AL, et al. (2018)
Plant and Soil 422(1-2): 467-478. -
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918275Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochraceaPUB | DOI | WoS | PubMed | Europe PMC
Fleming EJ, Woyke T, Donatello AR, Kuypers MMM, Sczyrba A, Littmann S, Emerson D (2018)
Applied and Environmental Microbiology 84(9): e02239-17. -
2017 | Zeitschriftenaufsatz | PUB-ID: 2913876Benchmark data sets, software results and reference data for the first CAMI challengePUB | DOI
Sczyrba A, Hofman P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, et al. (2017)
GigaScience Database. -
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics softwarePUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, et al. (2017)
Nature Methods 14(11): 1063-1071. -
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelismPUB | PDF | DOI | WoS | PubMed | Europe PMC
Yu J, Blom J, Sczyrba A, Goesmann A (2017)
Journal of Biotechnology 257: 58-60. -
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516
Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomesPUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, et al. (2017)
Biotechnology for Biofuels 10(1): 264. -
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556Bioinformatics for NGS-based metagenomics and the application to biogas researchPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum S, Schlüter A, Goesmann A, Sczyrba A, et al. (2017)
Journal of Biotechnology 261(SI): 10-23. -
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904836Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor typePUB | DOI | WoS | PubMed | Europe PMC
Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U (2016)
Biotechnology for Biofuels 9(1): 155. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905260Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolatesPUB | DOI | WoS | PubMed | Europe PMC
Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, et al. (2016)
Biotechnology for Biofuels 9(1): 171. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729MeCorS: Metagenome-enabled error correction of single cell sequencing readsPUB | DOI | WoS | PubMed | Europe PMC
Bremges A, Singer E, Woyke T, Sczyrba A (2016)
Bioinformatics 32(14): 2199-2201. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900928Back to the future of soil metagenomicsPUB | DOI | WoS | PubMed | Europe PMC
Nesme J, Achouak W, Agathos S, Bailey M, Baldrian P, Brunel D, Frostegard A, Heulin T, Jansson JK, Jurkevitch E, Kowalchuk GA, et al. (2016)
Frontiers in Microbiology 7: 73. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plantsPUB | PDF | DOI | WoS | PubMed | Europe PMC
Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A (2016)
Biotechnology for Biofuels 9(1): 156. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633
acdc – Automated Contamination Detection and Confidence estimation for single-cell genome dataPUB | PDF | DOI | WoS | PubMed | Europe PMC
Lux M, Krüger J, Rinke C, Maus I, Schlüter A, Woyke T, Sczyrba A, Hammer B (2016)
BMC Bioinformatics 17(1): 543. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitmentPUB | DOI | WoS | PubMed | Europe PMC
Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, Schlüter A (2016)
Journal of Biotechnology 232: 50-60. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencingPUB | DOI | WoS | PubMed | Europe PMC
Wibberg D, Bremges A, Dammann-Kalinowski T, Maus I, Igeño MI, Vogelsang R, König C, Luque-Almagro VM, Roldán MD, Sczyrba A, Moreno-Vivián C, et al. (2016)
Journal of Biotechnology 232: 61-68. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineeringPUB | DOI | WoS | PubMed | Europe PMC
Stiefel F, Fischer S, Sczyrba A, Otte K, Hesse F (2016)
Journal of Biotechnology 225: 31-43. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901418Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systemsPUB | DOI | WoS
Campos SB, Lisboa BB, Camargo FAO, Bayer C, Sczyrba A, Dirksen P, Albersmeier A, Kalinowski J, Beneduzi A, Costa PB, Passaglia LMP, et al. (2016)
Soil Biology and Biochemistry 96: 191-197. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901675Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene.PUB | DOI | WoS | PubMed | Europe PMC
Krahn T, Wibberg D, Maus I, Winkler A, Bontron S, Sczyrba A, Nordmann P, Pühler A, Poirel L, Schlüter A (2016)
