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Novel Systems Biology Techniques

  • Open Access
    SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
    Methods and Protocols | Novel Systems Biology Techniques
    SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control

    Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is...

    Gabriel A. Al-Ghalith, Benjamin Hillmann, Kaiwei Ang, Robin Shields-Cutler, Dan Knights
  • Open Access
    Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity
    Research Article | Novel Systems Biology Techniques
    Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

    Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and...

    Luis M. Rodriguez-R, Santosh Gunturu, James M. Tiedje, James R. Cole, Konstantinos T. Konstantinidis
  • Open Access
    Developing a <em>Bacteroides</em> System for Function-Based Screening of DNA from the Human Gut Microbiome
    Research Article | Novel Systems Biology Techniques
    Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome

    Human gut microbiome research has been supported by advances in DNA sequencing that make it possible to obtain gigabases of sequence data from metagenomes but is limited by a lack of knowledge of gene function that leads to incomplete annotation of these data sets. There is a need for the development of methods that can provide experimental data regarding microbial gene function. Functional metagenomics is one such method, but...

    Kathy N. Lam, Eric C. Martens, Trevor C. Charles
  • Open Access
    From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
    Minireview | Novel Systems Biology Techniques
    From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

    An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities.

    Eugen Bauer, Ines Thiele
  • Open Access
    Toward Personalized Control of Human Gut Bacterial Communities
    Special Issue Perspective | Novel Systems Biology Techniques
    Toward Personalized Control of Human Gut Bacterial Communities

    A key challenge in microbiology will be developing tools for manipulating human gut bacterial communities. Our ability to predict and control the dynamics of these communities is now in its infancy.

    Lawrence A. David
  • Open Access
    Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <em>Nitrosomonas europaea</em> and <em>Nitrobacter winogradskyi</em>
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi

    Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH4+). Up to 60% of NH4+-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO3−), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO2], and nitrous oxide [N2O] gases), the latter being a...

    Brett L. Mellbye, Andrew T. Giguere, Ganti S. Murthy, Peter J. Bottomley, Luis A. Sayavedra-Soto, Frank W. R. Chaplen
  • Open Access
    KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples
    Research Article | Novel Systems Biology Techniques
    KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

    Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to...

    Jeremiah J. Minich, Qiyun Zhu, Stefan Janssen, Ryan Hendrickson, Amnon Amir, Russ Vetter, John Hyde, Megan M. Doty, Kristina Stillwell, James Benardini, Jae H. Kim, Eric E. Allen, Kasthuri Venkateswaran, Rob Knight
  • Open Access
    On the Road to Strain-Resolved Comparative Metagenomics
    Special Issue Perspective | Novel Systems Biology Techniques
    On the Road to Strain-Resolved Comparative Metagenomics

    Metagenomics has transformed microbiology, but its potential has not been fully expressed yet. From computational methods for digging deeper into metagenomes to study designs for addressing specific hypotheses, the Segata Lab is pursuing an integrative metagenomic approach to describe and model human-associated microbial communities as collections of strains.

    Nicola Segata
  • Open Access
    Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology
    Special Issue Perspective | Novel Systems Biology Techniques
    Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

    Microbial and plant specialized metabolites, also known as natural products, are key mediators of microbe-microbe and host-microbe interactions and constitute a rich resource for drug development. In the past decade, genome mining has emerged as a prominent strategy for natural product discovery.

    Marnix H. Medema
  • Open Access
    Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria
    Research Article | Novel Systems Biology Techniques
    Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

    Molecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The...

    Hualan Liu, Morgan N. Price, Robert Jordan Waters, Jayashree Ray, Hans K. Carlson, Jacob S. Lamson, Romy Chakraborty, Adam P. Arkin, Adam M. Deutschbauer

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