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Microbial Genomics|April 27, 2026
bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilizationNicholas Pucci, Daniel R MendeFrontiers in Microbiology|October 22, 2019
Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical GyreDaniel R Mende, Dominique Boeuf, Edward F DeLongNature Methods|July 30, 2013
Accurate and universal delineation of prokaryotic speciesDaniel R Mende, Shinichi Sunagawa, Georg Zeller, et al.Genome Biology|April 22, 2015
Inter-individual differences in the gene content of human gut bacterial speciesAna Zhu, Shinichi Sunagawa, Daniel R Mende, et al.Mbio|November 30, 2017
Bacteriophage Distributions and Temporal Variability in the Ocean's InteriorElaine Luo, Frank O Aylward, Daniel R Mende, et al.Peerj|January 27, 2025
Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiomeNicholas Pucci, Joanne Ujčič-Voortman, Arnoud P Verhoeff, et al.The ISME Journal|February 16, 2020
Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water columnElaine Luo, John M Eppley, Anna E Romano, et al.Proceedings of the National Academy of Sciences of the United States of America|May 6, 2015
Metabolic dependencies drive species co-occurrence in diverse microbial communitiesAleksej Zelezniak, Sergej Andrejev, Olga Ponomarova, et al.Microbial Genomics|March 15, 2022
Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolutionBoas C L van der Putten, Niek A H Huijsmans, Daniel R Mende, et al.Frontiers in Microbiology|February 24, 2016
Improved Environmental Genomes via Integration of Metagenomic and Single-Cell AssembliesDaniel R Mende, Frank O Aylward, John M Eppley, et al.Pageof 7