Category Archives: Research
OAST visits the South Bay Saltworks
Last week we were busy hosting the inaugural Oceans Across Space and Time (OAST, @Space Oceans OAST on Facebook) combined first year meeting and field effort. It was a crazy week but a huge success. The goal of OAST is … Continue reading
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New paper on seagrass microbial ecology
We have a new paper out today on the impacts of coastal seagrasses on the microbial community structure of San Diego Bay. I’m excited about this paper as the first student-led study to come out of my lab. The study … Continue reading
Posted in Research, Uncategorized
Tagged Natalia Erazo, paprica, Sahra Webb, seagrass microbiome, Tia Rabsatt
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Analyzing flow cytometry data with R
We recently got our CyFlow Space flow cytometer in the lab and have been working out the kinks. From a flow cytometry perspective the California coastal environment is pretty different from the western Antarctic Peninsula where I’ve done most of … Continue reading
Posted in Computer tutorials, Research
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Microbial community segmentation with R
In my previous post I discussed our recent paper in ISME J, in which we used community structure and flow cytometry data to predict bacterial production. The insinuation is that if you know community structure, and have the right measure … Continue reading
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New paper published in ISME Journal
I’m happy to report that a paper I wrote during my postdoc at the Lamont-Doherty Earth Observatory was published online today in the ISME Journal. The paper, Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of … Continue reading
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Antarctic Long Term Ecological Research
I’m very excited that our manuscript “Microbial community dynamics in two polar extremes: The lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem” has been published as an overview article in the journal BioScience. The article … Continue reading
Creating a landmask for the West Antarctic Peninsula in R
This is going to be a pretty niche topic, but probably useful for someone out there. Lately I’ve been working with a lot of geospatial data for the West Antarctic Peninsula. One of the things that I needed to do … Continue reading
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Astrobiology Primer v2
The long-awaited version 2 of the Astrobiology Primer was published (open access) yesterday in the journal Astrobiology. I’m not sure who first conceived of the Astrobiology Primer, first published in 2006, but the v2 effort was headed by co-lead editors … Continue reading
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How I learned to stop worrying and love subsampling (rarifying)
I have had the 2014 paper “Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissable” by McMurdie and Holmes sitting on my desk for a while now. Yesterday I finally got around to reading it and was immediately a … Continue reading
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The Database Dilemma
Microbial ecologists know they have a problem with data archiving, particularly when it comes to sequence data. I’m not entirely sure why this is the case; in theory it would be pretty straightforward to build a database searchable by the … Continue reading
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