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A road map for the development of community systems (CoSy) biology
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/bit.10803openalex-snapshot
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
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Systematizing the generation of missing metabolic knowledge
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Bacteria and Marine Biogeochemistry
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Phototrophic consortia: model systems for symbiotic interrelations between prokaryotes
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The Salmonella enterica Pan-genome
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A proteomic fingerprint of dissolved organic carbon and of soil particles
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A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
inferredcites →https://doi.org/10.1016/j.cell.2011.01.015openalex-snapshot
Intercellular Nanotubes Mediate Bacterial Communication
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Adaptive laboratory evolution — harnessing the power of biology for metabolic engineering
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Metabolic systems biology
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Comparative genomics: the bacterial pan-genome
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Construction and optimization of synthetic pathways in metabolic engineering
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Hierarchical thinking in network biology: the unbiased modularization of biochemical networks
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When microbial conversations get physical
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Missing genes in metabolic pathways: a comparative genomics approach
inferredcites →https://doi.org/10.1038/ismej.2010.117openalex-snapshot
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
inferredcites →https://doi.org/10.1038/ismej.2010.178openalex-snapshot
The Future of microbial metagenomics (or is ignorance bliss?)
inferredcites →https://doi.org/10.1038/ismej.2010.200openalex-snapshot
Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions
inferredcites →https://doi.org/10.1038/ismej.2011.107openalex-snapshot
Defining seasonal marine microbial community dynamics
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RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture
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Applications of genome‐scale metabolic reconstructions
inferredcites →https://doi.org/10.1038/msb.2010.66openalex-snapshot
Emergent cooperation in microbial metabolism
inferredcites →https://doi.org/10.1038/msb.2010.68openalex-snapshot
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
inferredcites →https://doi.org/10.1038/msb.2011.42openalex-snapshot
Microbial laboratory evolution in the era of genome‐scale science
inferredcites →https://doi.org/10.1038/msb4100131openalex-snapshot
Metabolic modeling of a mutualistic microbial community
inferredcites →https://doi.org/10.1038/nature01906openalex-snapshot
Evolution of cooperation and conflict in experimental bacterial populations
inferredcites →https://doi.org/10.1038/nature02340openalex-snapshot
Community structure and metabolism through reconstruction of microbial genomes from the environment
inferredcites →https://doi.org/10.1038/nature02456openalex-snapshot
Integrating high-throughput and computational data elucidates bacterial networks
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A microbial consortium couples anaerobic methane oxidation to denitrification
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Resource competition and social conflict in experimental populations of yeast
inferredcites →https://doi.org/10.1038/nature06279openalex-snapshot
Cooperation and conflict in quorum-sensing bacterial populations
inferredcites →https://doi.org/10.1038/nature07921openalex-snapshot
Snowdrift game dynamics and facultative cheating in yeast
inferredcites →https://doi.org/10.1038/nature08790openalex-snapshot
Electric currents couple spatially separated biogeochemical processes in marine sediment
inferredcites →https://doi.org/10.1038/nature08821openalex-snapshot
