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Novel Systems Biology Techniques

  • Open Access
    Systematic Localization of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Membrane Proteins
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Systematic Localization of Escherichia coli Membrane Proteins

    Current knowledge of protein localization, particularly outer membrane proteins, is highly dependent on bioinformatic predictions. To date, no systematic experimental studies have directly compared protein localization spanning the inner and outer membranes of E. coli. By combining sucrose density gradient fractionation of inner membrane (IM) and outer membrane (OM)...

    Anna Sueki, Frank Stein, Mikhail M. Savitski, Joel Selkrig, Athanasios Typas
  • Open Access
    manta: a Clustering Algorithm for Weighted Ecological Networks
    Methods and Protocols | Novel Systems Biology Techniques
    manta: a Clustering Algorithm for Weighted Ecological Networks

    manta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.

    Lisa Röttjers, Karoline Faust
  • Open Access
    Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
    Research Article | Novel Systems Biology Techniques
    Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines

    Method choice throughout the workflow of a microbiome study, from sample collection to DNA extraction and sequencing procedures, can greatly affect results. This study evaluated three different DNA extraction methods and two bioinformatic pipelines by including positive and negative controls and various biological specimens. By identifying an optimal combination of DNA extraction method and bioinformatic pipeline use, we hope to...

    Q. R. Ducarmon, B. V. H. Hornung, A. R. Geelen, E. J. Kuijper, R. D. Zwittink
  • Open Access
    The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities
    Research Article | Novel Systems Biology Techniques
    The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities

    This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can...

    Thomas Yssing Michaelsen, Jakob Brandt, Caitlin Margaret Singleton, Rasmus Hansen Kirkegaard, Johanna Wiesinger, Nicola Segata, Mads Albertsen
  • Open Access
    Geometry-Aware Cell Detection with Deep Learning
    Research Article | Novel Systems Biology Techniques
    Geometry-Aware Cell Detection with Deep Learning

    Automated diagnostic microscopy powered by deep learning is useful, particularly in rural areas. However, there is no general method for object detection of different cells. In this study, we developed GFS-ExtremeNet, a geometry-aware deep-learning method which is based on the detection of four extreme key points for each object (topmost, bottommost, rightmost, and leftmost) and its center point. A postprocessing step, namely, adjacency...

    Hao Jiang, Sen Li, Weihuang Liu, Hongjin Zheng, Jinghao Liu, Yang Zhang
  • Open Access
    Transfer Learning for <span class="named-content genus-species" id="named-content-1">Toxoplasma gondii</span> Recognition
    Research Article | Novel Systems Biology Techniques
    Transfer Learning for Toxoplasma gondii Recognition

    Toxoplasma gondii, one of the world’s most common parasites, can infect all types of warm-blooded animals, including one-third of the world’s human population. Artificial intelligence (AI) could provide accurate and rapid diagnosis in fighting Toxoplasma. So far, none of the previously reported deep learning methods have attempted to explore the advantages of...

    Sen Li, Aijia Li, Diego Alejandro Molina Lara, Jorge Enrique Gómez Marín, Mario Juhas, Yang Zhang
  • Open Access
    Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation
    Research Article | Novel Systems Biology Techniques
    Extreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting Translation

    Bacterial persistence is a fascinating phenomenon in which a small subpopulation of bacteria becomes phenotypically tolerant to lethal antibiotic exposure. There is growing evidence that populations of bacteria in chronic clinical infections develop a hyperpersistent phenotype, enabling a substantially larger subpopulation to survive repeated antibiotic treatment. The mechanisms of persistence and modes of increasing persistence rates...

    Anupama Khare, Saeed Tavazoie
  • Open Access
    MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
    Research Article | Novel Systems Biology Techniques
    MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

    The bacterial communities that live within the human gut have been linked to health and disease. However, we are still just beginning to understand how those bacteria interact and what potential interventions to our gut microbiome can make us healthier. Here, we present a mathematical modeling framework (named MICOM) that can recapitulate the growth rates of diverse bacterial species in the gut and can simulate metabolic interactions...

    Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
  • Open Access
    Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes
    Observation | Novel Systems Biology Techniques
    Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes

    Every branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to “remember” past infections in order to better fight them in the future. There has been much interest among molecular...

    Jake L. Weissman, Philip L. F. Johnson
  • Open Access
    Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies
    Research Article | Novel Systems Biology Techniques
    Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies

    Identifying the key microbial taxa responsible for metabolic differences between microbiomes is an important step toward understanding and manipulating microbiome metabolism. To achieve this goal, researchers commonly conduct microbiome-metabolome association studies, comprehensively measuring both the composition of species and the concentration of metabolites across a set of microbial community samples and then testing for...

    Cecilia Noecker, Hsuan-Chao Chiu, Colin P. McNally, Elhanan Borenstein

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