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Novel Systems Biology Techniques

  • Open Access
    Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
    Editor's Pick Observation | Novel Systems Biology Techniques
    Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

    Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time.

    Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez, Rob Knight
  • Open Access
    Integrated Regulatory and Metabolic Networks of the Marine Diatom <em>Phaeodactylum tricornutum</em> Predict the Response to Rising CO<sub>2</sub> Levels
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels

    Using a systems biology approach, we studied the response of the marine diatom Phaeodactylum tricornutum to changing atmospheric carbon concentrations on an ocean-wide scale. By integrating an available genome-scale metabolic model and a newly developed transcriptional regulatory network inferred from transcriptome sequencing expression data, we demonstrate that carbon metabolism and nitrogen metabolism are strongly connected...

    Jennifer Levering, Christopher L. Dupont, Andrew E. Allen, Bernhard O. Palsson, Karsten Zengler
  • Open Access
    Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research
    Methods and Protocols | Novel Systems Biology Techniques
    Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

    As the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results....

    André M. Comeau, Gavin M. Douglas, Morgan G. I. Langille
  • Open Access
    Spatial Molecular Architecture of the Microbial Community of a <em>Peltigera</em> Lichen
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

    Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and...

    Neha Garg, Yi Zeng, Anna Edlund, Alexey V. Melnik, Laura M. Sanchez, Hosein Mohimani, Alexey Gurevich, Vivian Miao, Stefan Schiffler, Yan Wei Lim, Tal Luzzatto-Knaan, Shengxin Cai, Forest Rohwer, Pavel A. Pevzner, Robert H. Cichewicz, Theodore Alexandrov, Pieter C. Dorrestein
  • Open Access
    Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota
    Allison L. Richards, Michael B. Burns, Adnan Alazizi, Luis B. Barreiro, Roger Pique-Regi, Ran Blekhman, Francesca Luca
  • Open Access
    Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

    Soil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches,...

    Richard Allen White, Eric M. Bottos, Taniya Roy Chowdhury, Jeremy D. Zucker, Colin J. Brislawn, Carrie D. Nicora, Sarah J. Fansler, Kurt R. Glaesemann, Kevin Glass, Janet K. Jansson
  • Open Access
    A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses
    Research Article | Novel Systems Biology Techniques
    A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

    This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities...

    Lindsey A. Moser, Lisbeth Ramirez-Carvajal, Vinita Puri, Steven J. Pauszek, Krystal Matthews, Kari A. Dilley, Clancy Mullan, Jennifer McGraw, Michael Khayat, Karen Beeri, Anthony Yee, Vivien Dugan, Mark T. Heise, Matthew B. Frieman, Luis L. Rodriguez, Kristen A. Bernard, David E. Wentworth, Timothy B. Stockwell, Reed S. Shabman
  • Open Access
    MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses
    Editor's Pick Research Article | Novel Systems Biology Techniques
    MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

    In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such...

    Ernesto S. Nakayasu, Carrie D. Nicora, Amy C. Sims, Kristin E. Burnum-Johnson, Young-Mo Kim, Jennifer E. Kyle, Melissa M. Matzke, Anil K. Shukla, Rosalie K. Chu, Athena A. Schepmoes, Jon M. Jacobs, Ralph S. Baric, Bobbie-Jo Webb-Robertson, Richard D. Smith, Thomas O. Metz
  • Open Access
    An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria
    Editor's Pick Research Article | Novel Systems Biology Techniques
    An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria

    We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known to produce a broad spectrum of...

    Maria Maansson, Nikolaj G. Vynne, Andreas Klitgaard, Jane L. Nybo, Jette Melchiorsen, Don D. Nguyen, Laura M. Sanchez, Nadine Ziemert, Pieter C. Dorrestein, Mikael R. Andersen, Lone Gram
  • Open Access
    From Sample to Multi-Omics Conclusions in under 48 Hours
    Research Article | Novel Systems Biology Techniques
    From Sample to Multi-Omics Conclusions in under 48 Hours

    Polymicrobial 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...

    Robert A. Quinn, Jose A. Navas-Molina, Embriette R. Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J. Minich, Alexey V. Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J. Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C. Dorrestein, Rob Knight

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