Daniel R. Mende
Daniel R. Mende
Asst. Professor, Amsterdam University Medical Center, University of Amsterdam
Verified email at amsterdamumc.nl
Title
Cited by
Cited by
Year
A human gut microbial gene catalogue established by metagenomic sequencing
J Qin, R Li, J Raes, M Arumugam, KS Burgdorf, C Manichanh, T Nielsen, ...
nature 464 (7285), 59-65, 2010
84672010
Enterotypes of the human gut microbiome
M Arumugam, J Raes, E Pelletier, D Le Paslier, T Yamada, DR Mende, ...
nature 473 (7346), 174-180, 2011
52302011
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
J Huerta-Cepas, D Szklarczyk, K Forslund, H Cook, D Heller, MC Walter, ...
Nucleic acids research 44 (D1), D286-D293, 2016
11452016
Structure and function of the global ocean microbiome
S Sunagawa, LP Coelho, S Chaffron, JR Kultima, K Labadie, G Salazar, ...
Science 348 (6237), 2015
11332015
Genomic variation landscape of the human gut microbiome
S Schloissnig, M Arumugam, S Sunagawa, M Mitreva, J Tap, A Zhu, ...
Nature 493 (7430), 45-50, 2013
5972013
Potential of fecal microbiota for early‐stage detection of colorectal cancer
G Zeller, J Tap, AY Voigt, S Sunagawa, JR Kultima, PI Costea, A Amiot, ...
Molecular systems biology 10 (11), 766, 2014
5112014
Metagenomic species profiling using universal phylogenetic marker genes
S Sunagawa, DR Mende, G Zeller, F Izquierdo-Carrasco, SA Berger, ...
Nature methods 10 (12), 1196-1199, 2013
3372013
Metabolic dependencies drive species co-occurrence in diverse microbial communities
A Zelezniak, S Andrejev, O Ponomarova, DR Mende, P Bork, KR Patil
Proceedings of the National Academy of Sciences 112 (20), 6449-6454, 2015
3322015
Country-specific antibiotic use practices impact the human gut resistome
K Forslund, S Sunagawa, JR Kultima, DR Mende, M Arumugam, A Typas, ...
Genome research 23 (7), 1163-1169, 2013
3122013
Accurate and universal delineation of prokaryotic species
DR Mende, S Sunagawa, G Zeller, P Bork
Nature methods 10 (9), 881-884, 2013
2332013
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
J Huerta-Cepas, D Szklarczyk, D Heller, A Hernández-Plaza, SK Forslund, ...
Nucleic acids research 47 (D1), D309-D314, 2019
2312019
Role for urea in nitrification by polar marine Archaea
L Alonso-Sáez, AS Waller, DR Mende, K Bakker, H Farnelid, PL Yager, ...
Proceedings of the National Academy of Sciences 109 (44), 17989-17994, 2012
1872012
Deciphering a global network of functionally associated post‐translational modifications
P Minguez, L Parca, F Diella, DR Mende, R Kumar, M Helmer‐Citterich, ...
Molecular systems biology 8 (1), 599, 2012
1782012
Assessment of metagenomic assembly using simulated next generation sequencing data
DR Mende, AS Waller, S Sunagawa, AI Järvelin, MM Chan, M Arumugam, ...
PloS one 7 (2), e31386, 2012
1702012
MOCAT: a metagenomics assembly and gene prediction toolkit
JR Kultima, S Sunagawa, J Li, W Chen, H Chen, DR Mende, ...
PloS one 7 (10), e47656, 2012
1592012
Inter-individual differences in the gene content of human gut bacterial species
A Zhu, S Sunagawa, DR Mende, P Bork
Genome biology 16 (1), 82, 2015
1112015
Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean
RM Boiteau, DR Mende, NJ Hawco, MR McIlvin, JN Fitzsimmons, ...
Proceedings of the National Academy of Sciences 113 (50), 14237-14242, 2016
992016
Environmental drivers of a microbial genomic transition zone in the ocean’s interior
DR Mende, JA Bryant, FO Aylward, JM Eppley, T Nielsen, DM Karl, ...
Nature microbiology 2 (10), 1367-1373, 2017
632017
Microbial abundance, activity and population genomic profiling with mOTUs2
A Milanese, DR Mende, L Paoli, G Salazar, HJ Ruscheweyh, M Cuenca, ...
Nature communications 10 (1), 1-11, 2019
552019
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
DR Mende, I Letunic, J Huerta-Cepas, SS Li, K Forslund, S Sunagawa, ...
Nucleic acids research, gkw989, 2016
532016
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