A human gut microbial gene catalogue established by metagenomic sequencing
inferredcites →https://doi.org/10.1038/nature10363openalex-snapshot
Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase
inferredcites →https://doi.org/10.1038/nbt.1582openalex-snapshot
The transcription unit architecture of the Escherichia coli genome
inferredcites →https://doi.org/10.1038/nbt.1672openalex-snapshot
High-throughput generation, optimization and analysis of genome-scale metabolic models
inferredcites →https://doi.org/10.1038/nbt1401openalex-snapshot
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
inferredcites →https://doi.org/10.1038/nchembio.266openalex-snapshot
Automatic policing of biochemical annotations using genomic correlations
inferredcites →https://doi.org/10.1038/nchembio.462openalex-snapshot
The challenges of integrating multi-omic data sets
inferredcites →https://doi.org/10.1038/nchembio.499openalex-snapshot
Laboratory evolution of glutathione biosynthesis reveals natural compensatory pathways
inferredcites →https://doi.org/10.1038/ncomms1597openalex-snapshot
Competitive and cooperative metabolic interactions in bacterial communities
inferredcites →https://doi.org/10.1038/nprot.2009.203openalex-snapshot
A protocol for generating a high-quality genome-scale metabolic reconstruction
inferredcites →https://doi.org/10.1038/nrg3033openalex-snapshot
Systems-biology approaches for predicting genomic evolution
inferredcites →https://doi.org/10.1038/nrmicro1023openalex-snapshot
Genome-scale models of microbial cells: evaluating the consequences of constraints
inferredcites →https://doi.org/10.1038/nrmicro1949openalex-snapshot
Reconstruction of biochemical networks in microorganisms
inferredcites →https://doi.org/10.1038/nrmicro2456openalex-snapshot
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling
inferredcites →https://doi.org/10.1038/nrmicro2634openalex-snapshot
Imaging mass spectrometry in microbiology
inferredcites →https://doi.org/10.1073/pnas.0603364103openalex-snapshot
Systems approach to refining genome annotation
inferredcites →https://doi.org/10.1073/pnas.0704189104openalex-snapshot
Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
inferredcites →https://doi.org/10.1073/pnas.0708897105openalex-snapshot
Microbial community gene expression in ocean surface waters
inferredcites →https://doi.org/10.1073/pnas.0807935105openalex-snapshot
Defined spatial structure stabilizes a synthetic multispecies bacterial community
inferredcites →https://doi.org/10.1073/pnas.0908456107openalex-snapshot
Rapid evolution of stability and productivity at the origin of a microbial mutualism
inferredcites →https://doi.org/10.1073/pnas.97.10.5528openalex-snapshot
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
inferredcites →https://doi.org/10.1074/jbc.274.25.17410openalex-snapshot
Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype
inferredcites →https://doi.org/10.1101/gr.104521.109openalex-snapshot
A global network of coexisting microbes from environmental and whole-genome sequence data
inferredcites →https://doi.org/10.1101/gr.107540.110openalex-snapshot
Structural and operational complexity of the Geobacter sulfurreducens genome
inferredcites →https://doi.org/10.1101/gr.116103.110openalex-snapshot
Transcript amplification from single bacterium for transcriptome analysis
inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02279.xopenalex-snapshot
Bioturbation and the role of microniches for sulfate reduction in coastal marine sediments
inferredcites →https://doi.org/10.1111/j.1751-7915.2009.00087.xopenalex-snapshot
Coupling a genome‐scale metabolic model with a reactive transport model to describe in situ uranium bioremediation
inferredcites →https://doi.org/10.1126/science.1093857openalex-snapshot
Environmental Genome Shotgun Sequencing of the Sargasso Sea
inferredcites →https://doi.org/10.1126/science.1107851openalex-snapshot
Comparative Metagenomics of Microbial Communities
inferredcites →https://doi.org/10.1126/science.1109070openalex-snapshot
Community Proteomics of a Natural Microbial Biofilm
inferredcites →https://doi.org/10.1126/science.1124234openalex-snapshot
Metagenomic Analysis of the Human Distal Gut Microbiome
inferredcites →https://doi.org/10.1126/science.1140516openalex-snapshot
Signals from chloroplasts converge to regulate nuclear gene expression.
