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bioinformatics

  • Open Access
    Computational Analysis of Microbial Flow Cytometry Data
    Minireview | Applied and Environmental Science
    Computational Analysis of Microbial Flow Cytometry Data

    Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution.

    Peter Rubbens, Ruben Props
  • Open Access
    A Simplified and Efficient Method for Himar-1 Transposon Sequencing in Bacteria, Demonstrated by Creation and Analysis of a Saturated Transposon-Mutant Library in <span class="named-content genus-species" id="named-content-1">Mycobacterium abscessus</span>
    Research Article | Novel Systems Biology Techniques
    A Simplified and Efficient Method for Himar-1 Transposon Sequencing in Bacteria, Demonstrated by Creation and Analysis of a Saturated Transposon-Mutant Library in Mycobacterium abscessus

    Transposon insertion sequencing is a powerful tool, but many researchers are discouraged by the apparent technical complexity of preparing the genomic library for deep sequencing and by the complicated computational analysis needed for insertion site identification. Our proposed method makes the preparation of the library easy and straightforward, relying on well-known molecular biology techniques. In addition, the results obtained from...

    Mark Foreman, Moran Gershoni, Daniel Barkan
  • Open Access
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
    Research Article | Novel Systems Biology Techniques
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

    Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary...

    Alexander M. Kloosterman, Kyle E. Shelton, Gilles P. van Wezel, Marnix H. Medema, Douglas A. Mitchell
  • Open Access
    Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations
    Methods and Protocols | Molecular Biology and Physiology
    Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations

    The correct mapping of promoter elements is a crucial step in microbial genomics. Also, when combining new DNA elements into synthetic sequences, predicting the potential generation of new promoter sequences is critical. Over the last years, many bioinformatics tools have been created to allow users to predict promoter elements in a sequence or genome of interest. Here, we assess the predictive power of some of the main prediction tools...

    Murilo Henrique Anzolini Cassiano, Rafael Silva-Rocha
  • Open Access
    Computational Basis for On-Demand Production of Diversified Therapeutic Phage Cocktails
    Research Article | Therapeutics and Prevention
    Computational Basis for On-Demand Production of Diversified Therapeutic Phage Cocktails

    The antibiotic resistance crisis has led to renewed interest in phage therapy as an alternative means of treating infection. However, conventional methods for isolating pathogen-specific phage are slow, labor-intensive, and frequently unsuccessful. We have demonstrated that computationally identified prophages carried by near-neighbor bacteria can serve as starting material for production of engineered phages that kill the target...

    Catherine M. Mageeney, Anupama Sinha, Richard A. Mosesso, Douglas L. Medlin, Britney Y. Lau, Alecia B. Rokes, Todd W. Lane, Steven S. Branda, Kelly P. Williams
  • 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
    A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination
    Editor's Pick Editorial
    A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination
    Chase M. Clark, Brian T. Murphy, Laura M. Sanchez
  • 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
    Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
    Research Article | Ecological and Evolutionary Science
    Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

    There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is...

    Matthew R. Olm, Alexander Crits-Christoph, Spencer Diamond, Adi Lavy, Paula B. Matheus Carnevali, Jillian F. Banfield
  • Open Access
    Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019
    Perspective | Applied and Environmental Science
    Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019

    Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses.

    ...
    Eric Sakowski, Gherman Uritskiy, Rachel Cooper, Maya Gomes, Michael R. McLaren, Jacquelyn S. Meisel, Rebecca L. Mickol, C. David Mintz, Emmanuel F. Mongodin, Mihai Pop, Mohammad Arifur Rahman, Alvaro Sanchez, Winston Timp, Jeseth Delgado Vela, Carly Muletz Wolz, Joseph P. Zackular, Jessica Chopyk, Seth Commichaux, Meghan Davis, Douglas Dluzen, Sukirth M. Ganesan, Muyideen Haruna, Dan Nasko, Mary J. Regan, Saul Sarria, Nidhi Shah, Brook Stacy, Dylan Taylor, Jocelyne DiRuggiero, Sarah P. Preheim

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