Antimicrobial Agents and Chemotherapy 60(5): 3032-3040. -
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plantPUB | DOI | WoS | PubMed | Europe PMC
Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum S, Jaenicke S, Fracowiak J, Pühler A, Schlüter A (2016)
Journal of Biotechnology 231: 268-279. -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906
Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plantPUB | PDF | DOI | WoS | PubMed | Europe PMC
Bremges A, Maus I, Belmann P, Eikmeyer FG, Winkler A, Albersmeier A, Pühler A, Schlüter A, Sczyrba A (2015)
GigaScience 4(1): 33. -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501Bioboxes: standardised containers for interchangeable bioinformatics softwarePUB | DOI | WoS | PubMed | Europe PMC
Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD (2015)
GigaScience 4(1): 47. -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156Targeted diversity generation by intraterrestrial archaea and archaeal virusesPUB | DOI | WoS | PubMed | Europe PMC
Paul BG, Bagby SC, Czornyj E, Arambula D, Handa S, Sczyrba A, Ghosh P, Miller JF, Valentine DL (2015)
Nature Communications 6(1): 6585. -
2015 | Preprint | Veröffentlicht | PUB-ID: 2901613Automated Contamination Detection in Single-Cell SequencingPUB
Lux M, Hammer B, Sczyrba A (2015)
bioRxiv. -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communitiesPUB | DOI | WoS | PubMed | Europe PMC
Kohrs F, Wolter S, Benndorf D, Heyer R, Hoffmann M, Rapp E, Bremges A, Sczyrba A, Schlüter A, Reichl U (2015)
Proteomics 15(20): 3585-3589. -
2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466A Bioinformatics Pipeline for the Detection of β-lactamase Genes in Metagenome Sequence Data and its Application to Production-Scale Biogas PlantsPUB
Osterholz B, Wiebke P, Fust A, Rumming M, Schlüter A, Sczyrba A (2015)
Presented at the 3rd International Symposium on the environmental Dimension of Antibiotic Resistance, Wernigerode. -
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi SeamountPUB | DOI | WoS | PubMed | Europe PMC
Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D (2015)
The ISME journal 9(4): 857-870. -
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901612Automatic discovery of metagenomic structurePUB | DOI
Lux M, Sczyrba A, Hammer B (2015)
In: 2015 International Joint Conference on Neural Networks (IJCNN). Institute of Electrical & Electronics Engineers (IEEE). -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profilingPUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe SG, Mackie RI, Yeoman CJ, Hess M (2014)
Frontiers in Microbiology 5(307): 307. -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2698163Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass SpectrometryPUB | DOI | WoS | PubMed | Europe PMC
Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, et al. (2014)
ACS chemical biology 9(9): 2082-2091. -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic FeaturesPUB | DOI | WoS | PubMed | Europe PMC
Kamke J, Rinke C, Schwientek P, Mavromatis K, Ivanova N, Sczyrba A, Woyke T, Hentschel U (2014)
PLoS ONE 9(1): e87353. -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689051Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineagePUB | DOI | WoS | PubMed | Europe PMC
Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan L-K, Martinez-Garcia M, Sczyrba A, et al. (2014)
The ISME Journal 8(12): 2503-2516. -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2672695Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyresPUB | DOI | WoS | PubMed | Europe PMC
Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland EDP, Harris CC, Sczyrba A, Chain PSG, Koren S, et al. (2014)
PloS one 9(4): e95380. -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral CarcinomaPUB | DOI | WoS | PubMed | Europe PMC
Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gerlach W, Gombert M, Rahn S, Stoye J, Borkhardt A, Fischer U (2014)
PLoS ONE 9(3): e92297. -
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2662055Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344PUB | DOI | WoS | PubMed | Europe PMC
Wibberg D, Luque-Almagro VM, Igeño MI, Bremges A, Roldán MD, Merchán F, Sáez LP, Guijo MI, Manso MI, Macías D, Cabello P, et al. (2014)
