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Novel Systems Biology Techniques

  • Open Access
    Metabolic Responses to Polymyxin Treatment in <em>Acinetobacter baumannii</em> ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
    Research Article | Novel Systems Biology Techniques
    Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling

    Combating antimicrobial resistance has been highlighted as a critical global health priority. Due to the drying drug discovery pipeline, polymyxins have been employed as the last-line therapy against Gram-negative “superbugs”; however, the detailed mechanisms of antibacterial killing remain largely unclear, hampering the improvement of polymyxin therapy. Our integrative modeling using the constructed genome-scale metabolic model i...

    Yan Zhu, Jinxin Zhao, Mohd Hafidz Mahamad Maifiah, Tony Velkov, Falk Schreiber, Jian Li
  • Open Access
    Calour: an Interactive, Microbe-Centric Analysis Tool
    Methods and Protocols | Novel Systems Biology Techniques
    Calour: an Interactive, Microbe-Centric Analysis Tool

    Calour allows us to identify interesting microbial patterns and generate novel biological hypotheses by interactively inspecting microbiome studies and incorporating annotation databases and convenient statistical tools. Calour can be used as a first-step tool for microbiome data exploration.

    Zhenjiang Zech Xu, Amnon Amir, Jon Sanders, Qiyun Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
  • Open Access
    q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
    Editor's Pick Methods and Protocols | Novel Systems Biology Techniques
    q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

    Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity. We describe q2-longitudinal, a software plugin for longitudinal analysis of microbiome data sets in QIIME 2. The availability of longitudinal statistics and visualizations in the QIIME 2 framework will make the analysis of longitudinal data more accessible to microbiome researchers.

    Nicholas A. Bokulich, Matthew R. Dillon, Yilong Zhang, Jai Ram Rideout, Evan Bolyen, Huilin Li, Paul S. Albert, J. Gregory Caporaso
  • Open Access
    Evaluating the Information Content of Shallow Shotgun Metagenomics
    Methods and Protocols | Novel Systems Biology Techniques
    Evaluating the Information Content of Shallow Shotgun Metagenomics

    A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S...

    Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Daryl M. Gohl, Kenneth B. Beckman, Rob Knight, Dan Knights
  • Open Access
    High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity
    Methods and Protocols | Novel Systems Biology Techniques
    High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity

    Reduced costs of sequencing have tremendously impacted the field of microbial ecology, allowing scientists to design more studies with larger sample sizes that often exceed 10,000 samples. Library preparation costs have not kept pace with sequencing prices, although automated liquid handling robots provide a unique opportunity to bridge this gap while also decreasing human error. Here, we take advantage of an acoustic liquid handling...

    Jeremiah J. Minich, Greg Humphrey, Rodolfo A. S. Benitez, Jon Sanders, Austin Swafford, Eric E. Allen, Rob Knight
  • Open Access
    Ribosome Profiling of <em>Synechocystis</em> Reveals Altered Ribosome Allocation at Carbon Starvation
    Research Article | Novel Systems Biology Techniques
    Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation

    Ribosome profiling accesses the translational step of gene expression via deep sequencing of ribosome-protected mRNA footprints. Pairing of ribosome profiling and transcriptomics data provides a translational efficiency for each gene. Here, the translatome and transcriptome of the model cyanobacterium Synechocystis were compared under carbon-replete and carbon starvation conditions. The latter may be experienced when...

    Jan Karlsen, Johannes Asplund-Samuelsson, Quentin Thomas, Michael Jahn, Elton P. Hudson
  • Open Access
    Comprehensive Functional Analysis of the <span class="named-content genus-species" id="named-content-1">Enterococcus faecalis</span> Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF
    Resource Report | Novel Systems Biology Techniques
    Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF

    The robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome...

    Jennifer L. Dale, Kenneth B. Beckman, Julia L. E. Willett, Jennifer L. Nilson, Nagendra P. Palani, Joshua A. Baller, Adam Hauge, Daryl M. Gohl, Raymond Erickson, Dawn A. Manias, Michael J. Sadowsky, Gary M. Dunny
  • Open Access
    Modeling the <em>Pseudomonas</em> Sulfur Regulome by Quantifying the Storage and Communication of Information
    Research Article | Novel Systems Biology Techniques
    Modeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of Information

    Bacteria sense and respond to their environments using a sophisticated array of sensors and regulatory networks to optimize their fitness and survival in a constantly changing environment. Understanding how these regulatory and sensory networks work will provide the capacity to predict bacterial behaviors and, potentially, to manipulate their interactions with an environment or host. Leveraging the information theory provides useful...

    Peter E. Larsen, Sarah Zerbs, Philip D. Laible, Frank R. Collart, Peter Korajczyk, Yang Dai, Philippe Noirot
  • 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

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