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About me

Originally, I am from a town called Oxford, Ohio.  I graduated Miami University in 2014, obtaining degrees in Computer Science, Mathematics & Statistics, Electrical Engineering and Engineering Physics.  During that time, I have worked in numerous bioinformatics labs, at Miami University, Cold Spring Harbor Laboratories and Johns Hopkins University.  In addition, I was heavily involved with Miami University's autonomous robot, Redblade.

Now, my focus in microbiome studies.  I am currently a PhD student in Computer Science at University of California, San Diego working in Rob Knight's lab.  Specifically,  I am interested in developing algorithms and statistical theory to better understand microbial ecosystems.

I am currently involved with scikit-bio, Emperor the American-Gut project, and the Earth Microbiome project.






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ANCOM explained

In case you have not heard, ANCOM is another differential abundance test, designed specifically for tweezing out differentially abundance bacteria between groups.  Now, note that there are a ton of differential abundance techniques out there.  And one might ask why are there so many people focused on this seemingly simple problem. It turns out that this problem is actually impossible.   And this is rooted into the issue of relative abundances.  A change of 1 species between samples can be also explained by the change of all of the other species between samples.   Let's take a look at simple, concrete example. Here we have ten species, and 1 species doubles after the first time point.  If we know the original abundances of this species, it's pretty clear that species 1 doubled.  However, if we can only obtain the proportions of species within the environment, the message isn't so clear. Above are the proportions of the species in the e...

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