# or ^ denotes authors contribute equally, * denotes (co-)corresponding author and _ _ denotes a lab member. An up-to-date list of all publications is available on Google Scholar.
Dissecting sequence determinants of DNA methylation and in silico perturbation.
Chen, F.#, Zhang, Q.#, Zhu, S.#, Liang, J.#, Zhong, S., Zhang, Z., Su, J., Guo, Y.*, Fan, X.*, Zhang, Y.*, Yu, F.*.
CAPTAIN: A multimodal foundation model pretrained on co-assayed single-cell RNA and protein.
Ji, B.#, Hu, T.#, Wang, J.#, Liu, M., Xu, L., Zhang, Q., Zhong, S., Qiao, L., Zhang, Y.*, Peng, S.*, Yu, F.*.
Disentangled multimodal evolutionary representations for cross-virus predictive modeling of antigenic change.
Zhang, Z.#, Lin, Y.#, Zhong, S., Zhou, P., Li, Y. & Yu, F.*.
Explainable AI multiomics analysis reveals shared and divergent host responses in COVID-19 and influenza.
Zhang, Y., Zhang, L., Zhang, Z., Lin, Y., Jiang, Z., Yu, F.*. npj Digital Medicine
Decoding Translation-Related Functional Sequences in 5’UTRs Using Interpretable Deep Learning Models.
Lin, Y.#, Fang, Y.#, Zhang, Z.#, Liu, Z., Zhong, S., Wang, Z.*, Yu, F.*. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
Ad5-boosted COVID-19 vaccine reduces symptomatic BA. 5 infection via cross-neutralizing antibodies and NK cell immunity.
Cui, T., Liu, S., Wang, T., Liu, Y., Liang, X., Chen, F., Huang, M., Su, X., Song, T., Su, J., Deng, S., Zhao, J.*, Yu, F.* & Wang, Z.* BMC Medicine
Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood.
Jakubek, Y., Ma, X., Stilp, A., Yu, F., et al., , Auer, P.*. The American Journal of Human Genetics
Context-aware single-cell multiomics approach identifies cell-type-specific lung cancer susceptibility genes.
Long, E., Yin, J., Shin, J., Li, Y., Li, B., Kane, A., Patel, L. D., Sun, N., Wang, C., Luong, TG., Xia, S., Han, W., Byun, S., Zhang, C., Zhao, D., Landi Rothman, E., Lan, E., Chang, C., Yu, F., Christopher, N., Shi, J. J., Lee, X., Young, Kim.*, Chiang, C.*, Choi, J.*. Nature Commnications
A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children.
Smith, A.#*, Wahlster, L.#, Jeon, S.#, Kachuri, L.,Black, S., Langie, J., Cato, L. D., Nakatsuka, N., Chan, T.-F., Xia, G., Mazumder, S., Yang, W., Gazal, S., Eng, C., Hu, D., González Burchard, E., Ziv, E., Metayer, C., Mancuso, N., Yang, J. J., Ma, X., Wiemels, J. L., Yu, F.^, Chiang, C.^, V., G.*^. Cell Genomics
Deciphering cell states and genealogies of human hematopoiesis.
Weng, C., Yu, F., Yang, D., Poeschla,, M., Liggett, L. A., Jones, M. G., Qiu, X., Wahlster, L., Caulier, A., Hussmann, J. A., Schnell, A., Yost, K. E., Koblan, L. W., Martin-Rufino, J. D., Min, J., Hammond, A., Ssozi, D., Bueno, R., Mallidi, H., Kreso, A., Escabi, J., Rideout, W. M. III, Jacks, T., Hormoz, S., van Galen, P., Weissman, J. S., Sankaran, V. G.*. Nature
Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution.
Zhang, H., Yu, X., Ye, J., Li, H., Hu, J., Tan, H., Fang, Y., Akbay, E., Yu, F., Weng, C., Sankaran, V., G., Bachoo, R., Maher, E., Minna, J., Zhang, A., Bo Li* Cancer Cell
Selected publications before 2022
A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia.
Voit, R.#, Tao, L.#, Yu, F.#, Cato, L., Cohen, B., Liao, X., Claudia, F., Nandakumar, S., Wahlster, L., Kristian, T., Regev, A.*, and Sankaran, V., G.* Nature Immunology
[Github], [Data], Highlight by [Boston Children’s Hospital, BioArt]
Variant to function mapping at single-cell resolution through network propagation.
Yu, F., Cato L., D., Weng, C., Liggett L., A., Jeon, S., Xu, K., Chiang, C., Wiemels J., L., Weissman J., S., , Smith A. J., and Sankaran V., G.* Nature Biotechnology
[Github], Highlight by [Nature Genetics, New York Stem Cell Foundation, Broad Institute, BioArt]
A pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis.
Yu, F., Sankaran V., G., and Yuan G., C.* Bioinformatics
[Github]
scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures.
Zhang, Y#., Zhang, Y#., Hu, J.#, Zhang, J., Guo, F., Zhou, M., Zhang, G.*, Yu, F.*, and Su, J.* Bioinformatics
[Website]
CFEA: a cell-free epigenome atlas in human diseases.
Yu, F.#, Li, K.#, Li, S.#, Liu, J., Zhang, Y., Zhou, M., Zhao, H., Chen, H., Wu, N., Liu, Z.*, and Su, J.* Nucleic Acids Research
[Website]
Breast cancer prognosis signature: linking risk stratification to disease subtypes.
Yu, F.#, Quan, F.#, Xu, J.#, Zhang, Y.#, Xie, Y., Zhang, J., Lan, Y., Yuan, H., Zhang, H., Cheng, S.*, Xiao, Y.*, and Li, X.* Briefings in Bioinformatics
Systematic Characterization of Circular RNA-Associated CeRNA Network Identified Novel circRNA Biomarkers in Alzheimer’s Disease.
Zhang, Y.#, Yu, F.#, Bao, S., and & Sun, J.* Frontiers in Bioengineering and Biotechnology
LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse.
Yu, F.#, Zhang, G.#, Shi, A.#, Hu, J., Li, F., Zhang, X., Zhang, Y., Huang, J., Xiao, Y.*, Li, X.*, and & Cheng, S.* Database
MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq.
Xiao, Y.#, Yu, F.#, Pang, L.#, Zhao, H., Liu, L., Zhang, G., Liu, T., Zhang, H., Fan, H., Zhang, Y., Pang, B., and & Li, X.* Scientific Reports