Author Archives: Jeff

New paper on microbial community structure in coastal Southern California

Congrats to postdoctoral researcher Jesse Wilson for his new paper in Environmental Microbiology Recurrent microbial community types driven by nearshore and seasonal processes in coastal Southern California. Although considerable microbiology work has taken place at the Ellen Browning Scripps Pier … Continue reading

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New paper on microbial life in hypersaline environments

Congrats to Benjamin Klempay for his first, first-authored publication in the lab! (wow, didn’t I just write that??) Benjamin is part of the Oceans Across Space and Time (OAST) project and his paper, Microbial diversity and activity in Southern California … Continue reading

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New paper on shrimp aquaculture in mangrove forests

Congrats to Natalia Erazo for her first first-authored publication in the lab! Her paper, Sensitivity of the mangrove-estuarine microbial community to aquaculture effluent, appears in a special issue of the journal iScience. The publication is the culmination of our 2017 … Continue reading

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New paper on microbial community dynamics in up-flow bioreactors

Congrats to Avishek Dutta for his first publication in the Bowman Lab: Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring. Avishek did a remarkable job of resurrecting a stagnant dataset and turning it into … Continue reading

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New paper linking the SCCOOS and AGAGE datasets

Postdoctoral researcher Jesse Wilson has a new paper titled Using empirical dynamic modeling to assess relationships between atmospheric trace gases and eukaryotic phytoplankton populations in coastal Southern California in press in the journal Marine Chemistry. This paper is the culmination … Continue reading

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Finding those lost data files

It’s been a long time since I’ve had the bandwidth to write up a code snippet here. This morning I had not quite enough time between Zoom meetings to tackle something more involved, so here goes! In this case I … Continue reading

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MOSAiC Interview on The Not Old-Better Show

I was fortunate to have the chance to talk about some of our experiences on MOSAiC Leg 3 with Paul Vogelzang, host of the Smithsonian’s Not Old-Better podcast. The full interview can be found here:

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Looking back to South Bay Salt Works 2019

Many thanks to Michelle Babcock, communications specialist for the OAST project, for producing this great video of our 2019 field effort at the South Bay Salt Works in San Diego. This field effort was supposed to be a low-key opportunity … Continue reading

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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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