Standout Papers
Citation Impact
Citing Papers
Metabolic dependencies drive species co-occurrence in diverse microbial communities
2015
Rhizobium induces DNA damage in Caenorhabditis elegans intestinal cells
2019 StandoutNobel
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
2019 Science
The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis
2013 StandoutScience
Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots
2019
Increasing homogeneity in global food supplies and the implications for food security
2014 Standout
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
2018
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
2009 StandoutScience
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
2013
High-level classification of the Fungi and a tool for evolutionary ecological analyses
2018
Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir
2016
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
2013
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
2015
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality
2020 Standout
Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa
2015
ColabFold: making protein folding accessible to all
2022 Standout
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming
2018
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
2022 StandoutNobel
Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production
2014
An Expanded View of Complex Traits: From Polygenic to Omnigenic
2017 Standout
Marine microbial community dynamics and their ecological interpretation
2015
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
2012 Standout
Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history
2021
Syndemics and the biosocial conception of health
2017 Standout
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
2010 Standout
Species–function relationships shape ecological properties of the human gut microbiome
2016
Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments
2016
Massive expansion of human gut bacteriophage diversity
2021
The microbiota in adaptive immune homeostasis and disease
2016 StandoutNature
Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds
2016
Microbial tryptophan catabolites in health and disease
2018 Standout
Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
2018 Standout
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
2014 StandoutNature
Plant–microbiome interactions: from community assembly to plant health
2020 Standout
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
2013
Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere
2019
Categorization of the gut microbiota: enterotypes or gradients?
2012
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
2009
Host genetic variation impacts microbiome composition across human body sites
2015
Microbiome Datasets Are Compositional: And This Is Not Optional
2017 Standout
STRING v10: protein–protein interaction networks, integrated over the tree of life
2014 Standout
Network-based metabolic analysis and microbial community modeling
2016
Viruses in the faecal microbiota of monozygotic twins and their mothers
2010 StandoutNature
The Human Intestinal Microbiome in Health and Disease
2016 Standout
Microbiota and Host Nutrition across Plant and Animal Kingdoms
2015
RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes
2017 StandoutNobel
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016 Standout
Proportionality: A Valid Alternative to Correlation for Relative Data
2015
Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales
2013
Role of the Microbiota in Immunity and Inflammation
2014 Standout
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease
2016 Standout
Deciphering microbial interactions and detecting keystone species with co-occurrence networks
2014
Biofilms: an emergent form of bacterial life
2016 Standout
Differential abundance analysis for microbial marker-gene surveys
2013 Standout
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
2016 Standout
Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study
2019 Standout
Diet–microbiota interactions as moderators of human metabolism
2016 StandoutNature
Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc
2016
Innate and Adaptive Immunity Interact to Quench Microbiome Flagellar Motility in the Gut
2013
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
2021
Quantitative microbiome profiling links gut community variation to microbial load
2017 Nature
It's all relative: analyzing microbiome data as compositions
2016
Current understanding of the human microbiome
2018 Standout
Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health
2014
Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
2014
Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research
2017
Gut microbiota, metabolites and host immunity
2016 Standout
Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes
2016
Keystone taxa as drivers of microbiome structure and functioning
2018 Standout
Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity
2015 StandoutNature
Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation
2020 StandoutNobel
SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks
2009
A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links
2018
Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy
2017 Standout
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
2010 Standout
Leveraging models of cell regulation and GWAS data in integrative network-based association studies
2012
Diversity, stability and resilience of the human gut microbiota
2012 StandoutNature
Compositional data analysis of the microbiome: fundamentals, tools, and challenges
2016
Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease
2014
The resilience of the intestinal microbiota influences health and disease
2017
Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression
2014
STRING 8--a global view on proteins and their functional interactions in 630 organisms
2008 Standout
The pros, cons, and many unknowns of probiotics
2019 Standout
Gut microbiota in human metabolic health and disease
2020 Standout
2015 Standout
Computational meta'omics for microbial community studies
2013
Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments
2016
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China
2016
Decoupling function and taxonomy in the global ocean microbiome
2016 StandoutScience
Remarkable Mechanisms in Microbes to Resist Phage Infections
2014
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
2018 Standout
Classification of Intrinsically Disordered Regions and Proteins
2014 Standout
The Dynamic Codon Biaser: calculating prokaryotic codon usage biases
2021
Influence of resistance breeding in common bean on rhizosphere microbiome composition and function
2017
A phylogenetic transform enhances analysis of compositional microbiota data
2017
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
2018 Standout
Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies
2016
Establishment of Intestinal Microbiota during Early Life: a Longitudinal, Explorative Study of a Large Cohort of Danish Infants
2014
Prospective randomized controlled study on the effects of Saccharomyces boulardii CNCM I-745 and amoxicillin-clavulanate or the combination on the gut microbiota of healthy volunteers
2016
The ecology of the microbiome: Networks, competition, and stability
2015 StandoutScience
Computational Approaches for Integrative Analysis of the Metabolome and Microbiome
2017
jClust: a clustering and visualization toolbox
2009
Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns
2016
The Long-Term Stability of the Human Gut Microbiota
2013 StandoutScience
The identification of short linear motif-mediated interfaces within the human interactome
2012
Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota
2013
Network topology reveals high connectance levels and few key microbial genera within soils
2014
Caenorhabditis elegans responses to bacteria from its natural habitats
2016 StandoutNobel
The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis
2013
Analysis of a summary network of co-infection in humans reveals that parasites interact most via shared resources
2014
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights
2021 Standout
Application of multivariate statistical techniques in microbial ecology
2016
The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
2015
The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages
2016
Works of Karoline Faust being referenced
Using metabolic networks to resolve ecological properties of microbiomes
2017
Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil
2016
Metagenomics meets time series analysis: unraveling microbial community dynamics
2015
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
2012
Microbial Co-occurrence Relationships in the Human Microbiome
2012 Standout
Cross-biome comparison of microbial association networks
2015
Microbial interactions: from networks to models
2012 Standout
Can we predict keystones?
2018
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
2008
Computational approaches to predict bacteriophage–host relationships
2015
Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes
2016
Pathway discovery in metabolic networks by subgraph extraction
2010
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
2016
From hairballs to hypotheses–biological insights from microbial networks
2018