Using public data to evaluate global dynamics in biology publishing and the human microbiome
2022-02
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Using public data to evaluate global dynamics in biology publishing and the human microbiome
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2022-02
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The last decade has seen a rapid growth of research interest in the human microbiome, the bacterial communities that live on and in human bodies. Complex dynamics in the world of academic publishing have changed over almost the same period, during which time it has become increasingly common for researchers in the life sciences to share their manuscripts online as “preprints,” making them freely available prior to conventional peer review. Both are analyzed here by using publicly available data to quantify trends, patterns, and risks developing in both systems. First, I evaluate the growth of preprints posted to bioRxiv.org in its first five years. I describe the process for compiling the first comprehensive characterization of biology preprints and evaluate patterns in readership and outcomes for more than 37,000 manuscripts. Secondly, I examine changing trends in country-level preprint authorship and find patterns of international collaboration that suggest the supposedly egalitarian practice of preprinting may be replicating some of the same entrenched power dynamics found in conventional publishing. Third, I apply a similar approach to metadata for publicly available human microbiome samples: I characterize the origins of more than 440,000 samples and use country-level research activity to determine which countries are overrepresented in the characterization of the human microbiome relative to their population. Finally, I describe how we used this metadata in the construction of the largest human gut microbiome dataset in the world, consisting of more than 170,000 samples in one unified dataset that can be used to characterize broad patterns in microbial ecological dynamics.
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University of Minnesota Ph.D. dissertation. 2022. Major: Biomedical Informatics and Computational Biology. Advisor: Ran Blekhman. 1 computer file (PDF); 168 pages.
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Abdill, Richard. (2022). Using public data to evaluate global dynamics in biology publishing and the human microbiome. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/226944.
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