Jason Carter

Jason CarterJason Carter


B.A. University of California, San Diego (2014)

M.S. University of California, San Diego (2015)

Current Position:

6th Year MSTP

4th Year Med Student


Mickey Atwal, PhD

Graduate Program:

Applied Mathematics and Statistics

Research Interests:

I am interested in development and application of new computational approaches to address
translational questions in immunology and tumor biology. My undergraduate research focused
on the biophysics of regeneration in planarians and Hydra. My doctoral work in the Atwal Lab at
Cold Spring Harbor Laboratory took advantage of recent advances in high-throughput single-cell
sequencing to capture hundreds-of-thousands of paired αβ T cell receptors (TCRs). Employing
tools from machine learning, information theory, and statistical modeling, we explored the
importance of αβ TCR pairing in healthy individuals with respect to (i) accurately inferring TCR
repertoire diversity, (ii) fully understanding repertoire functionality, and (iii) inferring the rate of
allelic inclusion (ααβ/αββ) T cells. Additional work in the lab has focused on topics in
computational cancer genomics, including the prediction of individual response to immune
checkpoint blockade (ICB) therapy in metastatic melanoma and the bioinformatic identification
of novel cancer/testis (CT) antigens as potentially targetable neoantigens for immunotherapy.

Carter, J.A., Harris, B., and Atwal, G.S. (2020) “A pan-cancer germness score is correlated with
tumor progression and immune response.” In preparation

Carter, J.A., Gilbo, P., and Atwal, G.S. (2019) “IMPRES does not reproducibly predict
response to immune checkpoint blockade therapy in metastatic melanoma.” Nature Medicine

Carter, J.A., Preall, J., and Atwal, G.S. (2019) “Bayesian inference of allelic inclusion rates in
the human T cell receptor repertoire.” Cell Systems 9(5):475-482

Carter, J.A., Preall, J., Grigaityte, K., Goldfless, S.J., Jeffery, E., Briggs, A.W., Vigneault, F.,
and Atwal, G.S. (2019) “Single T Cell Sequencing Demonstrates the Functional Role of αβ TCR
Pairing in Cell Lineage and Antigen Specificity.” Frontiers in Immunology 10:1516

Grigaityte, K., Carter, J.A., Goldfless, S.J., Jeffery, E.W., Hause, R.J., Jiang, Y., Koppstein, D.,
Briggs, A.W., Church, G.M., Vigneault, F., and Atwal, G.S. (2017) “Single-cell sequencing
reveals αβ pairing shapes the T-cell repertoire.” bioRxiv: 213462

Cochet-Escartin, O.,* Carter, J.A.,* Chakraverti-Wuerthwein, M.,* Sinha, J., and Collins,
E.M.S. (2016) “Slo1 regulates ethanol-induced scrunching in freshwater planarians.” Physical
Biology 13(5): 055001. (*Equal Contribution)

Carter, J.A.,* Hyland, C.,* Steele, R.E., and Collins, E.M.S. (2016) “Dynamics of Mouth
Opening in Hydra. Biophysical Journal 11(5):1191-201. (*Equal Contribution)

Carter, J.A., Lind, C.H., Truong, M.P., and Collins, E.M.S. (2015) “To Each His Own.
Reproductive Strategies and Success of Three Common Planarian Species: Schmidtea
mediterranea, Dugesia japonica, and Dugesia tigrina.” Journal of Statistical Physics