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Daniel R. Mende
Daniel R. Mende
Asst. Professor, Amsterdam University Medical Center, University of Amsterdam
Verified email at amsterdamumc.nl
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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
134722010
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
84912011
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
31542019
Structure and function of the global ocean microbiome
S Sunagawa, LP Coelho, S Chaffron, JR Kultima, K Labadie, G Salazar, ...
Science 348 (6237), 1261359, 2015
25042015
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
19972016
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
11152014
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
9692013
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
6952015
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
5232013
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
4522013
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), 1014, 2019
3992019
Accurate and universal delineation of prokaryotic species
DR Mende, S Sunagawa, G Zeller, P Bork
Nature methods 10 (9), 881-884, 2013
3322013
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
2812012
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
2782012
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
2722012
Critical assessment of metagenome interpretation: the second round of challenges
F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ...
Nature methods 19 (4), 429-440, 2022
2322022
MOCAT: a metagenomics assembly and gene prediction toolkit
JR Kultima, S Sunagawa, J Li, W Chen, H Chen, DR Mende, ...
Public Library of Science 7 (10), e47656, 2012
2302012
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
2152016
Inter-individual differences in the gene content of human gut bacterial species
A Zhu, S Sunagawa, DR Mende, P Bork
Genome biology 16, 1-13, 2015
2142015
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
1572017
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