* denotes equal contribution; # denotes correspondence; Yang lab members are in bold.
2025
Huang, A.Y.*, Burke, K.P.*, Porter, R., Fatouros, P., Vokes, N., Ricker, C., Robitschek, E., Tarantino, G., Aprati, T.J., Glettig, M.C., Chen, J., He, Y., Yang, J., Wang, C., Ho, L.-L., Galani, K., Freeman, G., Van Allen, E.M., Kellis, M., Boland, G.M., Sharpe, A.H., Liu, D., 2025. Immune infiltrate predicts response to αPD1/αCTLA4 but not αPD1 and distinguishes programs of primary resistance in metastatic melanoma. Science Translational Medicine (under review). https://doi.org/10.1101/2024.10.29.620300 (bioRxiv)
Qiu, M., Hu, X., Zhan, F., Yun, S., Peng, J., Zhang, R., Kailkhura, B., Yang, J., Chen, T., 2025. GRNFormer: A biologically-guided framework for integrating gene regulatory networks into RNA foundation models. Association for Computational Linguistics. https://doi.org/10.48550/arXiv.2503.01682
Yang, J.*#, Wang, C.*, Fu, D.*, Ho, L.-L., Galani, K., Chen, L., Gonzalez, J., Fu, J., Huang, A.Y., Frederick, D.T., He, L., Asnani, M., Tacke, R., Robitschek, E.J., Yadav, S.K., Deng, W., Burke, K.P., Sharova, T., Sullivan, R.J., Weiss, S., Rai, K., Liu, D., Boland, G.M.#, Kellis, M.#, 2025. Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma. Nature Communications (accepted). https://doi.org/10.1101/2024.06.20.599945
Babu, S., Chen, J., Baron, C.S., Sun, K., Robitschek, E., McConnell, A., Wu, C., Dedeilia, A., Sade-Feldman, M., Modhurima, R., Manos, M.P., Chen, K.Y., Cox, A.M., Ludwig, C.G., Kellis, M., Buchbinder, E.I., Hacohen, N., Yang, J., Boland, G.M., Abraham, B.J., Liu, D., Zon, L.I., Insco, M.L., 2025. Specific oncogene activation of the cell of origin in mucosal melanoma. Nature Communications (accepted). https://doi.org/10.1101/2024.04.22.590595
Revach, O., Cicerchia, A.M., Shorer, O., Palin, C.A., Petrova, B., Anderson, S., Liu, B., Park, J., Chen, L., Mehta, A., Wright, S.J., McNamee, N., Tal-Mason, A., Cattaneo, G., Tiwari, P., Xie, H., Sweere, J.M., Cheng, L., Sigal, N., Enrico, E., Milijkovic, M., Evans, S.A., Nguyen, N., Whidden, M.E., Srinivasan, R., Spitzer, M.H., Sun, Y., Sharova, T., Lawless, A., Michaud, W.A., Rasmussen, M.Q., Fang, J., Brook, J.R., Chen, F., Wang, X., Ferrone, C.R., Lawrence, D.P., Sullivan, R.J., Liu, D., Sachdeva, U.M., Sen, D.R., Flaherty, K.T., Manguso, R.T., Bod, L., Kellis, M., Boland, G.M., Yizhak, K., Yang, J., Kanarek, N., Sade-Feldman, M., Hacohen, N., Jenkins, R.W., 2025. Overcoming resistance to immunotherapy by targeting CD38 in human tumor explants. Cell Reports Medicine 6. https://doi.org/10.1016/j.xcrm.2025.102210.
Ellington, C.N., Lengerich, B.J., Watkins, T.B.K., Yang, J., Adduri, A.K., Mahbub, S., Xiao, H., Kellis, M., Xing, E.P., 2025. Learning to estimate sample-specific transcriptional networks for 7,000 tumors. Proceedings of the National Academy of Sciences 122(21). https://doi.org/10.1073/pnas.2411930122
2024
Pujadas Liwag, E.M., Wei, X., Acosta, N., Carter, L.M., Yang, J., Almassalha, L.M., Jain, S., Daneshkhah, A., Rao, S.S.P., Seker-Polat, F., MacQuarrie, K.L., Ibarra, J., Agrawal, V., Aiden, E.L., Kanemaki, M.T., Backman, V.#, Adli, M.#, 2024. Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism. Genome Biol 25, 77. https://doi.org/10.1186/s13059-024-03212-y
2023
[Review] Wendi Liu*, Anusha Puri*, Doris Fu*, Lee Chen, Cassia Wang, Manolis Kellis, Jiekun Yang#, Dissecting the tumor microenvironment in response to immune checkpoint inhibitors via single-cell and spatial transcriptomics, Clinical & Experimental Metastasis (2023). https://doi.org/10.1007/s10585-023-10246-2
[Review] Cassia Wang*, Lee Chen*, Doris Fu, Wendi Liu, Anusha Puri, Manolis Kellis, Jiekun Yang#, Antigen presenting cells in cancer immunity and mediation of immune checkpoint blockade, Clinical & Experimental Metastasis (2024). https://doi.org/10.1007/s10585-023-10257-z
2022
Jiekun Yang*, Maria Vamvini*, Pasquale Nigro*, Li-Lun Ho, Kyriakitsa Galani, Marcus Alvarez, Yosuke Tanigawa, Ashley Renfro, Nicholas P. Carbone, Markku Laakso, Leandro Z. Agudelo, Päivi Pajukanta, Michael F. Hirshman, Roeland J.W. Middelbeek, Kevin Grove, Laurie J. Goodyear#, Manolis Kellis#, Single-cell dissection of the obesity-exercise axis in adipose-muscle tissues implies a critical role for mesenchymal stem cells, Cell Metabolism, Volume 34, Issue 10, 2022, Pages 1578-1593.e6, ISSN 1550-4131,
https://doi.org/10.1016/j.cmet.2022.09.004. (https://www.sciencedirect.com/science/article/pii/S1550413122003941)