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<p>Hello! My name is Elizabeth McDaniel and I am a Scientist passionate about microbes, bioinformatics, and open science.</p>
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<p>I’m currently a Scientist at the <ahref="https://astera.org/">Astera Institute</a> working on a project at the intersection of fermented foods and human health, where we are exploring ways of getting the health benefits of fermented foods to people in an accessible way and producing public datasets to spur innovative research in this area.</p>
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<p>Previously I was a scientist at <ahref="https://www.arcadiascience.com/">Arcadia Science</a>, where I created computational tools and approaches towards understanding diverse organisms across the tree of life, and contributed to pubs released through a non-journal based publishing platform.</p>
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<p>Hello! My name is Elizabeth McDaniel and I am a scientist passionate about bioinformatics, reproducibility, and open science.</p>
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<p>I’m currently a computational biologist at <ahref="https://microcosmfoods.com/">Microcosm Foods</a>, a company working towards making the benefits of fermented foods accessible to all through open datasets and novel products. Microcosm Foods is currently incubated at the <ahref="https://astera.org/">Astera Institute</a>, a nonprofit focused on producing public goods.</p>
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<p>Previously, I was a scientist at <ahref="https://www.arcadiascience.com/">Arcadia Science</a>, where I created computational tools and workflows for harnessing the evolutionary biology of diverse organisms across the tree of life for developing novel therapeutics, and contributed to pubs released through a non-journal based publishing platform.</p>
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<p>I received my PhD in the <ahref="https://microbiology.wisc.edu/">Microbiology Doctoral Training Program</a> at the University of Wisconsin-Madison studying lab-scale enrichment systems simulating phosphorus removal using multi-omics techniques. Prior to moving to industry, I was a postdoctoral researcher at the University of British Columbia in the Departments of Civil Engineering and Microbiology and Immunology working on the microbial ecology of anaerobic digestion systems.</p>
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<p>You can find more information about <ahref="./work.html">my work</a>, what I’m <ahref="./writing.html">writing about</a>, and how to get <ahref="./contact.html">in contact</a> with me!</p>
<p>Listed below are links to the work I’ve contributed to in various industry settings and a list of my academic publications. You can find a full listing of publications that are indexed on my <ahref="https://scholar.google.com/citations?user=OJFxBWMAAAAJ&hl=en">Google Scholar Profile</a>. For all publications I’ve made a concerted effort to provide links to open access versions of the article or preprint, the underlying code, and data repositories. If you have trouble accessing a paper, dataset, or code, please don’t hesitate to <ahref="./contact.html">contact me</a>!</p>
<p>All Microcosm Foods datasets are deposited primarily through Zenodo with a CC0 open-access license. Additionally we have partnered with other organizations to make datasets such as curated microbial genomes from fermented foods and annotated bacterial genomes available.</p>
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<p>Explore <ahref="https://zenodo.org/communities/microcosmfoods/records?q=&l=list&p=1&s=10&sort=newest">Microcosm Foods Datasets on Zenodo</a> such as curated genomes, annotations, and peptide bioactivity predictions using machine learning classifications.</p>
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<p>Interactively explore a <ahref="https://kbase.us/n/218406/47/">curated set of microbial genomes from fermented foods</a> on KBase, a free platform for curating, analyzing, and sharing genomes.</p>
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<p>Interactively explore functional annotations for a subset of bacterial genomes from fermented foods on Tatta Bio’s <ahref="https://seqhub.org/rachel-dutton/collections/microcosm-fermented-food-genomes">SeqHub platform</a>, and read about our partnership <ahref="https://seqhub.org/blog/seqhub-microcosm-foods-partnership">here</a>.</p>
<p>Arcadia Science is <ahref="https://research.arcadiascience.com/reimagining-scientific-publishing">reimagining scientific publishing</a> and does not publish work in traditional peer-reviewed journals. You can check out their work at <ahref="https://research.arcadiascience.com/">research.arcadiascience.com</a>. See pubs that I specifically contributed to <ahref="https://research.arcadiascience.com/user/elizabeth-a.-mcdaniel/">here</a>, with a select few pubs listed below that I led:</p>
