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

por Zhu, Ana, Sunagawa, Shinichi, Mende, Daniel R, Bork, Peer
Publicado 2015

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

por Mende, Daniel R., Boeuf, Dominique, DeLong, Edward F.
Publicado 2019

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior

por Luo, Elaine, Aylward, Frank O., Mende, Daniel R., DeLong, Edward F.
Publicado 2017

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

por Luo, Elaine, Eppley, John M., Romano, Anna E., Mende, Daniel R., DeLong, Edward F.
Publicado 2020

Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution

por van der Putten, Boas C. L., Huijsmans, Niek A. H., Mende, Daniel R., Schultsz, Constance
Publicado 2022

Country-specific antibiotic use practices impact the human gut resistome

por Forslund, Kristoffer, Sunagawa, Shinichi, Kultima, Jens Roat, Mende, Daniel R., Arumugam, Manimozhiyan, Typas, Athanasios, Bork, Peer
Publicado 2013

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

por Mende, Daniel R., Aylward, Frank O., Eppley, John M., Nielsen, Torben N., DeLong, Edward F.
Publicado 2016

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

por Mende, Daniel R., Letunic, Ivica, Huerta-Cepas, Jaime, Li, Simone S., Forslund, Kristoffer, Sunagawa, Shinichi, Bork, Peer
Publicado 2017

Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage

por Boeuf, Dominique, Eppley, John M., Mende, Daniel R., Malmstrom, Rex R., Woyke, Tanja, DeLong, Edward F.
Publicado 2021

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

por Mende, Daniel R., Waller, Alison S., Sunagawa, Shinichi, Järvelin, Aino I., Chan, Michelle M., Arumugam, Manimozhiyan, Raes, Jeroen, Bork, Peer
Publicado 2012

GUNC: detection of chimerism and contamination in prokaryotic genomes

por Orakov, Askarbek, Fullam, Anthony, Coelho, Luis Pedro, Khedkar, Supriya, Szklarczyk, Damian, Mende, Daniel R., Schmidt, Thomas S. B., Bork, Peer
Publicado 2021

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

por Sosa, Oscar A., Repeta, Daniel J., Ferrón, Sara, Bryant, Jessica A., Mende, Daniel R., Karl, David. M., DeLong, Edward F.
Publicado 2017

Evidence of Genomic Diversification in a Natural Symbiotic Population Within Its Host

por Bongrand, Clotilde, Koch, Eric, Mende, Daniel, Romano, Anna, Lawhorn, Susannah, McFall-Ngai, Margaret, DeLong, Edward F., Ruby, Edward G.
Publicado 2022

Deciphering a global network of functionally associated post-translational modifications

por Minguez, Pablo, Parca, Luca, Diella, Francesca, Mende, Daniel R, Kumar, Runjun, Helmer-Citterich, Manuela, Gavin, Anne-Claude, van Noort, Vera, Bork, Peer
Publicado 2012

Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review

por Luchen, Charlie C., Chibuye, Mwelwa, Spijker, Rene, Simuyandi, Michelo, Chisenga, Caroline, Bosomprah, Samuel, Chilengi, Roma, Schultsz, Constance, Mende, Daniel R., Harris, Vanessa C.
Publicado 2023

Consistent mutational paths predict eukaryotic thermostability

por van Noort, Vera, Bradatsch, Bettina, Arumugam, Manimozhiyan, Amlacher, Stefan, Bange, Gert, Creevey, Chris, Falk, Sebastian, Mende, Daniel R, Sinning, Irmgard, Hurt, Ed, Bork, Peer
Publicado 2013

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

por Aylward, Frank O., Boeuf, Dominique, Mende, Daniel R., Wood-Charlson, Elisha M., Vislova, Alice, Eppley, John M., Romano, Anna E., DeLong, Edward F.
Publicado 2017

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments

por Ruscheweyh, Hans-Joachim, Milanese, Alessio, Paoli, Lucas, Karcher, Nicolai, Clayssen, Quentin, Keller, Marisa Isabell, Wirbel, Jakob, Bork, Peer, Mende, Daniel R., Zeller, Georg, Sunagawa, Shinichi
Publicado 2022

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

por Kultima, Jens Roat, Sunagawa, Shinichi, Li, Junhua, Chen, Weineng, Chen, Hua, Mende, Daniel R., Arumugam, Manimozhiyan, Pan, Qi, Liu, Binghang, Qin, Junjie, Wang, Jun, Bork, Peer
Publicado 2012

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

por Huerta-Cepas, Jaime, Szklarczyk, Damian, Heller, Davide, Hernández-Plaza, Ana, Forslund, Sofia K, Cook, Helen, Mende, Daniel R, Letunic, Ivica, Rattei, Thomas, Jensen, Lars J, von Mering, Christian, Bork, Peer
Publicado 2019