Journal of biotechnology 175: 67-68. -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 cladePUB | DOI | WoS | PubMed | Europe PMC
Zaremba-Niedzwiedzka K, Viklund J, Zhao W, Ast J, Sczyrba A, Woyke T, McMahon K, Bertilsson S, Stepanauskas R, Andersson SG (2013)
Genome biology 14(11): R130. -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613567Insights into the phylogeny and coding potential of microbial dark matterPUB | DOI | WoS | PubMed | Europe PMC
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, et al. (2013)
Nature 499(7459): 431-437. -
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500Nonlinear dimensionality reduction for cluster identification in metagenomic samplesPUB | DOI
Gisbrecht A, Hammer B, Mokbel B, Sczyrba A (2013)
In: 17th International Conference on Information Visualisation IV 2013. Banissi E (Ed); Piscataway, NJ: IEEE: 174-179. -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563543Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral CavityPUB | DOI | WoS | PubMed | Europe PMC
Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M (2013)
PLoS ONE 8(3): e59361. -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiotaPUB | DOI | WoS | PubMed | Europe PMC
Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M (2013)
Proceedings of the National Academy of Sciences of the United States of America 110(14): 5540-5545. -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine spongesPUB | DOI | WoS | PubMed | Europe PMC
Kamke J, Sczyrba A, Ivanova N, Schwientek P, Rinke C, Mavromatis K, Woyke T, Hentschel U (2013)
The ISME journal 7(12): 2287-2300. -
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613623Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface oceanPUB | DOI | WoS | PubMed | Europe PMC
Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, et al. (2013)
Proceedings of the National Academy of Sciences of the United States of America 110(28): 11463-11468. -
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2518330Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplanktonPUB | DOI | WoS | PubMed | Europe PMC
Garcia SL, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, Grossart H-P, Woyke T, Warnecke F (2012)
The ISME journal 7(1): 137-147. -
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2547307Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC packagePUB | DOI | WoS | PubMed | Europe PMC
El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P (2012)
BMC Bioinformatics 13(Suppl 17): S22. -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410148Decontamination of MDA Reagents for Single Cell Whole Genome AmplificationPUB | DOI | WoS | PubMed | Europe PMC
Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng J-F (2011)
PLoS ONE 6(10): e26161. -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2351462High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme DiscoveryPUB | DOI | PubMed | Europe PMC
Kim T-W, Chokhawala HA, Hess M, Dana CM, Baer Z, Sczyrba A, Rubin EM, Blanch HW, Clark DS (2011)
Angewandte Chemie 123(47): 11411-11414. -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2329885Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark OceanPUB | DOI | WoS | PubMed | Europe PMC
Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland EDP, Gomez ML, Sieracki ME, et al. (2011)
Science 333(6047): 1296-1300. -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2789582Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC | GenBank
Sales CM, Mahendra S, Grostern A, Parales RE, Goodwin LA, Woyke T, Nolan M, Lapidus A, Chertkov O, Ovchinnikova G, Sczyrba A, et al. (2011)
Journal of Bacteriology 193(17): 4549-4550. -
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991643Metagenomic discovery of biomass-degrading genes and genomes from cow rumenPUB | DOI | WoS | PubMed | Europe PMC
Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, et al. (2011)
Science 331(6016): 463-467. -
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991615Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome projectPUB | DOI | PubMed | Europe PMC
Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, et al. (2010)
Stand Genomic Sci 3(3): 243-248. -
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020