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<p><em>Authors are listed in alphabetical order and not by pub contribution</em></p>
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<p><strong>Discovering shared protein structure signatures connected to polyphosphate accumulation in diverse bacteria.</strong><ahref="https://research.arcadiascience.com/pub/result-ppk1-homology/release/1">pub</a><ahref="https://github.com/Arcadia-Science/2023-polyphosphate">code</a><ahref="https://zenodo.org/records/8378182">data</a> Avasthi P, Celebi FM, <strong>McDaniel EA</strong>. 2023. DOI: 10.57844/arcadia-ac10-23e7</p>
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<p><strong>Quickly processing and profiling microbial community sequencing data with a Nextflow workflow for metagenomics.</strong><ahref="https://research.arcadiascience.com/pub/resource-metagenomics-workflow/release/2">pub</a><ahref="https://github.com/Arcadia-Science/metagenomics/tree/v1.0.0">workflow</a> Dutton RJ, <strong>McDaniel EA.</strong> 2023. DOI: 10.57844/arcadia-7etp-pj24</p>
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<p><strong>Creating reproducible workflows for complex computational pipelines</strong>. <ahref="https://research.arcadiascience.com/pub/perspective-reproducible-workflows/release/3">pub</a> Celebi FM, <strong>McDaniel EA</strong>, Reiter T. 2023. DOI: 10.57844/arcadia-cc5j-a519</p>
<p><strong>17. Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism.</strong><ahref="https://www.biorxiv.org/content/10.1101/2025.07.15.664484v2.abstract">preprint</a><ahref="https://www.nature.com/articles/s41564-025-02146-w">publication</a> Friedline S., <strong>McDaniel E.A.</strong>, Scarborough M., Waring K., Lin V.S., Malmstrom R.R., Goudeau D., Chrisler W., Dueholm M.K.D., Gorham L.J., Kombala C.J., Griggs L.D., Olson H.M., Lehmann S.B., Munoz N., Trejo J., Tolic N., Pasa-Tolic L., Williams S.M., Lipton M., Hallam S.J., Ziels R.M. <em>Nature Microbiology.</em> Oct. 2025. DOI: 10.1038/s41564-025-02146-w</p>
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<p><strong>16. Sulfate Reduction Drives Elevated Methylmercury Formation in the Water Column of a Eutrophic Freshwater Lake.</strong><ahref="https://pubs.acs.org/doi/full/10.1021/acs.est.4c12759">publication</a>. Peterson B.D., Janssen S.E., Poulin B.A., Ogorek J.M., White A.M., <strong>McDaniel E.A.</strong>, Marick R.A., Armstrong G.J., Scheel N.D., Tate M.T., Krabbenhoft D.P., McMahon K.D. <em>Environmental Science and Technology.</em> Mar. 2025. DOI: 10.1021/acs.est.4c12759.</p>
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<p><strong>15. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium.</strong><ahref="https://www.nature.com/articles/s41396-023-01542-6">publication</a><ahref="https://github.com/ZielsLab/SAOB_Metaproteogenomics">code</a><ahref="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA885503">data</a><strong>McDaniel E.A</strong>, Scarborough M., Mulat D.G., Lin X., Sampara P.S., Olson H.M., Young R.P., Eder E.K., Attah I.K., Markillie L.M., Hoyt D.W., Lipton M.S., Hallam S.J., Ziels R.M. <em>ISMEJ.</em> Oct. 2023. DOI: 10.1038/s41396-023-01542-6.</p>
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<p><strong>14. Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria.</strong><ahref="https://www.biorxiv.org/content/10.1101/2021.11.30.467465v2.abstract">preprint</a><ahref="https://journals.asm.org/doi/full/10.1128/msystems.00201-23">publication</a> #Tran P.Q., #Bachand S.C., #Hotvedt J.C., Kieft K, <strong>McDaniel E.A.</strong>, McMahon K.D., Anantharaman K. <em>mSystems.</em> June 2023. DOI: 10.1138/msystems.00201-23.</p>
<p>I write on Substack about <ahref="https://themicrobialeconomy.substack.com/?r=uckqe&utm_campaign=pub-share-checklist">The Microbial Economy</a>, a dedicated newsletter about how microbial technologies make it (or not) to the marketplace.</p>
Hello! My name is Elizabeth McDaniel and I am a Scientist passionate about microbes, bioinformatics, and open science.
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Hello! My name is Elizabeth McDaniel and I am a scientist passionate about bioinformatics, reproducibility, and open science.
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I'm currently a Scientist at the [Astera Institute](https://astera.org/) working on a project at the intersection of fermented foods and human health, where we are exploring ways of getting the health benefits of fermented foods to people in an accessible way and producing public datasets to spur innovative research in this area.
