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76 Publikationen

2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2936223 OA
Belmann, P., Fischer, B., Krüger, J., Procházka, M., Rasche, H., Prinz, M., Hanussek, M., Lang, M., Bartusch, F., Gläßle, B., et al. (2019). de.NBI Cloud federation through ELIXIR AAI. F1000Research 8:842.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
Pankoke, H., Maus, I., Loh, G., Huser, A., Seifert, J., Tilker, A., Hark, S., Sczyrba, A., Pelzer, S., and Kleinbolting, J. (2019). F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota. FEMS microbiology letters.
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923 OA
Nelkner, J., Henke, C., Lin, T. W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., Pühler, A., Sczyrba, A., and Schlüter, A. (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 10:424.
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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., et al. (2019). CAMISIM: simulating metagenomes and microbial communities. Microbiome 7:17.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929
Stolze, Y., Bremges, A., Maus, I., Pühler, A., Sczyrba, A., and Schlüter, A. (2018). Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants. Microbial Biotechnology 11, 667-679.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777
Celis, J. S., Wibberg, D., Ramírez-Portilla, C., Rupp, O., Sczyrba, A., Winkler, A., Kalinowski, J., and Wilke, T. (2018). Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience 7:giy075.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593 OA
Linden, M., Prochazka, M., Lappalainen, I., Bucik, D., Vyskocil, P., Kuba, M., Silén, S., Belmann, P., Sczyrba, A., Newhouse, S., et al. (2018). Common ELIXIR Service for Researcher Authentication and Authorisation. F1000Research 7:1199.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723
Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A., and McHardy, A. C. (2018). AMBER: Assessment of Metagenome BinnERs. GigaScience:giy069.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890
Huang, L., Krüger, J., and Sczyrba, A. (2018). Analyzing large scale genomic data on the cloud with Sparkhit. Bioinformatics 34, 1457-1465.
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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., et al. (2018). Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnology for Biofuels 11:167.
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918275
Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, A., Littmann, S., and Emerson, D. (2018). Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology 84:e02239-17.
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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., et al. (2018). Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approach. Plant and Soil 422, 467-478.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516 OA
Maus, I., Bremges, A., Stolze, Y., Hahnke, S., Cibis, K. G., Koeck, D. E., Kim, Y. S., Kreubel, J., Hassa, J., Wibberg, D., et al. (2017). Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels 10:264.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
Yu, J., Blom, J., Sczyrba, A., and Goesmann, A. (2017). Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Journal of Biotechnology 257, 58-60.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556 OA
Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., Albaum, S., Schlüter, A., Goesmann, A., et al. (2017). Bioinformatics for NGS-based metagenomics and the application to biogas research. Journal of Biotechnology 261, 10-23.
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2017 | Datenpublikation | PUB-ID: 2914921 OA
Huang, L., Krüger, J., and Sczyrba, A. (2017). Sparkhit evaluation data set. Bielefeld University.
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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., et al. (2017). Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods 14, 1063-1071.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815 OA
Stolze, Y., Bremges, A., Rumming, M., Henke, C., Maus, I., Pühler, A., Sczyrba, A., and Schlüter, A. (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.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633 OA
Lux, M., Krüger, J., Rinke, C., Maus, I., Schlüter, A., Woyke, T., Sczyrba, A., and Hammer, B. (2016). acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data. BMC Bioinformatics 17:543.
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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., and Reichl, U. (2016). Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnology for Biofuels 9:155.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489
Maus, I., Cibis, K. G., Bremges, A., Stolze, Y., Wibberg, D., Tomazetto, G., Blom, J., Sczyrba, A., König, H., Pühler, A., 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.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302
Wibberg, D., Bremges, A., Dammann-Kalinowski, T., Maus, I., Igeño, M. I., Vogelsang, R., König, C., Luque-Almagro, V. M., Roldán, M. D., Sczyrba, A., 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.
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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., 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.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190
Stiefel, F., Fischer, S., Sczyrba, A., Otte, K., and 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.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729
Bremges, A., Singer, E., Woyke, T., and Sczyrba, A. (2016). MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics 32, 2199-2201.
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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., et al. (2016). Back to the future of soil metagenomics. Frontiers in Microbiology 7:73.
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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., and Schlüter, A. (2016). Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene. Antimicrobial Agents and Chemotherapy 60, 3032-3040.
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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., 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 9:171.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234
Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S., Jaenicke, S., Fracowiak, J., Pühler, A., and Schlüter, A. (2016). An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology 231, 268-279.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906 OA
Bremges, A., Maus, I., Belmann, P., Eikmeyer, F. G., Winkler, A., Albersmeier, A., Pühler, A., Schlüter, A., and Sczyrba, A. (2015). Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. GigaScience 4:33.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833
Kohrs, F., Wolter, S., Benndorf, D., Heyer, R., Hoffmann, M., Rapp, E., Bremges, A., Sczyrba, A., Schlüter, A., and Reichl, U. (2015). Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics 15, 3585-3589.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183
Field, E. K., Sczyrba, A., Lyman, A. E., Harris, C. C., Woyke, T., Stepanauskas, R., and Emerson, D. (2015). Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. The ISME journal 9, 857-870.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501
Belmann, P., Dröge, J., Bremges, A., McHardy, A. C., Sczyrba, A., and Barton, M. D. (2015). Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience 4:47.
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2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901612
Lux, M., Sczyrba, A., and Hammer, B. (2015). “Automatic discovery of metagenomic structure” in 2015 International Joint Conference on Neural Networks (IJCNN) (Institute of Electrical & Electronics Engineers (IEEE).
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156
Paul, B. G., Bagby, S. C., Czornyj, E., Arambula, D., Handa, S., Sczyrba, A., Ghosh, P., Miller, J. F., and Valentine, D. L. (2015). Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nature Communications 6, 6585.
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2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466
Osterholz, B., Wiebke, P., Fust, A., Rumming, M., Schlüter, A., and 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
 