inferredcites →https://doi.org/10.1126/science.1174671openalex-snapshot
Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima
inferredcites →https://doi.org/10.1126/science.1196526openalex-snapshot
Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria
inferredcites →https://doi.org/10.1126/science.1198914openalex-snapshot
Second-Order Selection for Evolvability in a Large Escherichia coli Population
inferredcites →https://doi.org/10.1126/science.1203163openalex-snapshot
Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists
inferredcites →https://doi.org/10.1126/science.1203980openalex-snapshot
Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria
inferredcites →https://doi.org/10.1126/science.289.5486.1902openalex-snapshot
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
inferredcites →https://doi.org/10.1126/science.7542800openalex-snapshot
Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd
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Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium
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Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms
inferredcites →https://doi.org/10.1128/aem.71.12.7838-7845.2005openalex-snapshot
Coaggregation Facilitates Interspecies Hydrogen Transfer betweenPelotomaculum thermopropionicumandMethanothermobacter thermautotrophicus
inferredcites →https://doi.org/10.1128/aem.72.1.135-143.2006openalex-snapshot
Identification of Eukaryotic Open Reading Frames in Metagenomic cDNA Libraries Made from Environmental Samples
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Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon
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A Periplasmic and Extracellular c -Type Cytochrome of Geobacter sulfurreducens Acts as a Ferric Iron Reductase and as an Electron Carrier to Other Acceptors or to Partner Bacteria
inferredcites →https://doi.org/10.1128/mmbr.00027-09openalex-snapshot
Central Role of the Cell in Microbial Ecology
inferredcites →https://doi.org/10.1128/mmbr.68.3.518-537.2004openalex-snapshot
Determination of the Core of a Minimal Bacterial Gene Set
inferredcites →https://doi.org/10.1146/annurev.micro.030608.101423openalex-snapshot
Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities
inferredcites →https://doi.org/10.1186/2042-5783-1-4openalex-snapshot
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset
inferredcites →https://doi.org/10.1186/gb-2008-9-11-r158openalex-snapshot
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
inferredcites →https://doi.org/10.1371/journal.pcbi.1000312openalex-snapshot
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization
inferredcites →https://doi.org/10.1371/journal.pcbi.1001002openalex-snapshot
Environments that Induce Synthetic Microbial Ecosystems
inferredcites →https://doi.org/10.3389/fmicb.2011.00146openalex-snapshot
Close Interspecies Interactions between Prokaryotes from Sulfureous Environments
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Nanoscale patchiness of bacteria in lake water studied with the spatial information preservation method
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Reactive Transport Modeling and Biogeochemical Cycling
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Harnessing In Silico Techniques for Bioremediation Solutions
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Programming Gut Microbiome Function Through Cross‐Feeding: From Ecological Mechanisms to Live Biotherapeutics
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Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach
inferred← citeshttps://doi.org/10.1002/wsbm.1308openalex-snapshot
Metabolic network modeling of microbial communities
inferred← citeshttps://doi.org/10.1007/10_2017_17openalex-snapshot
Microbial Electrosynthesis I: Pure and Defined Mixed Culture Engineering
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Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data
inferred← citeshttps://doi.org/10.1007/978-1-4614-6418-1_85-4openalex-snapshot
Integrated Lab-on-Chip System, Genome Sequencing of Single Microbial Cells, Project
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Investigating Host–Pathogen Behavior and Their Interaction Using Genome-Scale Metabolic Network Models
inferred← citeshttps://doi.org/10.1007/978-1-4939-2778-4_8openalex-snapshot
Weaving Knowledge into Biological Pathways in a Collaborative Manner
inferred← citeshttps://doi.org/10.1007/978-3-319-08575-3_43openalex-snapshot
The Minimal Rhizosphere Microbiome
inferred← citeshttps://doi.org/10.1007/978-3-319-33000-6_12openalex-snapshot
Marine Microbial Systems Ecology: Microbial Networks in the Sea
inferred← citeshttps://doi.org/10.1007/978-3-642-33636-2_5openalex-snapshot
Symmetry-Based Model Reduction for Approximate Stochastic Analysis
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Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming
inferred← citeshttps://doi.org/10.1007/978-3-642-53971-8_11openalex-snapshot
Microbial Bioprospecting in Marine Environments
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Symbiotic Interactions of Phototrophic Microbes: Engineering Synthetic Consortia for Biotechnology
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Proteome Engineering: An Evolutionary Perspective of Biochemical Systems
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Microbial cultivation and the role of microbial resource centers in the omics era
inferred← citeshttps://doi.org/10.1007/s11356-024-33474-9openalex-snapshot
Microbial remediation of petroleum-contaminated soil focused on the mechanism and microbial response: a review
