Faculty Directory
Zhe Ji

Assistant Professor of Biomedical Engineering

Assistant Professor of Pharmacology


2145 Sheridan Road
Evanston, IL 60208-3109

Email Zhe Ji


Zhe Ji Research Group


Biomedical Engineering


Postdoc Cancer Systems Biology, Harvard Medical School, Boston, MA

Postdoc Computational Biology, Broad Institute of MIT and Harvard, Cambridge, MA

Ph.D. Computational Genomics, Rutgers University, Newark, NJ

B.S. Biotechnology, Nanjing University, China


Research Interests

Our group develops integrated computational and experimental genomics approaches to examine the regulation of gene transcription and RNA translation underlying cell fate commitment and oncogenic processes. We aim to reveal novel disease therapeutic strategies for precision medicine and immunotherapy.

Keywords of our research: Data Science, Computational Biology, Functional Genomics, RNA, Cancer, Inflammation, and Machine Learning.

Selected Publications

Li, Q., Yang, H., Stroup, E.K., Wang, H., and Ji, Z. (2022). Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation. Genome Research, 32: 545-557. 

Wang, X., Frederick, J., Wang, H., Hui, S., Backman, V., and Ji, Z. (2021). Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anti-cancer drug response. NAR Genomics and Bioinformatics, 3(2): lqab054.

Botta, G., Lyons, N.J., Goodale, A., Kalani, Z., Fritchman, B., Brown, A., Alan, D., Green, T., Yang, X., Jaffe, J.D., Roth, J.A., Piccioni, F., Kirschner, M.W., Ji, Z., Root, D.E., and Golub, T.R. (2021). Non-canonical open reading frames encode functional proteins essential for cancer cell survival. Nature Biotechnology, 39, 694-704.

Ouspenskaia, T., Law, T., Clauser, K.R., Klaeger, S., Sarkizova, S., Aguet, F., Li, B., Christian, E., Knisbacher, B.A., Le, P.M., Hartigan, C.R., Keshishian, H., Apffel, A., Oliveira, G., Zhang, W., Chow, Y.T., Ji, Z., Jungreis, I., Shukla, S.A., Bachireddy, P., Kellis, M., Getz G., Hacohen, N., Keskin, D.B., Carr, S.A., Wu, C.J., and Regev, A. (2021). Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature Biotechnology.

Ji, Z., He, L., Regev, A. and Struhl, K. (2019). Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers. Proc Natl Acad Sci U S A, 116, 9453-9462.

Ji, Z. (2018). RibORF: Identifying genome-wide translated open reading frames using ribosome profiling. Current Protocols in Molecular Biology, e67.

Ji, Z. (2018). Rfoot: Transcriptome-scale identification of RNA-protein complexes from ribosome profiling data. Current Protocols in Molecular Biology, e66.

Ji, Z., He, L., Rotem, A., Janzer, A., Cheng, C.S., Regev, A. and Struhl, K. (2018). Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. Nature Communications, 9, 2068.

Adiconis, X., Haber, A., Simmons, S.K., Moonshine, A.L., Ji, Z., Busby, M., Shi, X., Jacques, J., Lancaster, M.A., Pan, J.Q., Regev, A. and Levin, J.Z. (2018). Comprehensive comparative analysis of 5’ end RNA sequencing methods. Nature Methods, 15, 505–511.

Zhang, P., He, D., Xu, Y., Hou, J., Pan, B.F., Wang, Y., Liu, T., Davis, C.M., Ehli, E.A., Tan, L., Zhou, F., Hu, J., Yu, Y., Chen, X., Nguyen, T.M., Rosen, J.M., Hawke, D.H., Ji, Z., and Chen, Y. (2017) Genome-wide identification and differential analysis of translational initiation. Nature Communications, 8, 1749.

Henry, W.*, Hendrickson, D.*, Beca, F., Glass, B., Lindahl-Allen, M., He, L., Ji, Z., Struhl, K., Beck, A, Rinn, J, and Toker, A. (2016). LINC00520 is Induced by Src, STAT3, and PI3K and Plays an Oncogenic Role in Breast Cancer. Oncotarget, 13;7(50):81981-81994.

Miotto, B.*, Ji, Z.* and Struhl, K. (2016). Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. Proc Natl Acad Sci U S A, 113, E4810-E4819.

Ji, Z., Song, R., Huang, H., Regev, A. and Struhl, K. (2016). Transcriptome-scale RNase-footprinting of RNA-protein complexes. Nature Biotechnology, 34 (4), 410-413.

Ji, Z.*, Song, R.*, Regev, A. and Struhl, K. (2015). Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins. eLife, 4: e08890.

Rotem, A., Janzer, A., Izar, B., Ji, Z., Doench J.G., Garraway L.A., and Struhl, K. (2015). An alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation. Proc Natl Acad Sci U S A, 112, 5708-5713.

Luo, W.*, Ji, Z.*, Pan, Z.*, You B., Hoque, M., Li, W., Gunderson, S., and Tian, B. (2013). The conserved intronic cleavage and polyadenylation site of CstF-77 gene imparts control of 3’ end processing by feedback autoregulation and U1 snRNP. PLoS Genetics 9, e1003613.

Hoque, M.*, Ji, Z.*, Zheng, D., Luo, W., Li, W., You, B., Park, J.Y., Yehia, G., and Tian, B. (2013). Analysis of alternative cleavage and polyadenylation by 3’ region extraction and deep sequencing. Nature Methods 10, 133-139.

Haenni, S.*, Ji, Z.*, Hoque, M., Rust, N., Sharpe, H., Eberhard, R., Browne, C., Hengartner, M.O., Mellor, J., McGhee, J., Tian, B. and Furger, A. (2012). Analysis of C. elegans intestinal nuclear gene expression using fluorescence-activated nuclei sorting and 3’ end-seq. Nucleic Acids Research 40, 6304-6318.

Ji, Z.*, Luo, W.*, Li, W., Hoque, M., Pan, Z., Zhao, Y., and Tian, B. (2011). Transcriptional activity regulates alternative cleavage and polyadenylation. Molecular Systems Biology 7, 534.

Ji, Z., and Tian, B. (2009). Reprogramming of 3’ untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One 4, e8419.

Ji, Z.*, Lee, J.Y.*, Pan, Z.*, Jiang, B. and Tian, B. (2009). Progressive lengthening of 3’ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106, 7028-7033.


Tian, B., Luo, W., Ji, Z., and Hoque, M., Methods of isolating RNA and mapping of polyadenylation isoforms, WO Patent 2,013,028,902, 2013