Preprint
38. Stroup, E.K., and Ji, Z.$ (2024). Delineating yeast cleavage and polyadenylation signals using deep learning. bioRxiv, 2023.10.10.561764. (Under revision)
2024
37. Yang, H.*, Li, Q.*, Stroup, E.K., Wang, S., and Ji, Z.$ (2024). Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features. Nature Communications, 15, 1932. (Highlighted by Northwestern News).
2023
36. Stroup, E.K., and Ji, Z.$ (2023). Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease. Nature Communications, 14, 7378. (Highlighted by Northwestern News and IEEE Spectrum).
35. Li, Q., Stroup, E.K., and Ji, Z.$ (2023). Rfoot-seq: Transcriptomic RNase footprinting for mapping stable RNA-protein complexes and rapid ribosome profiling. Current Protocols, e761.
2022
34. Zhang, Y., Wang, G., Huang, P., Sun, E., Kweon, J., Li, Q., Ji, Z., Ying, L.L., and Zhang, H. (2022). Minimizing molecular misidentification in imaging low-abundance protein interactions using spectroscopic single-molecule localization microscopy. Analytical Chemistry, 94(40), 13834-13841.
33. 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.
32. 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. (2022). Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature Biotechnology, 40 (2), 209-217.
2021
31. Qadir, A.S., Guégan, J.P., Ginestier, C., Chaibi, A., Bessede, A., Charafe-Jauffret, E., Macario, M., Lavoué, V., Rouge, T.D.L.M., Law, C., Vilker, J., Wang, H., Stroup, E., Schipma, M.J., Bridgeman, B., Murmann, A.E., Ji, Z., Legembre, P. and Peter, M.E. (2021). CD95/Fas protects triple negative breast cancer from anti-tumor activity of NK cells. iScience, 24, 11, 103348.
30. Prensner, J.R., Enache, O.M., Luria, V., Krug, K., Clauser, K.R., Dempster, J.M., Karger, A., Wang, L., Stumbraite, K., Wang, V. M., 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). Noncanonical open reading frames encode functional proteins essential for cancer cell survival. Nature Biotechnology, 39, 694-704.
29. 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.
28. Yi, Y., Li Y., Meng, Q., Li, Q., Li, F., Lu, B., Shen, J., Fazli, L, Zhao, D., Li, C., Jiang, W., Wang, R., Liu, Q., Szczepanski A.P., Li Q., Qin W., Weiner A.B., Lotan, T., Ji, Z., Kalantry, S., Wang, L., Schaeffer, E.M., Niu, H., Dong, X., Zhao, W., Chen, K., and Cao, Q. A PRC2-independent function for EZH2 in regulating rRNA 2′-O methylation and IRES-dependent translation. Nature Cell Biology, 23, 341-354.
27. Dhar, P., Basher, F., Ji, Z., Huang, L., Qin, S., Wainwright, D.A., Robinson, J., Hagler, S., Zhou, J., MacKay, S., and Wu, J.D. (2021) Tumor-derived NKG2D ligand sMIC reprograms NK cells to an inflammatory phenotype through CBM signalosome activation. Communications Biology, 4, 905.
2020
26. Chan, C.S.K., Lonfat, N., Zhao, R., Davis, A.E., Li, L., Wu, M.R., Lin, C.H., Ji, Z., Cepko, C.L., and Wang, S. (2020). Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina. Development, 147 (14), dev187922.
25. Basher, F., Dhar, P., Wang, X., Wainwright, D.A., Zhang, B., Sosman, J., Ji, Z., and Wu, J.D. (2020). Antibody targeting tumor-derived soluble NKG2D ligand sMIC reprograms NK cell homeostatic survival and function and enhances melanoma response to PDL1 blockade therapy. J Hematol Oncol, 13, 74.
2019
24. 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.
2018
23. Ji, Z. (2018). RibORF: Identifying genome-wide translated open reading frames using ribosome profiling. Current Protocols in Molecular Biology, e67.
22. Ji, Z. (2018). Rfoot: Transcriptome-scale identification of RNA-protein complexes from ribosome profiling data. Current Protocols in Molecular Biology, e66.
21. 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.
20. 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.
2017
19. 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.
18. Li, W.*, Li, W.*, Laishram, R.S., Hoque, M., Ji, Z., Tian, B.$ and Anderson, R.A.$ (2017). Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases. Nucleic Acids Research, 45(15):8930-8942.
2016
17. 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.
16. 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. (Commented by PNAS, “ORChestrating the human DNA replication program”; Recommended by Faculty of 1000)
15. 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. (Highlighted by Nature Methods, “RNase footprints re-examined”; Recommended by Faculty of 1000)
2015
14. 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. (Commented by Hepatology)
13. 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.
12. Li, W., You, B., Hoque, M., Luo, W., Park. J.Y., Ji, Z., Zheng, D., Gunderson, S.I., Kalsotra, A., Manley, J.L., and Tian, B. (2015). Systematic profiling of poly(A)+ transcripts modulated by core 3′ end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genetics 11, e1005166.
11. Jin, Y., Geisberg, J.V., Moqtaderi, Z., Ji, Z., Hoque, M., Tian, B., and Struhl, K. (2015). Mapping 3′ mRNA isoforms on a genomic scale. Curr Protoc Mol Biol 110, 4.23.1-4.23.17.
2013
10. 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.
9. 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.
2012
8. Li, W., Yeh, H.J., Shankarling, G.S., Ji, Z., Tian, B., and Macdonald, C.C. (2012). The tauCstF-64 polyadenylation protein controls genome expression in testis. PLoS One 7, e48373.
7. Henriques, T., Ji, Z., Tan-Wong, S.M., Carmo, A.M., Tian, B., Proudfoot, N.J., and Moreira, A. (2012). Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster. Transcription 3, 198-212.
6. 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.
5. Li, W.*, Laishram, R.S.*, Ji, Z., Barlow, C.A., Tian, B., and Anderson, R.A. (2012). Star-PAP control of BIK expression and apoptosis is regulated by nuclear PIPKIalpha and PKCdelta signaling. Molecular Cell 45, 25-37.
2011
4. 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. (Published as a featured article)
2009
3. 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.
2. 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. (Highlighted by Nature Review Genetics, Commented by Nature Journal Club)
2008
1. Lee, J.Y., Ji, Z., and Tian, B. (2008). Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes. Nucleic Acids Research 36, 5581-5590.
*equal contribution; $Corresponding authors.