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I'm currently a computational biologist at [Microcosm Foods](https://microcosmfoods.com/), a company working towards making the benefits of fermented foods accessible to all through open datasets and novel products. Microcosm Foods is currently incubated at the [Astera Institute](https://astera.org/), a nonprofit focused on producing public goods.
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Previously I was a scientist at [Arcadia Science](https://www.arcadiascience.com/), where I created computational tools and approaches towards understanding diverse organisms across the tree of life, and contributed to pubs released through a non-journal based publishing platform.
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Previously, I was a scientist at [Arcadia Science](https://www.arcadiascience.com/), where I created computational tools and workflows for harnessing the evolutionary biology of diverse organisms across the tree of life for developing novel therapeutics, and contributed to pubs released through a non-journal based publishing platform.
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I received my PhD in the [Microbiology Doctoral Training Program](https://microbiology.wisc.edu/) at the University of Wisconsin-Madison studying lab-scale enrichment systems simulating phosphorus removal using multi-omics techniques. Prior to moving to industry, I was a postdoctoral researcher at the University of British Columbia in the Departments of Civil Engineering and Microbiology and Immunology working on the microbial ecology of anaerobic digestion systems.
Listed below are links to the work I've contributed to in various industry settings and a list of my academic publications. You can find a full listing of publications that are indexed on my
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[Google Scholar Profile](https://scholar.google.com/citations?user=OJFxBWMAAAAJ&hl=en). For all publications I've made a concerted effort to provide links to open access versions of the article or preprint, the underlying code, and data repositories. If you have trouble accessing a paper, dataset, or code, please don't hesitate to [contact me](contact.qmd)!
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## Microcosm Foods
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All Microcosm Foods datasets are deposited primarily through Zenodo with a CC0 open-access license. Additionally we have partnered with other organizations to make datasets such as curated microbial genomes from fermented foods and annotated bacterial genomes available.
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Explore [Microcosm Foods Datasets on Zenodo ](https://zenodo.org/communities/microcosmfoods/records?q=&l=list&p=1&s=10&sort=newest) such as curated genomes, annotations, and peptide bioactivity predictions using machine learning classifications.
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Interactively explore a [curated set of microbial genomes from fermented foods](https://kbase.us/n/218406/47/) on KBase, a free platform for curating, analyzing, and sharing genomes.
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Interactively explore functional annotations for a subset of bacterial genomes from fermented foods on Tatta Bio's [SeqHub platform](https://seqhub.org/rachel-dutton/collections/microcosm-fermented-food-genomes), and read about our partnership [here](https://seqhub.org/blog/seqhub-microcosm-foods-partnership).
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## Arcadia Science
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Arcadia Science is [reimagining scientific publishing](https://research.arcadiascience.com/reimagining-scientific-publishing) and does not publish work in traditional peer-reviewed journals. You can check out their work at [research.arcadiascience.com](https://research.arcadiascience.com/). See pubs that I specifically contributed to [here](https://research.arcadiascience.com/user/elizabeth-a.-mcdaniel/), with a select few pubs listed below that I led:
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*Authors are listed in alphabetical order and not by pub contribution*
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**Discovering shared protein structure signatures connected to polyphosphate accumulation in diverse bacteria.**[pub](https://research.arcadiascience.com/pub/result-ppk1-homology/release/1)[code](https://github.com/Arcadia-Science/2023-polyphosphate)[data](https://zenodo.org/records/8378182) Avasthi P, Celebi FM, **McDaniel EA**. 2023. DOI: 10.57844/arcadia-ac10-23e7
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**Quickly processing and profiling microbial community sequencing data with a Nextflow workflow for metagenomics.**[pub](https://research.arcadiascience.com/pub/resource-metagenomics-workflow/release/2)[workflow](https://github.com/Arcadia-Science/metagenomics/tree/v1.0.0) Dutton RJ, **McDaniel EA.** 2023. DOI: 10.57844/arcadia-7etp-pj24
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*\# Denotes equal contribution.*
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**17. Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism.**
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categories: "Tags"
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---
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### Microbial Economy
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I write on Substack about [The Microbial Economy](https://themicrobialeconomy.substack.com/?r=uckqe&utm_campaign=pub-share-checklist), a dedicated newsletter about how microbial technologies make it (or not) to the marketplace.
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### Personal Blog
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Below are one-off posts about various topics, which span from generic advice to random musings.
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