Hi. My name is Christopher Small.
I am a Co-Founder and Chief Data Scientist of Polis, an AI powered surveying tool which uses machine learning and data visualization to facilitate large scale open ended feedback. We've been making waves in Taiwan's government, and more recently beginning to work the governments of Canada and Singapore, as well as other organizations around the world.
When I'm not working on Polis I'm at Fred Hutchinson Cancer Research Center with Erick Matsen, building tools for HIV vaccine researchers to better understand the adaptation of the human immune system to the virus.
Featured Programming Projects
I've got a number of open source projects I'm proud to share. A number of these constitute a set of libraries which have become vital to the work that I do with Clojure.
- I built and maintain the code powering Polis.
Clojure data science work
- oz: data visualization library for Clojure based on Vega & Vega-Lite, complete with publishing to Vega Editor and ozviz.io via GitHub gists.
- semantic-csv: A CSV parsing library for Clojure which adds some nice higher level features for working with tabular data.
- clojure-datascience: Compilation site of resources for data science in Clojure.
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.
Fruits of my time as a computational biologist:
- cft: Computational pipeline for processing deep sequenced B-cell receptor data.
- olmsted: Data exploration/visualization tool fed by cft (above) for analyzing the adaptive immune system.
- hyperfreq: The tool I developed for analysis of APOBEC hypermutation, a specific host defense mechanism again HIV and related viruses.
Misc Clojure projects:
- 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.
For a complete list of everything public/OS, please visit my github page.
During a previous stint at Fredhutch, I applied molecular epidemiology and statistical inference towards better 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.
Rapid development of an infant-derived HIV-1 broadly neutralizing antibody lineage
Cassandra A Simonich, Laura Doepker, Duncan Ralph, James A Williams, Amrit Dhar, Zak Yaffe, Lauren Gentles, Christopher T Small, Brian Oliver, Vladimir Vigdorovich, Vidya Mangala Prasad, Ruth Nduati, D Noah Sather, Kelly K Lee, Frederick A Matsen IV, Julie Overbaugh
In preprint, pending review
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
PLoS Pathogens, 2015.
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.
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.
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.
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.
I've also been a lifelong educator. I tutored math and science throughout high school and college. More recently, I spent several years building curriculum and teaching intro bioinformatics skills to biologists.
Teaching has always been integral to the way I learn, as nothing so crystallizes for you what you know and don't know than attempting to teach it to another person.
Lately I've been devouring history podcasts, specifically Mike Duncan's History of Rome and Revolutions series, and some of Dan Carlin's Hardcore History podcast. Looking to the past has helped me better understand our current moment in history.
I also love to make music (piano, guitar, bass and beat-box), and at one point spent a lot of time doing visual arts (painting, digital).
To top it all off I have a wife and a child who ensure that I never have a dull moment.
Other places on the internet
You'll typically find me elsewhere on the internet using the name