inferred← citeshttps://doi.org/10.1007/s12275-015-5060-1openalex-snapshot
Unraveling interactions in microbial communities - from co-cultures to microbiomes
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Plant-associated fungal communities in the light of meta’omics
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From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes
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Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization
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Exploiting the Molecular Genetics of Microalgae
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Modeling and analysis techniques: seed microbiome
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Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies
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Applications of synthetic light-driven microbial consortia for biochemicals production
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Signal Destruction Tunes the Zone of Activation in Spatially Distributed Signaling Networks
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Dynamic fluid layer around immotile yeast colonies mediates the spread of bacteria
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Determining Microbial Products and Identifying Molecular Targets in the Human Microbiome
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Advances in constraint-based modelling of microbial communities
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Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities
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A methodological framework for linking bioreactor function to microbial communities and environmental conditions
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Deciphering microbial community robustness through synthetic ecology and molecular systems synecology
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Better together: engineering and application of microbial symbioses
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The sum is greater than the parts: exploiting microbial communities to achieve complex functions
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Biotechnology for secure biocontainment designs in an emerging bioeconomy
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Synthetic gut microbiome: Advances and challenges
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Biofilms: How Structure Emerges from Conflict
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Trophic Interactions and the Drivers of Microbial Community Assembly
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Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques
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Derivation of species interactions strength in a plant community with game theory
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Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities
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Algal-yeast consortium alters bacterial community composition and predicted functional potential during early biological soil crust development
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Microbial interactions in fermented foods: Ecological mechanisms, environmental drivers, and implications for quality
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Mathematical modeling and comparative metabolomics analyses of interactions between Lactiplantibacillus plantarum and Morganella morganii
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Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production
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Enhanced biomethane production through synergistic interaction of Enterobacter aerogenes and Methanosarcina barkeri in a co-culture anaerobic digestion system
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Metabolic interactions in microbial communities: untangling the Gordian knot
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Principles for designing synthetic microbial communities
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Microbial synergistic interactions for reductive dechlorination of polychlorinated biphenyls
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Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry
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Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology
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Condensing the omics fog of microbial communities
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Interactions in multispecies biofilms: do they actually matter?
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Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
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Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing
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Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
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Computational meta'omics for microbial community studies
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Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association
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Nutritional stress induces exchange of cell material and energetic coupling between bacterial species
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Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms
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Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth
