75 Publikationen

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[75]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923
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. doi:10.3390/genes10060424
PUB | PDF | DOI | Download (ext.)
 
[74]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
Pankoke, H., Maus, I., Loh, G., Huser, A., Seifert, J., Tilker, A., Hark, S., et al. (2019). F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota. FEMS microbiology letters. doi:10.1093/femsle/fnz033
PUB | DOI | PubMed | Europe PMC
 
[73]
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, 17. doi:10.1186/s40168-019-0633-6
PUB | DOI | WoS | PubMed | Europe PMC
 
[72]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[71]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[70]
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, giy069. doi:10.1093/gigascience/giy069
PUB | DOI | WoS | PubMed | Europe PMC
 
[69]
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. doi:10.12688/f1000research.15161.1
PUB | DOI | Download (ext.) | PubMed | Europe PMC
 
[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
PUB | DOI | WoS | PubMed | Europe PMC
 
[67]
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, 167. doi:10.1186/s13068-018-1162-4
PUB | DOI | WoS | PubMed | Europe PMC
 
[66]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[65]
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
PUB | DOI | WoS
 
[64]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
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. doi:10.1016/j.jbiotec.2017.02.020
PUB | DOI | WoS | PubMed | Europe PMC
 
[63]
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
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[62]
2017 | Datenpublikation | PUB-ID: 2914921
Huang, L., Krüger, J., & Sczyrba, A. (2017). Sparkhit evaluation data set. Bielefeld University. doi:10.4119/unibi/2914921
PUB | Dateien verfügbar | DOI
 
[61]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516
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
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[60]
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. doi:10.1038/nmeth.4458
PUB | DOI | WoS | PubMed | Europe PMC
 
[59]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815
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, 156. doi:10.1186/s13068-016-0565-3
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633
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, 543. doi:10.1186/s12859-016-1397-7
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[57]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[56]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[55]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[54]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[53]
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
PUB | DOI | WoS
 
[52]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[51]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[50]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[49]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[48]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[47]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906
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. doi:10.1186/s13742-015-0073-6
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[45]
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, 857-870. doi:10.1038/ismej.2014.183
PUB | DOI | WoS | PubMed | Europe PMC
 
[44]
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, 47. doi:10.1186/s13742-015-0087-0
PUB | DOI | WoS | PubMed | Europe PMC
 
[43]
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
PUB | DOI
 
[42]
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, 6585. doi:10.1038/ncomms7585
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. (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
PUB
 
[40]
2015 | Report | Veröffentlicht | PUB-ID: 2901613
Lux, M., Hammer, B., & Sczyrba, A. (2015). Automated Contamination Detection in Single-Cell Sequencing. Cold Spring Harbor Laboratory Press. doi:10.1101/020859
PUB | DOI
 
[39]
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). doi:10.3389/fmicb.2014.00307
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[38]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[37]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[36]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[35]
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), 95380. doi:10.1371/journal.pone.0095380
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[33]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[32]
2013 | Konferenzbeitrag | PUB-ID: 2909357
Gisbrecht, A., Hammer, B., Mokbel, B., & Sczyrba, A. (2013). Nonlinear dimensionality reduction for cluster identification in metagenomic samples. IV, 174-179.
PUB
 
[31]
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).
PUB
 
[30]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[29]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[28]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[27]
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. doi:10.1038/ismej.2013.111
PUB | DOI | WoS | PubMed | Europe PMC
 
[26]
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
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., 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
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., 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
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. (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
PUB | DOI | WoS | PubMed | Europe PMC
 
[22]
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. doi:10.1126/science.1203690
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., et al. (2011). High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery. Angewandte Chemie, 123(47), 11411-11414. doi:10.1002/ange.201104685
PUB | DOI | PubMed | Europe PMC
 
[20]
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
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC | GenBank
 
[19]
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. doi:10.1371/journal.pone.0026161
PUB | DOI | WoS | PubMed | Europe PMC
 
[18]
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. doi:10.1126/science.1200387
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., et al. (2010). Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci, 3(3), 243-248. doi:10.4056/sigs.1433550
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. (2008). GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics, 9(Suppl 4), S13. doi:10.1186/1471-2105-9-S4-S13
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[15]
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. doi:10.1093/bib/bbm063
PUB | DOI | WoS | PubMed | Europe PMC
 
[14]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756
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. doi:10.1186/1471-2105-7-110
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. (2005). XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics, 6(1), 123. doi:10.1186/1471-2164-6-123
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. (2004). Genlight: Interactive high-throughput sequence analysis and comparative genomics. Journal of Integrative Bioinformatics, 1(1), 0008. doi:10.2390/biecoll-jib-2004-8
PUB | DOI
 
[11]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383536
Beckstette, M., Sczyrba, A., & Selzer, P. M. (2004). Genlight: Interactive high-throughput sequence analysis and comparative genomics. Proceedings of the German Conference on Bioinformatics, 179-186
PUB
 
[10]
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. Proceedings of the German Conference on Bioinformatics
PUB
 
[9]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607400
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. doi:10.1093/nar/gkh386
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[8]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607394
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. doi:10.1093/nar/gkh478
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[7]
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. doi:10.1016/j.jbiotec.2003.08.010
PUB | DOI | WoS | PubMed | Europe PMC
 
[6]
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. doi:10.1093/bioinformatics/btf882
PUB | DOI | WoS | PubMed | Europe PMC
 
[5]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773844
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. doi:10.1093/nar/gkg576
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
[4]
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. doi:10.1093/bioinformatics/btg181
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., et al. (2001). Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet, 27(3), 337-340.
PUB
 
[2]
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. doi:10.1006/dbio.2001.0298
PUB | DOI | WoS | PubMed | Europe PMC
 
[1]
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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[75]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923
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. doi:10.3390/genes10060424
PUB | PDF | DOI | Download (ext.)
 
