Related references
Note: Only part of the references are listed.?What I cannot create, I do not understand: elucidating microbe-microbe interactions to facilitate plant microbiome engineering
Alexander M. Geller et al.
CURRENT OPINION IN MICROBIOLOGY (2023)
Interactions between Culturable Bacteria Are Predicted by Individual Species' Growth
Einat Nestor et al.
MSYSTEMS (2023)
The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions
M. J. Poupin et al.
ENVIRONMENTAL MICROBIOME (2023)
Resolving metabolic interaction mechanisms in plant microbiomes
Alan R. Pacheco et al.
CURRENT OPINION IN MICROBIOLOGY (2023)
In vitro interaction network of a synthetic gut bacterial community
Anna S. Weiss et al.
ISME JOURNAL (2022)
Functional attractors in microbial community assembly
Sylvie Estrela et al.
CELL SYSTEMS (2022)
Network structure of resource use and niche overlap within the endophytic microbiome
Matthew Michalska-Smith et al.
ISME JOURNAL (2022)
Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ
Lucas Hemmerle et al.
NATURE COMMUNICATIONS (2022)
Mapping phyllosphere microbiota interactions in planta to establish genotype-phenotype relationships
Martin Schaefer et al.
NATURE MICROBIOLOGY (2022)
A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions
Evangelia Vayena et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)
Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability
Mariana Murillo-Roos et al.
ISME JOURNAL (2022)
A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology
Joanna Coker et al.
MSYSTEMS (2022)
Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria
Birgitta Ryback et al.
ISME JOURNAL (2022)
The immunity priming effect of the Arabidopsis phyllosphere resident yeast Protomyces arabidopsidicola strain C29
Kai Wang et al.
FRONTIERS IN MICROBIOLOGY (2022)
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Ilija Dukovski et al.
NATURE PROTOCOLS (2021)
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen
Christine M. Vogel et al.
NATURE MICROBIOLOGY (2021)
Positive interactions are common among culturable bacteria
Jared Kehe et al.
SCIENCE ADVANCES (2021)
Enhancing Microbiome Research through Genome-Scale Metabolic Modeling
Nana Y. D. Ankrah et al.
MSYSTEMS (2021)
Non-additive microbial community responses to environmental complexity
Alan R. Pacheco et al.
NATURE COMMUNICATIONS (2021)
Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness
Tomer Orevi et al.
FRONTIERS IN MICROBIOLOGY (2021)
Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
Liliana Angeles-Martinez et al.
PLOS COMPUTATIONAL BIOLOGY (2021)
A general non-self response as part of plant immunity
Benjamin A. Maier et al.
NATURE PLANTS (2021)
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
David B. Bernstein et al.
GENOME BIOLOGY (2021)
MEMOTE for standardized genome-scale metabolic model testing
Christian Lieven et al.
NATURE BIOTECHNOLOGY (2020)
Context-dependent dynamics lead to the assembly of functionally distinct microbial communities
Leonora S. Bittleston et al.
NATURE COMMUNICATIONS (2020)
Plant-microbiome interactions: from community assembly to plant health
Pankaj Trivedi et al.
NATURE REVIEWS MICROBIOLOGY (2020)
Crop microbiome and sustainable agriculture
Brajesh K. Singh et al.
NATURE REVIEWS MICROBIOLOGY (2020)
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
Emmanuel Paradis et al.
BIOINFORMATICS (2019)
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
Pierre Salvy et al.
BIOINFORMATICS (2019)
Niche and fitness differences determine invasion success and impact in laboratory bacterial communities
Shao-peng Li et al.
ISME JOURNAL (2019)
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Laurent Heirendt et al.
NATURE PROTOCOLS (2019)
Driving factors of epiphytic bacterial communities: A review
Rudolf O. Schlechter et al.
JOURNAL OF ADVANCED RESEARCH (2019)
Modelling approaches for studying the microbiome
Manish Kumar et al.
NATURE MICROBIOLOGY (2019)
Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere
Charlotte Carlstroem et al.
NATURE ECOLOGY & EVOLUTION (2019)
Multistability and regime shifts in microbial communities explained by competition for essential nutrients
Veronika Dubinkina et al.
ELIFE (2019)
A systematic assessment of current genome-scale metabolic reconstruction tools
Sebastian N. Mendoza et al.
GENOME BIOLOGY (2019)
Emerging whole-cell modeling principles and methods
Arthur P. Goldberg et al.
CURRENT OPINION IN BIOTECHNOLOGY (2018)
Statistical physics of community ecology: a cavity solution to MacArthur's consumer resource model
Madhu Advani et al.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2018)
Deciphering microbial interactions in synthetic human gut microbiome communities
Ophelia S. Venturelli et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
Daniel Machado et al.
NUCLEIC ACIDS RESEARCH (2018)
Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome
Eric J. N. Helfrich et al.
