| Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development Z Ji, JY Lee, Z Pan, B Jiang, B Tian Proceedings of the National Academy of Sciences 106 (17), 7028-7033, 2009 | 674 | 2009 |
| Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins Z Ji, R Song, A Regev, K Struhl eLife 4, e08890, 2015 | 556 | 2015 |
| Analysis of alternative cleavage and polyadenylation by 3 [prime] region extraction and deep sequencing M Hoque, Z Ji, D Zheng, W Luo, W Li, B You, JY Park, G Yehia, B Tian Nature methods 10 (2), 133-139, 2013 | 502 | 2013 |
| Reprogramming of 3′ untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types Z Ji, B Tian PloS one 4 (12), e8419, 2009 | 331 | 2009 |
| Systematic profiling of poly (A)+ transcripts modulated by core 3’end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation W Li, B You, M Hoque, D Zheng, W Luo, Z Ji, JY Park, SI Gunderson, ... PLoS genetics 11 (4), e1005166, 2015 | 272 | 2015 |
| Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer T Ouspenskaia, T Law, KR Clauser, S Klaeger, S Sarkizova, F Aguet, B Li, ... Nature biotechnology 40 (2), 209-217, 2022 | 237 | 2022 |
| Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers Z Ji, L He, A Regev, K Struhl Proceedings of the National Academy of Sciences 116 (19), 9453-9462, 2019 | 218 | 2019 |
| Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers B Miotto, Z Ji, K Struhl Proceedings of the National Academy of Sciences 113 (33), E4810-E4819, 2016 | 200 | 2016 |
| Transcriptional activity regulates alternative cleavage and polyadenylation Z Ji, W Luo, W Li, M Hoque, Z Pan, Y Zhao, B Tian Molecular systems biology 7 (1), 2011 | 150 | 2011 |
| Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes JY Lee, Z Ji, B Tian Nucleic acids research 36 (17), 5581-5590, 2008 | 143 | 2008 |
| Alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation A Rotem, A Janzer, B Izar, Z Ji, JG Doench, LA Garraway, K Struhl Proceedings of the National Academy of Sciences 112 (18), 5708-5713, 2015 | 135 | 2015 |
| Noncanonical open reading frames encode functional proteins essential for cancer cell survival JR Prensner, OM Enache, V Luria, K Krug, KR Clauser, JM Dempster, ... Nature biotechnology 39 (6), 697-704, 2021 | 134 | 2021 |
| Genome-wide identification and differential analysis of translational initiation P Zhang, D He, Y Xu, J Hou, BF Pan, Y Wang, T Liu, CM Davis, EA Ehli, ... Nature communications 8 (1), 1-14, 2017 | 131 | 2017 |
| Comprehensive comparative analysis of 5′-end RNA-sequencing methods X Adiconis, AL Haber, SK Simmons, A Levy Moonshine, Z Ji, MA Busby, ... Nature methods 15 (7), 505-511, 2018 | 117 | 2018 |
| A PRC2-independent function for EZH2 in regulating rRNA 2′-O methylation and IRES-dependent translation Y Yi, Y Li, Q Meng, Q Li, F Li, B Lu, J Shen, L Fazli, D Zhao, C Li, W Jiang, ... Nature cell biology 23 (4), 341-354, 2021 | 87 | 2021 |
| Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3′-end-seq S Haenni, Z Ji, M Hoque, N Rust, H Sharpe, R Eberhard, C Browne, ... Nucleic acids research 40 (13), 6304-6318, 2012 | 87 | 2012 |
| Star-PAP control of BIK expression and apoptosis is regulated by nuclear PIPKIα and PKCδ signaling W Li, RS Laishram, Z Ji, CA Barlow, B Tian, RA Anderson Molecular cell 45 (1), 25-37, 2012 | 71 | 2012 |
| The conserved intronic cleavage and polyadenylation site of CstF-77 gene imparts control of 3′ end processing activity through feedback autoregulation and by U1 snRNP W Luo, Z Ji, Z Pan, B You, M Hoque, W Li, SI Gunderson, B Tian PLoS genetics 9 (7), e1003613, 2013 | 61 | 2013 |
| Transcriptome-scale RNase-footprinting of RNA-protein complexes Z Ji, R Song, H Huang, A Regev, K Struhl Nature biotechnology 34 (4), 410-413, 2016 | 60 | 2016 |
| RibORF: Identifying Genome‐Wide Translated Open Reading Frames Using Ribosome Profiling Z Ji Current protocols in molecular biology 124 (1), e67, 2018 | 50 | 2018 |