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Staff at EMBL

Daniel Mende

Postdoctoral Fellow
Bork Group

EMBL Heidelberg, Meyerhofstra├če 1, 69117 Heidelberg, Germany

E-mail: send a mail

Publications

Metagenomic species profiling using universal phylogenetic marker genes. Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W.M., Wang, J., Li, J., Dore, J., Ehrlich, S.D., Stamatakis, A. & Bork, P. Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20. Europe PMC

Accurate and universal delineation of prokaryotic species. Mende, D.R., Sunagawa, S., Zeller, G. & Bork, P. Nat Methods. 2013 Sep;10(9):881-4. doi: 10.1038/nmeth.2575. Epub 2013 Jul 28. Europe PMC

Country-specific antibiotic use practices impact the human gut resistome. Forslund, K., Sunagawa, S., Kultima, J.R., Mende, D.R., Arumugam, M., Typas, A. & Bork, P. Genome Res. 2013 Jul;23(7):1163-9. doi: 10.1101/gr.155465.113. Epub 2013 Apr 8. Europe PMC

Genomic variation landscape of the human gut microbiome. Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., Kota, K., Sunyaev, S.R., Weinstock, G.M. & Bork, P. Nature. 2013 Jan 3;493(7430):45-50. doi: 10.1038/nature11711. Epub 2012 Dec 5. Europe PMC

Consistent mutational paths predict eukaryotic thermostability. van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D.R., Sinning, I., Hurt, E. & Bork, P. BMC Evol Biol. 2013 Jan 10;13:7. doi: 10.1186/1471-2148-13-7. Europe PMC

MOCAT: a metagenomics assembly and gene prediction toolkit. Kultima, J.R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D.R., Arumugam, M., Pan, Q., Liu, B., Qin, J., Wang, J. & Bork, P. PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17. Europe PMC

Assessment of metagenomic assembly using simulated next generation sequencing data. Mende, D.R., Waller, A.S., Sunagawa, S., Jarvelin, A.I., Chan, M.M., Arumugam, M., Raes, J. & Bork, P. PLoS One. 2012;7(2):e31386. Epub 2012 Feb 23. Europe PMC

Deciphering a global network of functionally associated post-translational modifications. Minguez, P., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., van Noort, V. & Bork, P. Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31. Europe PMC