Daniel R. Mende

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Peer BorkDirector of EMBL HeidelbergVerified email at embl.de
Shinichi SunagawaETH Zurich; Swiss Institute of BioinformaticsVerified email at ethz.ch
Jaime Huerta-CepasGroup Leader at CBGP (UPM-INIA-CSIC), Madrid, SpainVerified email at embl.de
Ivica Letunićbiobyte solutions GmbHVerified email at biobyte.de
edward francis delongProfessor, University of Hawaii, ManoaVerified email at hawaii.edu
Damian SzklarczykSIB Swiss Institute of Bioinformatics / University of ZurichVerified email at isb-sib.ch
Christian von MeringProfessor of Computational Biology, University of Zurich and Swiss Institute of BioinformaticsVerified email at imls.uzh.ch
Georg ZellerLUMC Leiden & EMBL HeidelbergVerified email at embl.de
Manimozhiyan ArumugamAssociate Professor, Faculty of Health and Medical Sciences, University of CopenhagenVerified email at sund.ku.dk
Jens Roat KultimaDanish Competition and Consumer Agency; Bioinformatics and Economic Fraud SpecialistVerified email at kfst.dk
Luis Pedro CoelhoCentre for Microbiome Research, Queensland University of TechnologyVerified email at qut.edu.au
Thomas Sebastian B. SchmidtSchool of Medicine & APC Microbiome, University College CorkVerified email at ucc.ie
Julien TapINRAE, Université Paris-SaclayVerified email at inrae.fr
Alison S. WallerBrock UniversityVerified email at brocku.ca
Vera van Noortprofessor, KULeuvenVerified email at biw.kuleuven.be
Henrik Bjørn NielsenChief Scientific Officer, Clinical-Microbiomics A/SVerified email at clinical-microbiomics.com
Nassos TypasGroup Leader, EMBLVerified email at embl.de
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

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	13674	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	8631	2011
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	3305	2019
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	2569	2015
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	2024	2016
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	1146	2014
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	986	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	723	2015
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	528	2013
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	459	2013
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	423	2019
Accurate and universal delineation of prokaryotic species DR Mende, S Sunagawa, G Zeller, P Bork Nature methods 10 (9), 881-884, 2013	333	2013
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	286	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	280	2012
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	279	2012
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	250	2022
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	233	2012
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	217	2016
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	216	2015
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	161	2017

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