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Large-scale reconstruction and phylogenetic analysis of metabolic environments

https://doi.org/10.1073/pnas.0806162105
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks
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A model of flexible uptake of two essential resources
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Pathway evolution, structurally speaking
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Robustness Analysis of the Escherichia coli Metabolic Network
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Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
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The large-scale organization of metabolic networks
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Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
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Metabolic network structure determines key aspects of functionality and regulation
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Global organization of metabolic fluxes in the bacterium Escherichia coli
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Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
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Oxygen content of transmembrane proteins over macroevolutionary time scales
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Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
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Multiple knockout analysis of genetic robustness in the yeast metabolic network
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Evolutionary changes of metabolic networks and their biosynthetic capacities
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Universality in intermediary metabolism
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Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module
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The evolution of modularity in bacterial metabolic networks
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On the Evolution of Biochemical Syntheses
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The connectivity structure, giant strong component and centrality of metabolic networks
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Constraint-based functional similarity of metabolic genes: going beyond network topology
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
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The COG database: a tool for genome-scale analysis of protein functions and evolution
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From genomics to chemical genomics: new developments in KEGG
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The outcomes of pathway database computations depend on pathway ontology
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Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes
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Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
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A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
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Substrate-specific diffusion of select dicarboxylates through Chlamydia trachomatis PorB
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Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
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Functional genomics of Buchnera and the ecology of aphid hosts
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1126/science.1089072openalex-snapshot
Biological Networks: The Tinkerer as an Engineer
inferredcites →https://doi.org/10.1126/science.1118439openalex-snapshot
The Effect of Oxygen on Biochemical Networks and the Evolution of Complex Life
inferredcites →https://doi.org/10.1126/science.1123061openalex-snapshot
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
inferredcites →https://doi.org/10.1126/science.1125937openalex-snapshot
Tracing Oxygen's Imprint on Earth's Metabolic Evolution
inferredcites →https://doi.org/10.1126/science.155.3760.279openalex-snapshot
Construction of Phylogenetic Trees
inferredcites →https://doi.org/10.1126/science.282.5389.754openalex-snapshot
Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis
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Biosynthesis of biotin from dethiobiotin by the biotin auxotroph Lactobacillus plantarum
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Depth-First Search and Linear Graph Algorithms
inferredcites →https://doi.org/10.1142/s021972000400079xopenalex-snapshot
ROBUSTNESS OF METABOLIC MAP RECONSTRUCTION
inferredcites →https://doi.org/10.1186/1471-2105-4-41openalex-snapshot
The COG database: an updated version includes eukaryotes
inferredcites →https://doi.org/10.1186/1471-2105-7-130openalex-snapshot