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Modelling approaches for studying the microbiome
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Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities
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Polymicrobial biofilms of ocular bacteria and fungi on ex vivo human corneas
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Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach
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Synthetic microbial consortia: from systematic analysis to construction and applications
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Functional metagenomic exploration identifies novel prokaryotic copper resistance genes from the soil microbiome
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Plant-wide systems microbiology for the wastewater industry
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Metagenomics research on PAH biodegradation in the lower reaches of the Shiwuli River in Chaohu, China
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A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community
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Networks of energetic and metabolic interactions define dynamics in microbial communities
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Cell-to-cell bacterial interactions promoted by drier conditions on soil surfaces
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Distantly related bacteria share a rigid proteome allocation strategy with flexible enzyme kinetics
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Impact and Remediation of Petroleum Hydrocarbon Pollutants on Agricultural Land: A Review
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Implications of microbial adaptation for the assessment of environmental persistence of chemicals
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Multilevel Research Strategies and Biological Systems
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Antibiotic-induced stress responses in Gram-negative bacteria and their role in antibiotic resistance
inferred← citeshttps://doi.org/10.1101/018010openalex-snapshot
Impact of the species compartment definition on quantitative modeling of microbial communities
inferred← citeshttps://doi.org/10.1111/1462-2920.12312openalex-snapshot
Software platforms to facilitate reconstructing genome‐scale metabolic networks
inferred← citeshttps://doi.org/10.1111/1462-2920.12343openalex-snapshot
Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities
inferred← citeshttps://doi.org/10.1111/1574-6976.12028openalex-snapshot
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms
inferred← citeshttps://doi.org/10.1111/1751-7915.12855openalex-snapshot
Elucidation of complexity and prediction of interactions in microbial communities
inferred← citeshttps://doi.org/10.1111/2049-632x.12146openalex-snapshot
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces
inferred← citeshttps://doi.org/10.1111/jre.12708openalex-snapshot
Pyrosequencing of the subgingival microbiome in peri‐implantitis after non‐surgical mechanical debridement therapy
inferred← citeshttps://doi.org/10.1111/jvp.12041openalex-snapshot
Veterinary pharmacology: history, current status and future prospects
inferred← citeshttps://doi.org/10.1128/9781555817466.ch16openalex-snapshot
Mechanisms of Competition in Biofilm Communities
inferred← citeshttps://doi.org/10.1128/aem.00101-15openalex-snapshot
Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico
inferred← citeshttps://doi.org/10.1128/aem.02004-24openalex-snapshot
Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes
inferred← citeshttps://doi.org/10.1128/mbio.01175-18openalex-snapshot
Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
inferred← citeshttps://doi.org/10.1128/mbio.01526-14openalex-snapshot
Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations
inferred← citeshttps://doi.org/10.1128/mbio.02288-14openalex-snapshot
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
inferred← citeshttps://doi.org/10.1128/microbiolspec.mb-0009-2014openalex-snapshot
Mechanisms of Competition in Biofilm Communities
inferred← citeshttps://doi.org/10.1128/msphere.00681-22openalex-snapshot
The Fashion Industry Needs Microbiology: Opportunities and Challenges
inferred← citeshttps://doi.org/10.1128/msystems.00265-18openalex-snapshot
Bridging the Holistic-Reductionist Divide in Microbial Ecology
inferred← citeshttps://doi.org/10.1142/s0219720016500207openalex-snapshot
Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources
inferred← citeshttps://doi.org/10.1146/annurev-micro-092412-155614openalex-snapshot
Archaea in Biogeochemical Cycles
inferred← citeshttps://doi.org/10.11606/d.17.2018.tde-17072024-095057openalex-snapshot
A multiscale approach for exploring bacterial transcriptional systems
inferred← citeshttps://doi.org/10.1186/1752-0509-8-41openalex-snapshot
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
inferred← citeshttps://doi.org/10.1186/1757-4749-4-16openalex-snapshot
Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes
inferred← citeshttps://doi.org/10.1186/2049-2618-1-14openalex-snapshot
From meta-omics to causality: experimental models for human microbiome research
inferred← citeshttps://doi.org/10.1186/s12862-017-0950-yopenalex-snapshot
A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations
inferred← citeshttps://doi.org/10.1186/s12866-025-04296-7openalex-snapshot
Metagenomic analysis of vitamins B and K2 biosynthesis in chicken gut microbiota across laying periods
inferred← citeshttps://doi.org/10.1201/9781351246101openalex-snapshot
Microbial Fuels : Technologies and Applications