2015 | Report | Veröffentlicht | PUB-ID: 2901613
Lux, M., Hammer, B., and Sczyrba, A. (2015). Automated Contamination Detection in Single-Cell Sequencing. Cold Spring Harbor Laboratory Press.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992
Piao, H., Lachman, M., Malfatti, S., Sczyrba, A., Knierim, B., Auer, M., Tringe, S. G., Mackie, R. I., Yeoman, C. J., and Hess, M. (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.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433
Kamke, J., Rinke, C., Schwientek, P., Mavromatis, K., Ivanova, N., Sczyrba, A., Woyke, T., and Hentschel, U. (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:e87353.
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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., et al. (2014). Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal 8, 2503-2516.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2698163
Heins, R. A., Cheng, X., Nath, S., Deng, K., Bowen, B. P., Chivian, D. C., Datta, S., Friedland, G. D., D'Haeseleer, P., Wu, D., et al. (2014). Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS chemical biology 9, 2082-2091.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2672695
Swan, B. K., Chaffin, M. D., Martinez-Garcia, M., Morrison, H. G., Field, E. K., Poulton, N. J., Masland, E. D. P., Harris, C. C., Sczyrba, A., Chain, P. S. G., et al. (2014). Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres. PloS one 9, 95380.
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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., et al. (2014). Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma. PLoS ONE 9, e92297.
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2662055
Wibberg, D., Luque-Almagro, V. M., Igeño, M. I., Bremges, A., Roldán, M. D., Merchán, F., Sáez, L. P., Guijo, M. I., Manso, M. I., Macías, D., et al. (2014). Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Journal of biotechnology 175, 67-68.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Konferenzbeitrag | PUB-ID: 2909357
Gisbrecht, A., Hammer, B., Mokbel, B., and Sczyrba, A. (2013). “Nonlinear dimensionality reduction for cluster identification in metagenomic samples” in IV 174-179.
PUB
 
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500
Gisbrecht, A., Hammer, B., Mokbel, B., and Sczyrba, A. (2013). “Nonlinear dimensionality reduction for cluster identification in metagenomic samples” in 17th International Conference on Information Visualisation IV 2013, Banissi, E. ed. 174-179.
PUB
 
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., et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424
Campbell, J. H., O'Donoghue, P., Campbell, A. G., Schwientek, P., Sczyrba, A., Woyke, T., Söll, D., and Podar, M. (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, 5540-5545.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352
Kamke, J., Sczyrba, A., Ivanova, N., Schwientek, P., Rinke, C., Mavromatis, K., Woyke, T., and Hentschel, U. (2013). Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. The ISME journal 7, 2287-2300.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234
Zaremba-Niedzwiedzka, K., Viklund, J., Zhao, W., Ast, J., Sczyrba, A., Woyke, T., McMahon, K., Bertilsson, S., Stepanauskas, R., and Andersson, S. G. (2013). Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology 14, R130.
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