281 results found
    1. Computational and Systems Biology

    Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

    Arnaud Belcour et al.
    Computational models and software connect metagenomics to metabolic network reconstruction, assess metabolic complementarity between species, and identify critical species associated to functions of interest.
    1. Computational and Systems Biology

    Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

    David B Bernstein et al.
    A novel metabolic network analysis method enables large-scale computational predictions of biosynthetic capabilities across the human oral microbiome, revealing a unique cluster of fastidious microorganisms and potential metabolic interdependencies.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

    Kevin D'hoe et al.
    Human gut bacteria alter their metabolism in response to each other's presence, which causes their community dynamics to deviate from predictions that are based on mono-culture data.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Modeling transfer of vaginal microbiota from mother to infant in early life

    Martin Steen Mortensen et al.
    Modeling weighted transfer ratios enable statistical analysis of maternal–infant transfer at a more general level and can indicate whether any transfer is persistent, transient, or originates from alternate sources.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Computer-guided design of optimal microbial consortia for immune system modulation

    Richard R Stein et al.
    A computational method is presented that quantifies the effect that specific bacteria in the gut have on the immune system and guides the design of therapeutically potent microbial consortia to cure auto-immune disease.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Quantifying antibiotic impact on within-patient dynamics of extended-spectrum beta-lactamase resistance

    Rene Niehus et al.
    A data-driven within-host model reveals that different antibiotics are associated with divergent effects on antibiotic resistance carriage and abundance in hospitalised patients, with important implications for antibiotic stewardship.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance

    Robert M Cooper et al.
    Killing their neighbors allows bacteria to steal genes, including antibiotic resistance genes, which we observed under a microscope, quantified, modeled, and predicted potentially guiding strategies to combat it.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Adjusting for age improves identification of gut microbiome alterations in multiple diseases

    Tarini S Ghosh et al.
    A multi-cohort analysis of 2,500 gut microbiomes and five major diseases discovers that disease-microbiome associations display specific age-centric trends, with diseases characterized by age-centric trends of species gain/loss.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A phylogenetic transform enhances analysis of compositional microbiota data

    Justin D Silverman et al.
    The PhILR transform uses an evolutionary model to overcome statistical challenges associated with microbiota surveys.
    1. Computational and Systems Biology

    Stochastic logistic models reproduce experimental time series of microbial communities

    Lana Descheemaeker, Sophie de Buyl
    Properties of various microbial communities time series, such as the noise color and neutrality, are captured by stochastic generalized Lotka-Volterra equations, even in the absence of interactions.

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