[74]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
Pankoke, H., Maus, I., Loh, G., Huser, A., Seifert, J., Tilker, A., Hark, S., et al. (2019). F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota. FEMS microbiology letters. doi:10.1093/femsle/fnz033
PUB | DOI | PubMed | Europe PMC
 
[73]
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, 17. doi:10.1186/s40168-019-0633-6
PUB | DOI | WoS | PubMed | Europe PMC
 
[72]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[71]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[70]
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, giy069. doi:10.1093/gigascience/giy069
PUB | DOI | WoS | PubMed | Europe PMC
 
[69]
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. doi:10.12688/f1000research.15161.1
PUB | DOI | Download (ext.) | PubMed | Europe PMC
 
[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
PUB | DOI | WoS | PubMed | Europe PMC
 
[67]
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, 167. doi:10.1186/s13068-018-1162-4
PUB | DOI | WoS | PubMed | Europe PMC
 
[66]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[65]
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
PUB | DOI | WoS
 
[64]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
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. doi:10.1016/j.jbiotec.2017.02.020
PUB | DOI | WoS | PubMed | Europe PMC
 
[63]
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
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[62]
2017 | Datenpublikation | PUB-ID: 2914921
Huang, L., Krüger, J., & Sczyrba, A. (2017). Sparkhit evaluation data set. Bielefeld University. doi:10.4119/unibi/2914921
PUB | Dateien verfügbar | DOI
 
[61]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516
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
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[60]
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. doi:10.1038/nmeth.4458
PUB | DOI | WoS | PubMed | Europe PMC
 
[59]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815
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, 156. doi:10.1186/s13068-016-0565-3
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633
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, 543. doi:10.1186/s12859-016-1397-7
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[57]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[56]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[55]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[54]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[53]
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
PUB | DOI | WoS
 
[52]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[51]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[50]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[49]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[48]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[47]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906
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. doi:10.1186/s13742-015-0073-6
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[45]
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, 857-870. doi:10.1038/ismej.2014.183
PUB | DOI | WoS | PubMed | Europe PMC
 
[44]
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, 47. doi:10.1186/s13742-015-0087-0
PUB | DOI | WoS | PubMed | Europe PMC
 
[43]
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
PUB | DOI
 
[42]
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, 6585. doi:10.1038/ncomms7585
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. (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
PUB
 
[40]
2015 | Report | Veröffentlicht | PUB-ID: 2901613
Lux, M., Hammer, B., & Sczyrba, A. (2015). Automated Contamination Detection in Single-Cell Sequencing. Cold Spring Harbor Laboratory Press. doi:10.1101/020859
PUB | DOI
 
[39]
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). doi:10.3389/fmicb.2014.00307
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[38]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[37]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[36]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[35]
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), 95380. doi:10.1371/journal.pone.0095380
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[33]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[32]
2013 | Konferenzbeitrag | PUB-ID: 2909357
Gisbrecht, A., Hammer, B., Mokbel, B., & Sczyrba, A. (2013). Nonlinear dimensionality reduction for cluster identification in metagenomic samples. IV, 174-179.
PUB
 
[31]
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).
PUB
 
[30]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[29]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[28]
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
PUB | DOI | WoS | PubMed | Europe PMC
 
[27]
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. doi:10.1038/ismej.2013.111
PUB | DOI | WoS | PubMed | Europe PMC
 
[26]
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
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., 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
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., 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
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. (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
PUB | DOI | WoS | PubMed | Europe PMC
 
[22]
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. doi:10.1126/science.1203690
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., et al. (2011). High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery. Angewandte Chemie, 123(47), 11411-11414. doi:10.1002/ange.201104685
PUB | DOI | PubMed | Europe PMC
 
[20]
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
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC | GenBank
 
[19]
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. doi:10.1371/journal.pone.0026161
PUB | DOI | WoS | PubMed | Europe PMC
 
[18]
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. doi:10.1126/science.1200387
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., et al. (2010). Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci, 3(3), 243-248. doi:10.4056/sigs.1433550
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. (2008). GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics, 9(Suppl 4), S13. doi:10.1186/1471-2105-9-S4-S13
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[15]
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. doi:10.1093/bib/bbm063
PUB | DOI | WoS | PubMed | Europe PMC
 
[14]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756
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. doi:10.1186/1471-2105-7-110
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. (2005). XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics, 6(1), 123. doi:10.1186/1471-2164-6-123
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. (2004). Genlight: Interactive high-throughput sequence analysis and comparative genomics. Journal of Integrative Bioinformatics, 1(1), 0008. doi:10.2390/biecoll-jib-2004-8
PUB | DOI
 
[11]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383536
Beckstette, M., Sczyrba, A., & Selzer, P. M. (2004). Genlight: Interactive high-throughput sequence analysis and comparative genomics. Proceedings of the German Conference on Bioinformatics, 179-186
PUB
 
[10]
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. Proceedings of the German Conference on Bioinformatics
PUB
 
[9]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607400
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. doi:10.1093/nar/gkh386
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[8]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607394
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. doi:10.1093/nar/gkh478
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[7]
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. doi:10.1016/j.jbiotec.2003.08.010
PUB | DOI | WoS | PubMed | Europe PMC
 
[6]
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. doi:10.1093/bioinformatics/btf882
PUB | DOI | WoS | PubMed | Europe PMC
 
[5]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773844
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. doi:10.1093/nar/gkg576
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
[4]
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. doi:10.1093/bioinformatics/btg181
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., et al. (2001). Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet, 27(3), 337-340.
PUB
 
[2]
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. doi:10.1006/dbio.2001.0298
PUB | DOI | WoS | PubMed | Europe PMC
 
[1]
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.
PUB
 

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