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List of works by Daniel R Mende

A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators

scientific article published on 23 September 2019

A human gut microbial gene catalogue established by metagenomic sequencing

scientific article

Accurate and universal delineation of prokaryotic species ⬇️

scientific article published on July 28, 2013

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

scientific article published on 07 July 2020

Assessment of metagenomic assembly using simulated next generation sequencing data

scientific article

Bacteriophage Distributions and Temporal Variability in the Ocean's Interior

scientific article

Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean

scientific article published on 08 October 2020

Combined pigment and metatranscriptomic analysis reveals synchronized diel patterns of phenotypic light response across domains in the open ocean

scientific article published on 14 May 2020

Complex marine microbial communities partition metabolism of scarce resources over the diel cycle

scientific article

Consistent mutational paths predict eukaryotic thermostability

scientific article

Country-specific antibiotic use practices impact the human gut resistome

scientific article published on 08 April 2013

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022

Deciphering a global network of functionally associated post-translational modifications

scientific article

Diel cycling and long-term persistence of viruses in the ocean's euphotic zone.

scientific article published on 11 October 2017

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

scientific article published on 11 February 2020

Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

scientific article published on 14 February 2020

Enterotypes of the human gut microbiome

scientific article

Environmental drivers of a microbial genomic transition zone in the ocean's interior.

scientific article published on 14 August 2017

Genomic variation landscape of the human gut microbiome

scientific article

Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies

scientific article

Individuality and temporal stability of the human gut microbiome.

scientific article published in January 2013

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

scientific article published on 14 January 2016

Inter-individual differences in the gene content of human gut bacterial species

scientific article published on 21 April 2015

Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter

scientific article published on 26 September 2017

MOCAT: a metagenomics assembly and gene prediction toolkit

scientific article

Metabolic dependencies drive species co-occurrence in diverse microbial communities

scientific article published on 4 May 2015

Metagenomic species profiling using universal phylogenetic marker genes

scientific article

Microbial abundance, activity and population genomic profiling with mOTUs2

scientific article published on 4 March 2019

Ocean plankton. Structure and function of the global ocean microbiome

scientific article published on May 2015

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre

scientific article published on 01 October 2019

Potential of fecal microbiota for early-stage detection of colorectal cancer

scientific article

Role for urea in nitrification by polar marine Archaea

scientific article

Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean

scientific article (publication date: 13 December 2016)

Towards the biogeography of prokaryotic genes

scientific article published in 2021

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

scientific article (publication date: 17 November 2015)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

scientific article published on 01 January 2019

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

scientific article published on 01 January 2020

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

scientific article

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