Extraction of phylogenetic network modules from the metabolic network
inferredcites →https://doi.org/10.1186/1471-2148-7-169openalex-snapshot
Environmental variability and modularity of bacterial metabolic networks
inferredcites →https://doi.org/10.1186/gb-2001-2-12-research0054openalex-snapshot
The process of genome shrinkage in the obligate symbiont Buchnera aphidicola
inferredcites →https://doi.org/10.1371/journal.pcbi.0020167openalex-snapshot
Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity
inferredcites →https://doi.org/10.1371/journal.pgen.0020021openalex-snapshot
Comparative Genomics of Emerging Human Ehrlichiosis Agents
inferredcites →https://doi.org/10.2307/2412116openalex-snapshot
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
inferredcites →https://doi.org/10.3109/10408419709115140openalex-snapshot
The Comparative Metabolism of the Mollicutes (Mycoplasmas): The Utility for Taxonomic Classification and the Relationship of Putative Gene Annotation and Phylogeny to Enzymatic Function in the Smallest Free-Living Cells
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Nouvelles recherches sur la distribution florale

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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The large-scale organization of the bacterial network of ecological co-occurrence interactions
inferred← citeshttps://doi.org/10.1093/oso/9780192847287.003.0019openalex-snapshot
Enzymes and Metabolic Pathways
inferred← citeshttps://doi.org/10.1094/mpmi-12-13-0368-ropenalex-snapshot
Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants
inferred← citeshttps://doi.org/10.1098/rsif.2011.0652openalex-snapshot
Evolutionary significance of metabolic network properties
inferred← citeshttps://doi.org/10.1098/rsif.2019.0610openalex-snapshot
Construction, comparison and evolution of networks in life sciences and other disciplines
inferred← citeshttps://doi.org/10.1099/jmm.0.000907openalex-snapshot
Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection
inferred← citeshttps://doi.org/10.1101/106856openalex-snapshot
Metabolic Network Analysis and Metatranscriptomics Reveals Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage aci
inferred← citeshttps://doi.org/10.1101/2021.05.17.444446openalex-snapshot
Unraveling microbial interactions in the gut microbiome
inferred← citeshttps://doi.org/10.1101/2022.07.27.501711openalex-snapshot
A system-level view on the function of natural eukaryotic biomes through taxonomically resolved metabolic pathway profiling
inferred← citeshttps://doi.org/10.1101/607531openalex-snapshot
Assessing the viability of biochemical networks across planets
inferred← citeshttps://doi.org/10.1101/gr.079715.108openalex-snapshot
Principles of transcriptional regulation and evolution of the metabolic system inE. coli
inferred← citeshttps://doi.org/10.1103/physrevlett.132.018401openalex-snapshot
Heterogeneous Popularity of Metabolic Reactions from Evolution
inferred← citeshttps://doi.org/10.1107/s1744309110029088openalex-snapshot
Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes
inferred← citeshttps://doi.org/10.1109/bibm58861.2023.10385992openalex-snapshot
Predicting Microbe-Metabolite Interactions by Integrating Non-negative Matrix Factorization and Generative Network
inferred← citeshttps://doi.org/10.1109/tgrs.2025.3586962openalex-snapshot
Dynamic Geometry-Aware Depth Hypotheses and Edge-Guided Depth Refinement for Aerial Multi-View Stereo
inferred← citeshttps://doi.org/10.1111/1751-7915.14396openalex-snapshot
Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing
inferred← citeshttps://doi.org/10.1111/ele.12048openalex-snapshot
The problem of pattern and scale in ecology: what have we learned in 20 years?
inferred← citeshttps://doi.org/10.1111/ele.13771openalex-snapshot
The evolutionary ecology of fatty‐acid variation: Implications for consumer adaptation and diversification
inferred← citeshttps://doi.org/10.1111/evo.13441openalex-snapshot
Emergent buffering balances evolvability and robustness in the evolution of phenotypic flexibility
inferred← citeshttps://doi.org/10.1111/jeb.13136openalex-snapshot
Beyond topology: coevolution of structure and flux in metabolic networks
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.03391-16openalex-snapshot
Global-Scale Structure of the Eelgrass Microbiome
inferred← citeshttps://doi.org/10.1128/mmbr.00007-19openalex-snapshot
Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection
inferred← citeshttps://doi.org/10.1128/msystems.00091-17openalex-snapshot
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
inferred← citeshttps://doi.org/10.1128/msystems.00688-26openalex-snapshot
misosoup: a metabolic modeling tool for identifying minimal microbial communities, facilitates the exploration of microbial ecology and biotechnological applications
