Novel Systems Biology Techniques
Research Article | Novel Systems Biology TechniquesFrom Sample to Multi-Omics Conclusions in under 48 HoursPolymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial...
Editor's Pick Research Article | Novel Systems Biology TechniquesADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host InteractionsThe quantity and breadth of genome-scale data sets that examine RNA expression in diverse bacterial and eukaryotic species are increasing more rapidly than for curated knowledge. Our ADAGE method integrates such data without requiring gene function, gene pathway, or experiment labeling, making practical its application to any large gene expression compendium. We built a ...
Editor's Pick Research Article | Novel Systems Biology TechniquesMetabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic VariationStudies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on...
Methods and Protocols | Novel Systems Biology Techniquescual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics StudiesThe adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis,...
Methods and Protocols | Novel Systems Biology TechniquesImproved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community SurveysWe continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is...