About

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Hi. My name is Christopher Small.

I am a Founder and Head Scientist of Pol.is, a startup tool using data visualization and machine learning to make sense of large scale conversations. We've been making waves in Taiwan's government, with "constitutional" implications, and are aiming to do the same across the globe.

As a consultant, I also build distributed systems, data analysis tools, dynamic web applications and design and teach technical curricula. I prefer to work with Clojure, ClojureScript and other functional languages (Elm, Haskell, Ocaml), but also work with R, Python, JavaScript and Ruby. Feel free to get in touch.

You can also download a copy of my CV.


Past Work

Prior to starting full time on Polis, I worked at Fred Hutchinson Cancer Research Center in the Computational Biology group with Erick Matsen. There I applied molecular epidemiology and statistics towards understanding viral transmission patterns and host defense mechanisms. Some of my work focused on novel methods for analyzing host defense activity in HIV and other retroviruses. I'm currently finishing research on a viral transmission study of atrovirus, which promises to greatly improve our understanding of the host ecology of the virus as a whole and as pertains to concerns of transmission to humans.

My activity in these areas ultimately stems from my love of mathematics. I studied Pure and Applied Mathematics at The Evergreen State College, and took that knowledge with me to industry, where programming became a natural application of my skills. Working at Fred Hutchinson gave me the opportunity to put computers and mathematics together in the context of really fascinating science.

I've also been a lifelong educator. I tutored and taught math and science throughout high school and college. Teaching has long been an integral part of how I learn, and I've been happy to continue with that trend in teaching bioinformatics skills to biologists.


Featured Programming Projects

I've been working on a set of tools for making full stack Clojure + ClojureScript applications using Datomic and DataScript as a data model. The most interesting pieces of this as of this writing:

  • Datsync: Datomic <-> DataScript syncing utilities.
  • Datview: A customizable/extensible set of utilities for building interactive views out of such data. (Be warned; this is currently in flux).
  • Datsys: The umbrella project for the above, in the form of a simple example application with these things hooked up together.

Some other Clojure projects:

  • semantic-csv: A CSV parsing library for Clojure which adds some nice higher level features for parsing.
  • clj-bots (WIP): A set of tools for working with Clojure for device programming, such as the BeagleBone Black, Raspberry Pi and (hopefully) soon Arduino via the Firmata protocol.
  • lein-clique: Contributed to a tool for analysis of clojure function dependencies.
  • clojure-datascience: Compilation of resources for data science in Clojure.

Fruits of my time as a computational biologist:

  • hyperfreq: The tool I developed for analysis of APOBEC hypermutation, a specific host defense mechanism again HIV and related viruses.

For a complete list of everything public, please visit my github page.


Publications


Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections

Erik A Karlsson *, Christopher T. Small *, Pamela Freiden, Mohammed M Feeroz, Frederick A. Matsen
IV, , Sorn San, M. Kamrul Hasan, Gunwha Oh, David Wang, Gregory Engel, Lisa Jones-Engel, Stacey
Schultz-Cherry.
PLoS Pathogens, 2015.

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A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
Frederick A. Matsen IV, Christopher T. Small, Khanh Soliven, Gregory A. Engel, Mostafa M. Feeroz, Xiaoxing Wang, Karen L. Craig, M. Kamrul Hasan, Michael Emerman, Maxine L. Linial, Lisa Jones-Engel
PLoS Comput. Biol., 2014.


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Simian Foamy Virus Infection of Rhesus Macaques in Bangladesh: Relationship of latent proviruses and transcriptionally active viruses
Soliven, Khanh, Wang, Xiaoxing, Small, Christopher T, Feeroz, Mostafa M, Lee, Eun-Gyung, Craig, Karen L, Hasan, Kamrul, Engel, Gregory A, Jones-Engel, Lisa, Matsen, Frederick A, and Linial, Maxine L.
Journal of virology, 2013.
[pdf]


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Zoonotic simian foamy virus in Bangladesh reflects diverse patterns of transmission and co-infection
Jones-Engel, L., Engel, G., Small, C., Soliven, K., Feeroz, M., Wang, X., Hasan, M., Oh, G., Alam, S. M. R., Craig, K., Jackson, D., IV, F. Matsen, and Linial, M. L.
Emerging Microbes and Infections, 2013.


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Population Dynamics of Rhesus Macaques and Associated Foamy Virus in Bangladesh
Feeroz, M.M., Soliven, K., Small, C.T., Engel, G.A., Pacheco-Delgado, M.A., Yee, J.L., Wang, X., Hasan, M. Kamrul, Oh, G., Levine, K.L., Alam, S.M.R., Craig, K. L., Jackson, D.L., Lee, E., Barry, P.A., Lerche, N.W., Escalante, A.A., Matsen, F.A., Linial, M.L., and Jones-Engel, L.
Emerging Microbes and Infections, 2013.


Other places on the internet

You'll typically find me elsewhere on the internet using the name metasoarous.

linkedin

twitter

profile for metasoarous on Stack Exchange, a network of free, community-driven Q&A sites


Extra-curricular

I am passionate about music, art, and philosophy. I play piano, guitar, bass and beat-box. I occasionally do some electronic art work, and some day would like to get back into oil painting and experiment with sculpture and other media.

I have a beautiful wife named Patricia, and a the cutest baby in the world (no seriously; his hair naturally grows in the shape of a mulhawk... yeah).




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