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Teaching

Metagenomics

I teach Metagenomics (CMSE 890:306) with Professor Alexis Black. This course is targeted to graduate and post-doc students. This course is offered every semester. This course is a way to increase your productivity as a researcher and to learn new computational skills. Topics include amplicon sequencing, diversity analysis, shotgun metagenome analysis, and assembled genomes.

Microbial Ecology

I co-teach Microbial Ecology (MMG 425) with Professor Ned Walker.  This course is targeted to upper-level students and is offered every spring semester.  Because the principles of microbial ecology are foundational to many fields, we welcome students majoring in a variety of disciplines, including microbiology, plant, soil and microbial sciences, environmental and biosystems engineering, geology, and other fields. The class is transitioning to be "flipped" such that content knowledge is consumed out of class  (e.g. via video recorded lectures and readings) while class time is dedicated to active learning exercises.

I am enthusiastic to mentor graduate students from any field in independent teaching-as-research (TAR) projects to develop and assess team-based, active-learning activities in MMG425. Check out a recent TAR project from Natalie VandePol here.

Statistical Analysis of Microbiomes

I teach Statistical Analysis of Microbiomes (MMG 991 Topics in Microbiology).  This course is targeted to graduate students, and post-docs and faculty are also welcome to join in the discussion. It may be offered every other fall semester (last offering was fall 2016). This is a foundational class that introduces the tools of ecological statistics and multivariate analysis for analyzing microbiome data that are organized in a table of genes/species by samples/communities.

EDAMAME workshop: microbial metagenome analysis

I lead the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop at Kellogg Biological Station. Enthusiastic and awesome co-instructors are Adina Howe at Iowa State and Tracy Teal of Data Carpentry.  This immersion, hands-on workshop takes learners through the basics of computing through cloud computing, amplicon and metagenome sequence analysis, and statistical analysis and visualizations.  All of our content is available on our wiki and more information is on our webpage.  This workshop is over-subscribed and has been attended by international and US grad students, post-docs, faculty, and scientists form governmental agencies (e.g. USGS, EPA).  It is and has been supported by an NIH R25 award (R25GM115335), the BEACON Center for the Study of Evolution in Action, the Michigan State Institute for Cyber-Enabled Research, and AWS Programs for Research and Education.

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