Recent Posts

Rust is increasingly being used for performant implmentations of various algorithms, including those used in computational biology. Some examples include a minhash algorithm implmented by OneCodex and a pseudo-aligner by 10X Genomics.

I thought it would be useful to start compiling a collection of these rust impementations as they appear, and so awesome-rust-biology-algorithms is born.


Everyone is always asking the age old question: R or Python? Why not both? I refuse to choose! They each have their own strengths and weaknesses, and I often find myself seamlessly interweaving between the two depending on the task at hand. Being ambidextrous with R and Python has never been easier, as cross-pollination across the two languages has resulted in many of the same constructs now existing for both. For example, data frame implementations such as pandas and tibble are largely converging on many of the same patterns and tooling.


After experimenting with several website/blog managers operable with Github Pages, it looks like Blogdown will be the winner. I really like the idea of maintaining a personal technical blog out of RStudio, as it feels a lot more like writing up technical reports with all the usual tools that RStudio affords (knitr cells, LaTeX, git, etc). The use of Hugo for theme management also looks like a good choice, and as such I’ve decided to go with the very snazzy looking Academic theme.


Create a beautifully simple website or blog in under 10 minutes.


R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see You can embed an R code chunk like this: summary(cars) ## speed dist ## Min. : 4.0 Min. : 2.00 ## 1st Qu.:12.0 1st Qu.: 26.00 ## Median :15.0 Median : 36.00 ## Mean :15.4 Mean : 42.98 ## 3rd Qu.



Microbial pathogen detection

Analytical framework to predict and classify pathogens.

External Project

An example of linking directly to an external project website using external_link.


I have been a teaching assistant for the following courses at Johns Hopkins University:

  • Spring 2018: 605.448.81 - Data Science
  • Spring 2018: 605.445.81 - Artificial Intelligence
  • Spring 2017: 605.448.81 - Data Science
  • Spring 2017: 605.445.81 - Artificial Intelligence
  • Fall 2016: 605.448.81 - Data Science
  • Fall 2016: 605.448.82 - Data Science