During my time at Fred Hutch with Erick Matsen in the computational biology department, I worked on several research projects, leading to a number of academic publications. Much of this research has revolved around the interactions between viruses and the human immune system, as well as patterns of transmission between species and host populations.
Through the course of most of this research, I was deeply involved in the scientific process together with our biological collaborators, helping write most of these papers, and producing a number of data visualizations, some of which are showcased below, next to the papers in which they were published.
Many thanks to the wonderful biologists I have had the pleasure of working with, for their fantastic work, and for the fruitful collaborations they sought fit to work together on.
My primary contribution towards this project has been a set of software which our biological collaborators used to process and analyze these datasets.
Kappa chain maturation helps drive rapid development of an infant 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 Nature Communications, 2019. web pdf
In this study, we looked at the first ever genetic sequencing of Astrovirus in non-human primates (NHP), and found evidence of very high interspecies transmission rates to and from NHP suggestive of high susceptibility to the virus.
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.
One of the first projects I cut my teeth on as a computational biologist was looking at fascinating data set of genetic sequence data from SFV infected humans and monkeys. The richness of the dataset warranted multiple papers, each of which looked at a certain angle of what the information was able to provide. One of the more major contributions of the work was finding evidence of the human viral restriction factor APOBEC3 as playing a role in the SFV's apparent inability to be transmitted between humans.
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.