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Cell Systems
This journal offers authors two options (open access or subscription) to publish research

Apr 27, 2016

Volume 2Issue 4p215-288
Open Archive
On the cover: Depth in the shallows. In RNA-seq data, key biological information, represented in here dark blue, is most prominent when coverage is deep (bottom) but still persists at shallow read depths (top). In this issue, Heimberg et al. (239–250) develop a mathematical framework that describes the tradeoff between mRNA-sequencing depth and error in the extraction of biological information....
On the cover: Depth in the shallows. In RNA-seq data, key biological information, represented in here dark blue, is most prominent when coverage is deep (bottom) but still persists at shallow read depths (top). In this issue, Heimberg et al. (239–250) develop a mathematical framework that describes the tradeoff between mRNA-sequencing depth and error in the extraction of biological information.

Editorial

  • The Power of Logic and Reason

    • Quincey Justman
    If you have a tenure-track job in science, then you’ve worked very hard. You’ve worked very hard. Therefore, you have a tenure-track job. This is what’s known in formal logic as a “converse error.” I’ve constructed a blatant example to make the logical fallacy obvious, but more reasonable arguments that follow this structure can be very seductive. Systems biology is rife with them, especially in papers that face the difficult job of marrying models and experiment—if my model is right, then it will match my experimental observations; model and experiment match, therefore my model is right.

Cell Systems Call

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Review

  • Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

    • Bernd Bodenmiller
    The study of organs and tissues on a molecular level is necessary as we seek an understanding of health and disease. Over the last few years, powerful highly multiplexed epitope-based imaging approaches that rely on the serial imaging of tissues with fluorescently labeled antibodies and the simultaneous analysis using metal-labeled antibodies have emerged. These techniques enable analysis of dozens of epitopes in thousands of cells in a single experiment providing a systems level view of normal and disease processes at the single-cell level with spatial resolution in tissues. In this Review, I discuss, first, the highly multiplexed epitope-based imaging approaches and the generated data. Second, I describe challenges that must be overcome to implement these imaging methods from bench to bedside, including issues with tissue processing and analyses of the large amounts of data generated. Third, I discuss how these methods can be integrated with readouts of genome, transcriptome, metabolome, and live cell information, and fourth, the novel applications possible in tissue biology, drug development, and biomarker discovery. I anticipate that highly multiplexed epitope-based imaging approaches will broadly complement existing imaging methods and will become a cornerstone of tissue biology and biomedical research and of precision medical applications.

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