Emily R. Davenport

Post-doctoral scholar

Cornell University

I am a postdoctoral scholar in the Department of Molecular Biology and Genetics at Cornell University. I’m working with Andy Clark, examining the host-microbiome interactions. I received my Ph.D. in September 2014 from the Department of Human Genetics at the University of Chicago, where I worked with Yoav Gilad. Scroll on to see more about my Research, Publications, Teaching, and how to Contact me.

Research

Research.

diet environment genotype

My long-term research interests revolve around understanding the complex interactions between the microbiome and the human host. Both my academic and industry experiences have led me to studying these complex interactions from a genomic perspective. As an undergraduate, I developed a strong interest in bacteriology while studying at the University of Wisconsin-Madison (Go Badgers!). After graduating, I gained experience in industry working for Roche Nimblegen, a microarray company. This experience introduced me to genomic techniques and I became proficient in the experimental skills necessary to perform high-throughput genomic research.

As a graduate student, I combined both my interests in microbial ecology and genomics by studying the human microbiome under Yoav Gilad at the University of Chicago. Specifically, I’ve lead projects examining the role of environmental and genetic factors on determining gut microbiome composition.

As a postdoc with Andy Clark, I’ve continued to examine the role the host genome plays in determining gut microbiome composition. In addition, I’ve begun other projects examining microbe-microbe interactions in health and disease and characterizing the microbiomes of non-US/European populations.

I’m now a jane-of-all-trades: doing all of my own experimental work and computational analyses. In addition, I’m interested in whether we’re studying the microbiome in the best way possible, and I’ve contributed to a project aimed at methods development for microbiome studies and an educational article for computational research methods.

Host diet/environment

Seasonal variation in gut microbiome composition

Many studies have shown the important role diet plays in determining gut microbiome composition, however, many of us eat fairly consistant diets seasonally because we have access to fresh produce grown all over the globe. To examine whether seasonal differences in diet might affect the microbiome, I examined the fecal bacterial content in an isolated, communally-living population: the Hutterites. Women in Hutterite colonies (a small town of a few hundred Hutterites) cook 3 huge, communal meals a day and the entire colony eats buffet style from that meal (check out some pictures). Because of this, inter-individual dietary variation in the Hutterites is much less than typical Americans at any given time. However, most of their produce is grown on the colony during the summer months and then canned, frozen, or pickled for the winter and spring. This means that they each many more serving of fresh produce during the summer than the winter. To examine whether or not these seasonal dietary differences affect the microbiome, we examined fecal microbiome sequencing using high-throughput 16S rRNA gene sequencing. We observe wide-spread, consistent shifts in the microbiome, many of which are likely driven by diet (as well as many other factors that change between season such as activity levels, vitamin D exposure, pathogen levels, immune activity, etc).

To read more, check out:


Genetic associations of the gut microbiome

Much of my work has been focused on elucidating the role of host genetics in determining gut microbiome composition. In addition to two study populations highlighted below, check out some reviews I’ve written on the subject:

Microbiome GWAS in the Hutterites

While many environmental factors are known to contribute to gut microbiome composition, the extent to which host genetic variation plays a role is unclear. Using the same population as the seasonal study (the Hutterites), where inter-individual variation in diet is limited, I examined the role of sex and age as well as host genetics in determining the relative abundances of the most common bacteria in the gut. To do so, I implemented methods that specifically account for the relatedness across individuals and examined genetic variation genome-wide. While this is an important first step at examining host genetics, I really can’t state enough the limitations of the sample size in this study and the number of tests performed. That being said, I do find bacteria that show evidence of heritability in my samples and have genome-wide (but not study-wide) significant associations with SNPs in the genome.

To read more, check out:

Genetics of the microbiome in UK Twins

As a postdoc, I’ve continued examining the role of host genetics using the TwinsUK cohort. This large, well-characterized cohort gives us much more power to detect associations between variation in the human genome and abundance of bacteria in the gut. We now have replication across multiple studies that show lactase persistence alleles are associated with lower levels of Bifidobacteria in the gut. The study was led by Julia Goodrich, while I contributed several analyses to study, including the replication of the LCT-Bifidobacterium association in the Hutterites, PrediXcan analyses, and microbiomeGWAS analyses.



To read more, check out:

Publications

Publications.

See my google scholar profile for an up-to-date list.

A recent-ish version of my CV can be found here. For a more current CV or more information, please contact me.

* denotes equal contribution

2016

2015

2014

2013

Teaching

Teaching.

Classroom

I never thought I would enjoy teaching, but after TAing several classes at UChicago I realized that I loved it.

To delve into it (as much as one can as a graduate student) I earned a certificate in University Teaching from the Center for Teaching and Learning at UChicago (now called Chicago Center for Teaching). This involved participating in a number of seminars and workshops related to designing curricula and assessment, generating a teaching portfolio, and being critiqued while teaching.

I even taught part of a course during my final year as a graduate student, covering topics in genomics such as current sequencing technology and applications, basic statistics, and genome organization and function. For an example of some prepared course material, see my introduction to linear models in R material. A summary of my TA evaluations can be found here.

To continue gaining experience as a teacher as a postdoc, I’m participating in workshops offered by the Center for Teaching Excellence at Cornell and Cornell University Center for the Integration of Research, Teaching, and Learning (CU-CIRTL). I’ve completed certificate programs in the Postdoc Leadership Program, Building Mentoring Skills for an Academic Career, and The Practice of Inclusive Teaching in STEM. Additionally, I’ve kept active in the classroom by teaching at Software Carpentry and Data Carpentry workshops (see below).


Software Carpentry and Data Carpentry

During graduate school I went to a Software Carpentry bootcamp and in two days learned all of the things I was hoping to learn about being a computational scientist (ok, it’s taking a lot more than two days, but the seeds were planted!). I became a certified Software Carpentry instructor in 2013 and taught at my first Data Carpentry workshop in 2015. I’ve been an instructor at 7 workshops (in Chicago, Ithaca, and State College) and lead instructor at 2 (in Toronto and Ithaca), typically teaching the shell, git, and/or R. It’s a great community and I’m constantly learning new skills (for instance, how to make this webpage using jekyll and github). Links to websites for these workshops are here:


2016

2015

2014

2013

Mentorship

Monica Guardado (2015 - )

Biology Undergraduate in the Perry Lab @ Pennsylvania State University

Monica became interested in host-microbiome dynamics during coursework for her Biology major. During her time in the Perry Lab at Penn State, she’s been examining whether termite-eating behavior in chimpanzees results in the transfer of termite microbiota into the chimpanzee gut. I’ve mentored her on both the wet lab and computational aspects of analyzing 16S rRNA sequencing data.


Xiaoling Gong (2016 - )

Visiting Scientist in the Clark Lab @ Cornell University

Xiaoling is interested in the population structure of Japanese Eels, an important aquaculture species in Asia. During her time as a visiting scientist in the Clark Lab, I’ve been mentoring her on the use of bioinformatic tools for analyzing RADseq data and application of population genetic statistics to answer the open question of whether Japanese Eels are panmictic.

contact

Contact.

Mailing address:

Emily Davenport
Biotechnology 101
Cornell University
Ithaca, NY 14853

Email:

ed379 - at - cornell.edu

Social Media:

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