inferred← citeshttps://doi.org/10.1128/msystems.00803-26openalex-snapshot
Integrated multi-omics and metabolic modeling links structure to function in high-performing electrosynthetic biofilm communities
inferred← citeshttps://doi.org/10.1128/msystems.01586-25openalex-snapshot
Screening of exogenous nutrients for pathogenic bacteria and development of highly active bactericides
inferred← citeshttps://doi.org/10.1128/spectrum.02342-23openalex-snapshot
Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications
inferred← citeshttps://doi.org/10.1140/epjb/e2013-40672-3openalex-snapshot
The prescribed output pattern regulates the modular structure of flow networks
inferred← citeshttps://doi.org/10.1146/annurev-cellbio-092910-154129openalex-snapshot
Beyond Homeostasis: A Predictive-Dynamic Framework for Understanding Cellular Behavior
inferred← citeshttps://doi.org/10.1155/2017/5296729openalex-snapshot
Novel Approach to Classify Plants Based on Metabolite-Content Similarity
inferred← citeshttps://doi.org/10.1158/0008-5472.can-11-1569openalex-snapshot
Systems Biology: Confronting the Complexity of Cancer
inferred← citeshttps://doi.org/10.11606/t.95.2015.tde-22092015-114705openalex-snapshot
Análise computacional da variação do potencial metabólico microbiano em metagenomas
inferred← citeshttps://doi.org/10.1186/1471-2105-11-s11-s13openalex-snapshot
Revealing parasite influence in metabolic pathways in Apicomplexa infected patients
inferred← citeshttps://doi.org/10.1186/1471-2105-11-s11-s7openalex-snapshot
Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species
inferred← citeshttps://doi.org/10.1186/1471-2105-12-s1-s27openalex-snapshot
Reconstructing phylogeny from metabolic substrate-product relationships
inferred← citeshttps://doi.org/10.1186/1471-2105-14-s2-s12openalex-snapshot
Reconstruction of phyletic trees by global alignment of multiple metabolic networks
inferred← citeshttps://doi.org/10.1186/1471-2148-11-20openalex-snapshot
Structural correlations in bacterial metabolic networks
inferred← citeshttps://doi.org/10.1186/1471-2148-9-231openalex-snapshot
Evolutionary constraints permeate large metabolic networks
inferred← citeshttps://doi.org/10.1186/1471-2164-11-217openalex-snapshot
Comparative genomics of metabolic networks of free-living and parasitic eukaryotes
inferred← citeshttps://doi.org/10.1186/1471-2164-13-157openalex-snapshot
Metabolic classification of microbial genomes using functional probes
inferred← citeshttps://doi.org/10.1186/1471-2164-13-438openalex-snapshot
Exploration of the core metabolism of symbiotic bacteria
inferred← citeshttps://doi.org/10.1186/1748-7188-7-25openalex-snapshot
Parsimonious reconstruction of network evolution
inferred← citeshttps://doi.org/10.1186/1752-0509-5-92openalex-snapshot
Cell functional enviromics: Unravelling the function of environmental factors
inferred← citeshttps://doi.org/10.1186/1752-0509-7-125openalex-snapshot
sybil – Efficient constraint-based modelling in R
inferred← citeshttps://doi.org/10.1186/gb-2008-9-11-239openalex-snapshot
Network-based approaches for linking metabolism with environment
inferred← citeshttps://doi.org/10.1186/gb-2009-10-6-r61openalex-snapshot
Metabolic-network-driven analysis of bacterial ecological strategies
inferred← citeshttps://doi.org/10.1186/s12859-015-0588-yopenalex-snapshot
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation
inferred← citeshttps://doi.org/10.1186/s12859-016-1088-4openalex-snapshot
RevEcoR: an R package for the reverse ecology analysis of microbiomes
inferred← citeshttps://doi.org/10.1186/s12859-017-1696-7openalex-snapshot
Limitations of a metabolic network-based reverse ecology method for inferring host–pathogen interactions
inferred← citeshttps://doi.org/10.1186/s12859-019-3112-yopenalex-snapshot
Robust structure measures of metabolic networks that predict prokaryotic optimal growth temperature
inferred← citeshttps://doi.org/10.1186/s12862-016-0731-zopenalex-snapshot
Structuring evolution: biochemical networks and metabolic diversification in birds
inferred← citeshttps://doi.org/10.1186/s12864-015-1379-6openalex-snapshot
Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci
inferred← citeshttps://doi.org/10.1186/s12934-023-02234-8openalex-snapshot
Plants and endophytes interaction: a “secret wedlock” for sustainable biosynthesis of pharmaceutically important secondary metabolites
inferred← citeshttps://doi.org/10.1186/s13059-021-02289-zopenalex-snapshot
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
inferred← citeshttps://doi.org/10.1186/s13059-025-03769-2openalex-snapshot
microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis
inferred← citeshttps://doi.org/10.1186/s13062-015-0073-6openalex-snapshot
Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification
inferred← citeshttps://doi.org/10.1186/s13321-022-00621-8openalex-snapshot
What makes a reaction network “chemical”?
