Author Archives: Jeff
Tutorial: SuperSOMS and an R script for detecting regions of interest
A common exercise in environmental microbiology is counting bacterial cells with an epifluorescent microscope. During my PhD I spend many hours hunched over a microscope in a darkened room, contemplating which points of light were bacteria (and should thus be … Continue reading
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Tutorial: Self Organizing Maps in R
Self-organizing maps (SOMs) are a form of neural network and a wonderful way to partition complex data. In our lab they’re a routine part of our flow cytometry and sequence analysis workflows, but we use them for all kinds of … Continue reading
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MOSAiC Leg 3
Where to begin… I started writing this post several days ago on a nearly empty plane flying from Charlotte, N.C. to San Diego. That flight marked the end of MOSAiC Leg 3 for me, though Leg 3 will continue for … Continue reading
CUREing microbes ASBMB2020 presentation
In a sign of the times here’s Ana Barral’s virtual presentation for the 2020 American Society for Biochemistry and Molecular Biology meeting (held remotely). It’s a nice summary of the initial results of our course-based undergraduate research experience (CURE) on … Continue reading
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Photos from MOSAiC Leg 1
Many thank to atmospheric chemist extraordinaire Jessie Creamean for participating in our NSF project on MOSAiC Leg 1. Jessie’s participation allowed us to have a physical presence during the critical setup phase and freeze in. Her participation was a double … Continue reading
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CURE-ing Microbes on Ocean Plastics Video
Over the last few months volunteer diver Caitlyn Webster has been putting together a quick outreach video on our CURE-ing Microbes on Ocean Plastics project with National University. In addition to highlighting the project, Caitlyn provides a nice overview of … Continue reading
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Article in San Diego Union Tribune
The San Diego Union Tribune published an article on our work at the South Bay Salt Works, part of the larger NASA-funded OAST project. Check it out here: https://www.sandiegouniontribune.com/news/environment/story/2019-11-05/seeking-life-in-the-solar-system.
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Antarctic ecosystem services paper published
We have a new paper published this week in Frontiers in Environmental Science on estimating ecosystem services along the western Antarctic Peninsula (WAP). This was one of the most challenging academic efforts I’ve been involved in, and is the culmination … Continue reading
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MOSAiC is go!
From the tropics to the Arctic… I spent last week in Tromsø , Norway helping prepare the German icebreaker Polarstern for the MOSAiC year-long polar drift expedition. As I’ve written in past posts, I’ve been waiting for this moment since … Continue reading
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Cayapas-Mataje Redux
Natalia Erazo and I are on our way back from an amazing week of sampling in the Cayapas-Mataje Ecological Reserve in northern Ecuador. We first visited the reserve in 2017 and have been anxious to return ever since. Our objectives … Continue reading
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