GeneFisher-P: variations of GeneFisher as processes in Bio-jETIPUB | PDF | DOI | WoS | PubMed | Europe PMC
Lamprecht A-L, Margaria T, Steffen B, Sczyrba A, Hartmeier S, Giegerich R (2008)
BMC Bioinformatics 9(Suppl 4): S13. -
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588303Two interactive bioinformatics courses at the bielefeld university bioinformatics serverPUB | DOI | WoS | PubMed | Europe PMC
Sczyrba A, Konermann S, Giegerich R (2008)
BRIEFINGS IN BIOINFORMATICS 9(3): 243-249. -
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756
IsoSVM - Distinguishing isoforms and paralogs on the protein levelPUB | PDF | DOI | WoS | PubMed | Europe PMC
Spitzer M, Lorkowski S, Cullen P, Sczyrba A, Fuellen G (2006)
BMC Bioinformatics 7(1): 110. -
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773613
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevisPUB | PDF | DOI | WoS | PubMed | Europe PMC
Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR (2005)
BMC Genomics 6(1): 123. -
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383529Genlight: Interactive high-throughput sequence analysis and comparative genomicsPUB | DOI
Beckstette M, Mailänder JT, Marhöfer RJ, Sczyrba A, Ohlebusch E, Giegerich R, Selzer PM (2004)
Journal of Integrative Bioinformatics 1(1): 90-107. -
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383536Genlight: Interactive high-throughput sequence analysis and comparative genomicsPUB
Beckstette M, Sczyrba A, Selzer PM (2004)
In: German Conference on Bioinformatics. GCB 2004 ; October 4 - 6, 2004, Bielefeld, Germany . Giegerich R (Ed); GI-Edition / Proceedings, 53. Bonn: Gesellschaft für Informatik: 179-186. -
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383561Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence AnalysisPUB
Sczyrba A, Beckstette M, Giegerich R, Altman C (2004)
In: German Conference on Bioinformatics 2004 : GCB 2004, October 4 - 6, 2004, Bielefeld, Germany . Giegerich R, Stoye J (Eds); GI-Edition / Proceedings, 53. Bonn: Gesellschaft für Informatik: 6-7. -
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607400
AGenDA: gene prediction by cross-species sequence comparisonPUB | PDF | DOI | WoS | PubMed | Europe PMC
Taher L, Rinner O, Garg S, Sczyrba A, Morgenstern B (2004)
Nucleic Acids Research 32(Web Server): W305-W308. -
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607394
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequencesPUB | PDF | DOI | WoS | PubMed | Europe PMC
Krüger J, Sczyrba A, Kurtz S, Giegerich R (2004)
NUCLEIC ACIDS RESEARCH 32(Web Server): W301-W304. -
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610494AGenDA: homology-based gene predictionPUB | DOI | WoS | PubMed | Europe PMC
Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B (2003)
BIOINFORMATICS 19(12): 1575-1577. -
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773844
RNA-related tools on the Bielefeld Bioinformatics ServerPUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
Sczyrba A, Krüger J, Mersch H, Kurtz S, Giegerich R (2003)
Nucleic Acids Research 31(13): 3767-3770. -
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612470AltAVisT: Comparing alternative multiple sequence alignmentsPUB | DOI | WoS | PubMed | Europe PMC
Morgenstern B, Goel S, Sczyrba A, Dress A (2003)
BIOINFORMATICS 19(3): 425-426. -
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609260EMMA: a platform for consistent storage and efficient analysis of microarray dataPUB | DOI | WoS | PubMed | Europe PMC
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F (2003)
JOURNAL OF BIOTECHNOLOGY 106(2-3): 135-146. -
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897716Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genomePUB
Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, Gaasterland T (2001)
Nat Genet 27(3): 337-340. -
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1616752Microarray-based analysis of early development in Xenopus laevisPUB | DOI | WoS | PubMed | Europe PMC
Altmann CR, Bell E, Sczyrba A, Pun J, Bekiranov S, Gaasterland T, Brivanlou AH (2001)
DEVELOPMENTAL BIOLOGY 236(1): 64-75. -
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897767MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh regionPUB
Gaasterland T, Sczyrba A, Thomas E, Kurban G (2000)
Genome Res 10(4): 502-510.