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003695openalex-snapshot
Emergent Biosynthetic Capacity in Simple Microbial Communities
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005079openalex-snapshot
The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005544openalex-snapshot
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005809openalex-snapshot
Quantifying the strength of quorum sensing crosstalk within microbial communities
inferred← citeshttps://doi.org/10.1371/journal.pone.0151722openalex-snapshot
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves
inferred← citeshttps://doi.org/10.1371/journal.pone.0171744openalex-snapshot
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems
inferred← citeshttps://doi.org/10.1371/journal.pone.0173183openalex-snapshot
Model-based quantification of metabolic interactions from dynamic microbial-community data
inferred← citeshttps://doi.org/10.1371/journal.pone.0216336openalex-snapshot
A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber
inferred← citeshttps://doi.org/10.18130/v3726fopenalex-snapshot
Comparative Systems Analysis of Opportunistic Gram-Negative Pathogens
inferred← citeshttps://doi.org/10.18307/2020.0125openalex-snapshot
Mini-review: Advances of metagenomics research for lake microbiomes
inferred← citeshttps://doi.org/10.2139/ssrn.5421696openalex-snapshot
Enhanced biomethane production through synergistic interaction of Enterobacter aerogenes and Methanosarcina barkeri in a co-culture anaerobic digestion system
inferred← citeshttps://doi.org/10.2217/fmb.13.38openalex-snapshot
Microbial Transformations of Arsenic: Perspectives for Biological Removal of Arsenic from Water
inferred← citeshttps://doi.org/10.3109/1040841x.2012.706250openalex-snapshot
Structure, mechanism and regulation of an artificial microbial ecosystem for vitamin C production
inferred← citeshttps://doi.org/10.3389/fmars.2014.00014openalex-snapshot
Systems biology solutions to challenges in marine biotechnology
inferred← citeshttps://doi.org/10.3389/fmicb.2014.00125openalex-snapshot
Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example
inferred← citeshttps://doi.org/10.3389/fmicb.2015.00213openalex-snapshot
Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure
inferred← citeshttps://doi.org/10.3389/fmicb.2015.01058openalex-snapshot
Emerging spatial patterns in Antarctic prokaryotes
inferred← citeshttps://doi.org/10.3389/fmicb.2016.00673openalex-snapshot
Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems
inferred← citeshttps://doi.org/10.3389/fmicb.2016.01366openalex-snapshot
Interspecific Bacterial Interactions are Reflected in Multispecies Biofilm Spatial Organization
inferred← citeshttps://doi.org/10.3389/fmicb.2016.01610openalex-snapshot
Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model
inferred← citeshttps://doi.org/10.3389/fmicb.2017.01106openalex-snapshot
Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds
inferred← citeshttps://doi.org/10.3389/fmicb.2017.01606openalex-snapshot
Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation
inferred← citeshttps://doi.org/10.3389/fmicb.2017.02299openalex-snapshot
From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality
inferred← citeshttps://doi.org/10.3389/fmicb.2018.02161openalex-snapshot
Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future
inferred← citeshttps://doi.org/10.3389/fmicb.2019.01095openalex-snapshot
Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity
inferred← citeshttps://doi.org/10.3389/fmicb.2020.02088openalex-snapshot
Understanding the Mechanisms of Positive Microbial Interactions That Benefit Lactic Acid Bacteria Co-cultures
inferred← citeshttps://doi.org/10.3389/fmicb.2022.883495openalex-snapshot
The Distinguishing Bacterial Features From Active and Remission Stages of Ulcerative Colitis Revealed by Paired Fecal Metagenomes
inferred← citeshttps://doi.org/10.3389/fnins.2020.00716openalex-snapshot
Systems Biology Approaches to Understand the Host–Microbiome Interactions in Neurodegenerative Diseases
inferred← citeshttps://doi.org/10.3390/bioengineering10010103openalex-snapshot
A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures
inferred← citeshttps://doi.org/10.3390/computation3010002openalex-snapshot
Computational Studies of the Intestinal Host-Microbiota Interactome
inferred← citeshttps://doi.org/10.3390/genes12081221openalex-snapshot
Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities
inferred← citeshttps://doi.org/10.3390/ijms231810761openalex-snapshot
Polymicrobial Biofilm Organization of Staphylococcus aureus and Pseudomonas aeruginosa in a Chronic Wound Environment
inferred← citeshttps://doi.org/10.3390/md20020108openalex-snapshot
Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications
inferred← citeshttps://doi.org/10.3390/microorganisms11020413openalex-snapshot
Differential Susceptibility of Mixed Polymicrobial Biofilms Involving Ocular Coccoid Bacteria (Staphylococcus aureus and S. epidermidis) and a Filamentous Fungus (Fusarium solani) on Ex Vivo Human Corneas
inferred← citeshttps://doi.org/10.3390/microorganisms13020234openalex-snapshot
Combined Analysis of Transcriptomes and Metabolomes Reveals Key Genes and Substances That Affect the Formation of a Multi-Species Biofilm by Nine Gut Bacteria
inferred← citeshttps://doi.org/10.3390/microorganisms7080236openalex-snapshot
Monitoring Biofilm Formation and Microbial Interactions that May Occur During a Salmonella Contamination Incident across the Network of a Water Bottling Plant
inferred← citeshttps://doi.org/10.3390/min7060106openalex-snapshot
Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage
inferred← citeshttps://doi.org/10.3390/molecules24183400openalex-snapshot
Petroleum Hydrocarbon Contamination in Terrestrial Ecosystems—Fate and Microbial Responses
inferred← citeshttps://doi.org/10.3390/pr2040711openalex-snapshot
Mathematical Modeling of Microbial Community Dynamics: A Methodological Review
inferred← citeshttps://doi.org/10.3724/1000-3207.2026.2026.0004openalex-snapshot
MICROBIAL COMMUNITY CHARACTERISTICS AND INTERACTION MECHANISMS DURING THE OUTBREAK OF HUANGTAI ALGAE IN ULANSUHAI LAKE
inferred← citeshttps://doi.org/10.47749/t/unicamp.2018.1062584openalex-snapshot
Construção de uma coleção de microorganismos representativos do microbioma da cana-de-açúcar
inferred← citeshttps://doi.org/10.5530/jam.4.1.5openalex-snapshot
Application of Computer Assisted Bimolecular Interaction Modelling in Predictive Microbiology, Current State and Future Prospects
inferred← citeshttps://doi.org/10.70675/175b6d22zc555z4155za9e1z77a323df2456openalex-snapshot
Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract
inferred← citeshttps://doi.org/10.70675/2b0a7354zc24dz4c20zae4cz6fab0ccf4752openalex-snapshot
Conception et optimisation d’un écosystème synthétique microbien pour la production de bio-hydrogène à partir de déchets de l’industrie laitière
inferred← citeshttps://doi.org/10.70675/3ac71e99z16f8z4171z96f3z5157b45cbb6dopenalex-snapshot
Etude d'un consortium microbien producteur d'hydrogène : de l'interaction inter-bactérienne au bioréacteur
inferred← citeshttps://doi.org/10.70675/97895b25zdfe7z4432z8766z801bf0b81cd6openalex-snapshot
Modeling Metabolic Networks and their Environment Interaction
inferred← citeshttps://doi.org/10.70675/c363a598z57b5z4fe6z9a8dz66b70f6521fcopenalex-snapshot
Metabolic modelling under non-balanced growth : application to microalgae growth for biofuels production
inferred← citeshttps://doi.org/10.7287/peerj.10911v0.1/reviews/1openalex-snapshot
Peer Review #1 of "A community perspective on the concept of marine holobionts: current status, challenges, and future directions (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10911v0.1/reviews/2openalex-snapshot
Peer Review #2 of "A community perspective on the concept of marine holobionts: current status, challenges, and future directions (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10911v0.1/reviews/3openalex-snapshot
Peer Review #3 of "A community perspective on the concept of marine holobionts: current status, challenges, and future directions (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10911v0.2/reviews/1openalex-snapshot
Peer Review #1 of "A community perspective on the concept of marine holobionts: current status, challenges, and future directions (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.10911v0.2/reviews/2openalex-snapshot
Peer Review #2 of "A community perspective on the concept of marine holobionts: current status, challenges, and future directions (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.10911v0.2/reviews/3openalex-snapshot
Peer Review #3 of "A community perspective on the concept of marine holobionts: current status, challenges, and future directions (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.9464v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Investigation of microbial community interactions between Lake Washington methanotrophs using genome-scale metabolic modeling (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.9464v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Investigation of microbial community interactions between Lake Washington methanotrophs using genome-scale metabolic modeling (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.9464v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Investigation of microbial community interactions between Lake Washington methanotrophs using genome-scale metabolic modeling (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.9464v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Investigation of microbial community interactions between Lake Washington methanotrophs using genome-scale metabolic modeling (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.preprints.27519v3openalex-snapshot
A community perspective on the concept of marine holobionts: current status, challenges, and future directions
inferred← citeshttps://doi.org/10.7554/elife.08208openalex-snapshot
Calibration and analysis of genome-based models for microbial ecology
inferred← citeshttps://doi.org/10.7554/elife.96719openalex-snapshot
Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways
inferred← citeshttps://doi.org/10.7554/elife.96719.1openalex-snapshot
From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways
inferred← citeshttps://doi.org/10.7554/elife.96719.2openalex-snapshot
From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways
inferred← citeshttps://doi.org/10.7554/elife.96719.2.sa0openalex-snapshot
Author response: From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways
inferred← citeshttps://doi.org/10.7554/elife.96719.2.sa3openalex-snapshot
eLife Assessment: From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways
inferred← citeshttps://doi.org/10.7554/elife.96719.3openalex-snapshot
Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways
inferred← citeshttps://doi.org/10.7717/peerj.10911openalex-snapshot
A community perspective on the concept of marine holobionts: current status, challenges, and future directions
inferred← citeshttps://doi.org/10.7717/peerj.9464openalex-snapshot
Investigation of microbial community interactions between Lake Washington methanotrophs using genome-scale metabolic modeling
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