inferred← citeshttps://doi.org/10.1186/s40168-018-0571-8openalex-snapshot
Competitive lottery-based assembly of selected clades in the human gut microbiome
inferred← citeshttps://doi.org/10.1186/s40168-019-0754-yopenalex-snapshot
A conceptual framework for the phylogenetically constrained assembly of microbial communities
inferred← citeshttps://doi.org/10.1186/s40168-022-01383-zopenalex-snapshot
Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome
inferred← citeshttps://doi.org/10.1186/s40793-023-00536-3openalex-snapshot
Designing a synthetic microbial community through genome metabolic modeling to enhance plant–microbe interaction
inferred← citeshttps://doi.org/10.1186/s42523-020-00028-6openalex-snapshot
Composition and co-occurrence patterns of the microbiota of different niches of the bovine mammary gland: potential associations with mastitis susceptibility, udder inflammation, and teat-end hyperkeratosis
inferred← citeshttps://doi.org/10.12677/hjcb.2012.21001openalex-snapshot
Reconstruction of Erwinia carotovora subsp. atroseptica SCRI1043 Metabolic Network and Its Application in Screening Potential Targets
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001185openalex-snapshot
Signatures of optimal codon usage in metabolic genes inform budding yeast ecology
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000690openalex-snapshot
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000904openalex-snapshot
Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1001002openalex-snapshot
Environments that Induce Synthetic Microbial Ecosystems
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003163openalex-snapshot
Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems
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.1003726openalex-snapshot
A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004338openalex-snapshot
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005361openalex-snapshot
Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005366openalex-snapshot
Genome composition and phylogeny of microbes predict their co-occurrence in the environment
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1007951openalex-snapshot
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species
inferred← citeshttps://doi.org/10.1371/journal.pone.0029096openalex-snapshot
A Genomic Reappraisal of Symbiotic Function in the Aphid/Buchnera Symbiosis: Reduced Transporter Sets and Variable Membrane Organisations
inferred← citeshttps://doi.org/10.1371/journal.pone.0077617openalex-snapshot
Metabolic Proximity in the Order of Colonization of a Microbial Community
inferred← citeshttps://doi.org/10.1371/journal.pone.0089618openalex-snapshot
The Use of Weighted Graphs for Large-Scale Genome Analysis
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/10.1504/ijdmb.2015.072103openalex-snapshot
Towards rule-based metabolic databases: a requirement analysis based on KEGG
inferred← citeshttps://doi.org/10.1609/icaps.v21i1.13485openalex-snapshot
The Minimal Seed Set Problem
inferred← citeshttps://doi.org/10.18130/v34p5bopenalex-snapshot
Novel Computational Tools for Linking Genotypes to Microbial Community Phenotypes
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1183956/v1openalex-snapshot
Inter-Cluster Competition and Resource Partitioning May Govern the Ecology of Frankia
inferred← citeshttps://doi.org/10.2147/agg.s57215openalex-snapshot
New insight into the gut microbiome through metagenomics
inferred← citeshttps://doi.org/10.2217/fvl-2019-0002openalex-snapshot
Gut Microbial Metabolites Associated With HIV Infection
inferred← citeshttps://doi.org/10.24072/pcjournal.685openalex-snapshot
Ecophylogenetic patterns of rhizosphere bacterial community assembly in Pisum spp. (Fabaceae, Fabeae) reveal strong plant-mediated ecological filtering
inferred← citeshttps://doi.org/10.29011/2577-2201/100030openalex-snapshot
Metabolite-Content-Guided Prediction of Medicinal/Edible Properties in Plants for Bioprospecting
inferred← citeshttps://doi.org/10.29011/crcam-130/100030openalex-snapshot
Metabolite-Content-Guided Prediction of Medicinal/Edible Properties in Plants for Bioprospecting
inferred← citeshttps://doi.org/10.3389/fgene.2017.00088openalex-snapshot
Perspectives and Challenges in Microbial Communities Metabolic Modeling
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.2016.00068openalex-snapshot
Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
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.2017.01606openalex-snapshot
Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation
inferred← citeshttps://doi.org/10.3389/fmicb.2017.01979openalex-snapshot
Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy
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