NATURE MICROBIOLOGY (2018)
Emergent simplicity in microbial community assembly
Joshua E. Goldford et al.
SCIENCE (2018)
Microbiome interactions shape host fitness
Alison L. Gould et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Nutrient limitation of soil microbial processes in tropical forests
Tessa Camenzind et al.
ECOLOGICAL MONOGRAPHS (2018)
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Stefania Magnusdottir et al.
NATURE BIOTECHNOLOGY (2017)
Strains, functions and dynamics in the expanded Human Microbiome Project
Jason Lloyd-Price et al.
NATURE (2017)
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
Eugen Bauer et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Community structure follows simple assembly rules in microbial microcosms
Jonathan Friedman et al.
NATURE ECOLOGY & EVOLUTION (2017)
Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research
Julia A. Vorholt et al.
CELL HOST & MICROBE (2017)
Marine Animal Microbiomes: Toward Understanding Host-Microbiome Interactions in a Changing Ocean
Amy Apprill
FRONTIERS IN MARINE SCIENCE (2017)
Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves
Florian Ryffel et al.
ISME JOURNAL (2016)
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
Zachary A. King et al.
NUCLEIC ACIDS RESEARCH (2016)
The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen
Unyarat Ritpitakphong et al.
NEW PHYTOLOGIST (2016)
Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico
Almut Heinken et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Tal Galili
BIOINFORMATICS (2015)
Spatially-resolved metabolic cooperativity within dense bacterial colonies
John A. Cole et al.
BMC SYSTEMS BIOLOGY (2015)
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Donovan H. Parks et al.
GENOME RESEARCH (2015)
Functional overlap of the Arabidopsis leaf and root microbiota
Yang Bai et al.
NATURE (2015)
Advanced methods of plant disease detection. A review
Federico Martinelli et al.
AGRONOMY FOR SUSTAINABLE DEVELOPMENT (2015)
Social behavior and the microbiome
Elizabeth A. Archie et al.
CURRENT OPINION IN BEHAVIORAL SCIENCES (2015)
Induced Systemic Resistance by Beneficial Microbes
Corne M. J. Pieterse et al.
ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 52 (2014)
Nutrient overlap, genetic relatedness and spatial origin influence interaction-mediated shifts in inhibitory phenotype among Streptomyces spp.
Patricia Vaz Jauri et al.
FEMS MICROBIOLOGY ECOLOGY (2014)
Constraint-based models predict metabolic and associated cellular functions
Aarash Bordbar et al.
NATURE REVIEWS GENETICS (2014)
Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice
Jeremiah J. Faith et al.
SCIENCE TRANSLATIONAL MEDICINE (2014)
The foliar microbiome
Josep Penuelas et al.
TRENDS IN PLANT SCIENCE (2014)
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
Almut Heinken et al.
GUT MICROBES (2013)
Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species
Kevin R. Foster et al.
CURRENT BIOLOGY (2012)
Bacterial Degradation of Benzoate CROSS-REGULATION BETWEEN AEROBIC AND ANAEROBIC PATHWAYS
J. Andres Valderrama et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2012)
Microbial life in the phyllosphere
Julia A. Vorholt
NATURE REVIEWS MICROBIOLOGY (2012)
Protection of Arabidopsis thaliana against Leaf-Pathogenic Pseudomonas syringae by Sphingomonas Strains in a Controlled Model System
Gerd Innerebner et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)
Microbial degradation of aromatic compounds - from one strategy to four
Georg Fuchs et al.
NATURE REVIEWS MICROBIOLOGY (2011)
Competitive and cooperative metabolic interactions in bacterial communities
Shiri Freilich et al.
NATURE COMMUNICATIONS (2011)
Omic data from evolved E-coli are consistent with computed optimal growth from genome-scale models
Nathan E. Lewis et al.
MOLECULAR SYSTEMS BIOLOGY (2010)
What is flux balance analysis?
Jeffrey D. Orth et al.
NATURE BIOTECHNOLOGY (2010)
A protocol for generating a high-quality genome-scale metabolic reconstruction
Ines Thiele et al.
NATURE PROTOCOLS (2010)
Bacterial competition: surviving and thriving in the microbial jungle
Michael E. Hibbing et al.
NATURE REVIEWS MICROBIOLOGY (2010)
Environments that Induce Synthetic Microbial Ecosystems
Niels Klitgord et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics
Remi Peyraud et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Thermodynamics-based metabolic flux analysis
Christopher S. Henry et al.
BIOPHYSICAL JOURNAL (2007)
Microbiology of the phyllosphere
SE Lindow et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)
A hydroponic culture system for growing Arabidopsis thaliana plantlets under sterile conditions
B Schlesier et al.
PLANT MOLECULAR BIOLOGY REPORTER (2003)
Appetite of an epiphyte: Quantitative monitoring of bacterial sugar consumption in the phyllosphere
JHJ Leveau et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Share Paper
