Daniel R. Mende

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	All	Since 2016
Citations	20924	14168
h-index	26	26
i10-index	30	28

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Co-authors

Peer BorkEMBLVerified email at embl.de
Shinichi SunagawaETH Zürich; Swiss Institute of BioinformaticsVerified email at ethz.ch
Manimozhiyan ArumugamAssociate Professor, Faculty of Health and Medical Sciences, University of CopenhagenVerified email at sund.ku.dk
Jaime Huerta-CepasGroup Leader at CBGP (UPM-INIA), Madrid, SpainVerified email at embl.de
edward francis delongProfessor, University of Hawaii, ManoaVerified email at hawaii.edu
Jens Roat KultimaDanish Competition and Consumer Agency; Bioinformatics and Economic Fraud SpecialistVerified email at kfst.dk
Sofia K. ForslundJunior Group Leader, ECRC (joint Max Delbrück Center and Charité University Hospital unit), BerlinVerified email at embl.de
Christian von MeringProfessor of Computational Biology, University of Zurich and Swiss Institute of BioinformaticsVerified email at imls.uzh.ch
Damian SzklarczykSIB Swiss Institute of Bioinformatics / University of ZurichVerified email at isb-sib.ch
Georg ZellerEMBL, HeidelbergVerified email at embl.de
Alison S. WallerBrock UniversityVerified email at brocku.ca
Luis Pedro CoelhoISTBI, Fudan UniversityVerified email at fudan.edu.cn
Julien TapDanone ResearchVerified email at danone.com
Vera van Noortprofessor, KULeuvenVerified email at biw.kuleuven.be
Nassos TypasGroup Leader, EMBLVerified email at embl.de
Jeroen RaesProfessor, Faculty of Medicine, Rega Institute, KU Leuven; Group Leader Microbiome, VIB, BelgiumVerified email at med.kuleuven.be
George WeinstockDirector of Microbial Genomics, Professor, Jackson LaboratoryVerified email at jax.org
Shamil SunyaevProfessor of Biomedical Informatics and of Medicine (BWH), Harvard Medical SchoolVerified email at rics.bwh.harvard.edu
Søren BrunakProfessor of Disease Systems Biology, University of CopenhagenVerified email at cpr.ku.dk
Alexandros StamatakisHeidelberg Institute for Theoretical Studies and Karlsruhe Institute of TechnologyVerified email at h-its.org

Daniel R. Mende

Asst. Professor, Amsterdam University Medical Center, University of Amsterdam

Verified email at amsterdamumc.nl

Computational Biology Bioinformatics Evolution Clinical Microbiology


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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	8800	2010
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	5428	2011
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	1239	2016
Structure and function of the global ocean microbiome S Sunagawa, LP Coelho, S Chaffron, JR Kultima, K Labadie, G Salazar, ... Science 348 (6237), 2015	1223	2015
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	634	2013
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	544	2014
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	352	2013
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	351	2015
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	345	2019
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	320	2013
Accurate and universal delineation of prokaryotic species DR Mende, S Sunagawa, G Zeller, P Bork Nature methods 10 (9), 881-884, 2013	239	2013
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	194	2012
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	182	2012
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	173	2012
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	166	2012
Inter-individual differences in the gene content of human gut bacterial species A Zhu, S Sunagawa, DR Mende, P Bork Genome biology 16 (1), 1-13, 2015	117	2015
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	108	2016
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	75	2017
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	74	2019
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	58	2016

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