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 with Yoav Gilad at the University of Chicago. Specifically, I’ve led projects examining the role of environmental and genetic factors on determining gut microbiome composition.

As a postdoc with Andy Clark and Ruth Ley, I’ve continued to examine the role the host genome plays in determining gut microbiome composition. In addition, I’m leading 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.

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Publications

* denotes equal contribution

. The human microbiome in evolution. BMC Biology, 2017.

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. The relationship between the human genome and microbiome comes into view. Annual Reviews of Genetics, 2017.

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. Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. Microbiome, 2017.

PDF Project Source Document

. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biology, 2016.

PDF Project Source Document

. ABO antigen and secretor statuses are not associated with gut microbiome composition in 1,500 twins. BMC Genomics, 2016.

PDF Project Source Document

. Genetic determinants of the gut microbiome in UK twins. Cell Host & Microbe, 2016.

PDF Project Source Document

. Cross-species comparisons of host genetic associations with the microbiome. Science, 2016.

PDF Project Source Document

. A quick introduction to version control with Git and GitHub. PLoS Computational Biology, 2016.

PDF Source Document Github repo

. Genome-wide association studies of the human gut microbiota. PLoS ONE, 2015.

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. Epigenetic modifications are associated with inter-species gene expression in primates. Genome Biology, 2014.

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. Seasonal variation in human gut microbiome composition. PLoS ONE, 2014.

PDF Project Source Document

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. See my CV for a full list of completed programs. 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 8 workshops (in Chicago, Ithaca, and State College) and lead instructor at 3 (in Toronto, Ithaca, and Phoenix), 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 with the content I taught are here:

2017

2016

2015

2014

2013


Mentorship

Adon Chowdhury (2017 - )

Biometry and Statistics Undergraduate in the Clark Lab @ Cornell University

Adon was a Biometry and Statistics major (graduated Spring 2018) who became interested in combining his interests in biology and data science by studying the microbiome. He is currently leading a project examining whether the dynamics of microbial community assembly in the gut are influenced by host genetics, using samples from the large TwinsUK cohort. Adon’s background has proven perfect for this project, as it requires strong statistical and computational skills, along with broad biological understanding.

Trang Dau (2017 - )

Human Biology, Health, & Society Undergraduate in the Clark Lab @ Cornell University

Trang is a Human Biology, Health, and Society major who became interested in the two-way relationship between the microbiome and the human host after taking courses in microbiology and ecology at Cornell. She has contributed to a number of projects during her time in lab, including examining the role of host genetics in microbial community assembly and the role of microbial networks in health and disease.

Monica Guardado (2015 - 2017)

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 examined 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.

—> Awarded an American Society of Microbiology (ASM) Research Capstone Fellowship for this work in 2017

Xiaoling Gong (2016 - 2017)

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.

Service

For a full list of my service activities, see my CV.

ASHG Training and Development Committee

I’ve been a member of the American Society of Human Genetics (ASHG) Training and Development Committee (TDC) since January 2017. Our goal as a society committee is to serve the needs of our trainee members (graduate students and postdocs). We provide trainee-related content at the annual meeting (career panels, workshops, networking events, etc.), community building throughout the year, and promoting trainee science.

In particular, I helped organize several events at the ASHG 2017 annual meeting in Orlando, including ASHG Peer Networking Trivia and the ASHG Trainee Professional Development Program: Academic Careers Panel: Open Q&A with Leading Scientists.

For ASHG 2018 in San Diego, I’m leading efforts to organize the ASHG Peer Networking Trivia, ASHG Trainee Professional Development Program: Resilience and Academic Training, and the Trainee Paper Spotlight CoLab.

In addition to events for the annual meetings, my year-round activities include leading the Trainee Paper Spotlight working group of the TDC and co-leading the Twitter #ASHGtrainee working group.

Cornell Consensual Relationships Policy Committee

I served as a postdoctoral representative on the university-level committee at Cornell to recommend a new policy for consensual relationships on campus. This committee consisted of selected representatives of groups on campus (undergraduates, graduate students, faculty, etc.) who had the goal of drafting an updated policy for consensual relationships to mitigate conflict and protect academic integrity and freedom. After researching similar policies at other institutions and dialog with groups on campus, we submitted a full policy proposal on May 1, 2018 to the University President. Martha Pollock endorsed our proposed policy, which is expected to roll out in the fall.

MBG Postdoc Invited Seminar Series

In 2017, Sarah Lower, Anne-Marie Dion-Côté, and I initiated a new departmental committee who organized postdoc-invited speakers as part of the Molecular Biology and Genetics (MBG) seminar series. Our goal was to increase the diversity of speakers included in our departmental seminar series, target speakers with reputations of being trainee-oriented, and providing extra chances for trainees in the department to network with invited speakers. Our first two visits in 2017 were an overwhelming success, with Dr. Harmit Malik and Dr. Abby Dernburg as our invited speakers.


Cornell University Postdoc advisory council

Starting in 2016, I joined the Cornell University Postdoctoral Advisory Council. This cross-campus council seeks to provide support, networking, and professional development opportunities to the large number of postdocs at Cornell. During my time on the committee, I led the effort to create a Postdoc Welcome packet for all new incoming postdocs to campus, and helped to organize a monthly social night.

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