Year |
Citation |
Score |
2023 |
Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee HRL, Tang X, He W, Islam N, Jain A, Chiu Y, ... ... Chen Y, et al. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nature Structural & Molecular Biology. PMID 37932451 DOI: 10.1038/s41594-023-01117-1 |
0.512 |
|
2023 |
Zhang L, He W, Fu R, Wang S, Chen Y, Xu H. Guide-specific loss of efficiency and off-target reduction with Cas9 variants. Nucleic Acids Research. PMID 37615574 DOI: 10.1093/nar/gkad702 |
0.394 |
|
2023 |
Zheng C, Wei Y, Zhang Q, Sun M, Wang Y, Hou J, Zhang P, Lv X, Su D, Jiang Y, Gumin J, Sahni N, Hu B, Wang W, Chen X, ... ... Chen Y, et al. Multiomics analyses reveal /YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Science Advances. 9: eadf3984. PMID 37540752 DOI: 10.1126/sciadv.adf3984 |
0.459 |
|
2023 |
Zheng C, Wei Y, Zhang P, Xu L, Zhang Z, Lin K, Hou J, Lv X, Ding Y, Chiu Y, Jain A, Islam N, Malovannaya A, Wu Y, Ding F, ... Chen Y, et al. CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer. The Journal of Clinical Investigation. 133. PMID 36856111 DOI: 10.1172/JCI159940 |
0.533 |
|
2022 |
Fu R, He W, Dou J, Villarreal OD, Bedford E, Wang H, Hou C, Zhang L, Wang Y, Ma D, Chen Y, Gao X, Depken M, Xu H. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Nature Communications. 13: 474. PMID 35078987 DOI: 10.1038/s41467-022-28028-x |
0.412 |
|
2021 |
Sun M, Wang Y, Zheng C, Wei Y, Hou J, Zhang P, He W, Lv X, Ding Y, Liang H, Hon CC, Chen X, Xu H, Chen Y. Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biology. 22: 240. PMID 34425866 DOI: 10.1186/s13059-021-02464-2 |
0.423 |
|
2021 |
He W, Wang H, Wei Y, Jiang Z, Tang Y, Chen Y, Xu H. GuidePro: A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. Bioinformatics (Oxford, England). PMID 33394026 DOI: 10.1093/bioinformatics/btaa1068 |
0.394 |
|
2019 |
Zi Z, Zhang Y, Zhang P, Ding Q, Chu M, Chen Y, Minna JD, Yu Y. A Proteomic Connectivity Map for Characterizing the Tumor Adaptive Response to Small Molecule Chemical Perturbagens. Acs Chemical Biology. PMID 31846293 DOI: 10.1021/Acschembio.9B00694 |
0.337 |
|
2018 |
Nguyen TM, Kabotyanski EB, Dou Y, Reineke LC, Zhang P, Zhang XH, Malovannaya A, Jung SY, Mo Q, Roarty KP, Chen Y, Zhang B, Neilson JR, Lloyd RE, Perou CM, et al. FGFR1-activated Translation of WNT Pathway Components with Structured 5' UTRs is Vulnerable to Inhibition of EIF4A-dependent Translation Initiation. Cancer Research. PMID 29844125 DOI: 10.1158/0008-5472.Can-18-0631 |
0.36 |
|
2018 |
Zhao N, Cao J, Xu L, Tang Q, Dobrolecki LE, Lv X, Talukdar M, Lu Y, Wang X, Hu DZ, Shi Q, Xiang Y, Wang Y, Liu X, Bu W, ... ... Chen Y, et al. Pharmacological targeting of MYC-regulated IRE1/XBP1 pathway suppresses MYC-driven breast cancer. The Journal of Clinical Investigation. PMID 29480818 DOI: 10.1172/Jci95873 |
0.411 |
|
2018 |
Bao X, Guo X, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan MJ, Zhu X, Luo Z, ... ... Chen Y, et al. Capturing the interactome of newly transcribed RNA. Nature Methods. PMID 29431736 DOI: 10.1038/Nmeth.4595 |
0.308 |
|
2017 |
Zhang P, He D, Xu Y, Hou J, Pan BF, Wang Y, Liu T, Davis CM, Ehli EA, Tan L, Zhou F, Hu J, Yu Y, Chen X, Nguyen TM, ... ... Chen Y, et al. Genome-wide identification and differential analysis of translational initiation. Nature Communications. 8: 1749. PMID 29170441 DOI: 10.1038/S41467-017-01981-8 |
0.411 |
|
2017 |
Fei T, Chen Y, Xiao T, Li W, Cato L, Zhang P, Cotter MB, Bowden M, Lis RT, Zhao SG, Wu Q, Feng FY, Loda M, He HH, Liu XS, et al. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proceedings of the National Academy of Sciences of the United States of America. PMID 28611215 DOI: 10.1073/Pnas.1617467114 |
0.622 |
|
2017 |
Li MJ, Zhang J, Liang Q, Xuan C, Wu J, Jiang P, Li W, Zhu Y, Wang P, Fernandez D, Shen Y, Chen Y, Kocher JA, Yu Y, Sham PC, et al. Exploring genetic associations with ceRNA regulation in the human genome. Nucleic Acids Research. PMID 28472449 DOI: 10.1093/Nar/Gkx331 |
0.599 |
|
2017 |
Nguyen TM, Kabotyanski EB, Reineke LC, Mo Q, Zhang P, Zhang X, Chen Y, Neilson J, Lloyd RE, Rosen JM. Abstract A03: FGF-WNT cooperativity and the role of lncRNAs in translational regulation in breast cancer Cancer Research. 77. DOI: 10.1158/1538-7445.Transcontrol16-A03 |
0.412 |
|
2016 |
T L, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang TH, Kim HM, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA. Addendum: REST and stress resistance in ageing and Alzheimer's disease. Nature. PMID 27851730 DOI: 10.1038/Nature20579 |
0.48 |
|
2016 |
Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, et al. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. Bmc Bioinformatics. 17: 404. PMID 27716038 DOI: 10.1186/S12859-016-1274-4 |
0.636 |
|
2016 |
Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nature Communications. 7: 10982. PMID 26975529 DOI: 10.1038/Ncomms10982 |
0.628 |
|
2016 |
Wang Y, Hou J, He D, Sun M, Zhang P, Yu Y, Chen Y. The Emerging Function and Mechanism of ceRNAs in Cancer. Trends in Genetics : Tig. PMID 26922301 DOI: 10.1016/J.Tig.2016.02.001 |
0.431 |
|
2016 |
Fei T, Chen Y, Brown M, Liu XS. Abstract IA11: Dependency of prostate cancer on HNRNPL and its associated RNAs Cancer Research. 76. DOI: 10.1158/1538-7445.Nonrna15-Ia11 |
0.35 |
|
2016 |
Fei T, Chen Y, Liu XS, Brown M. Abstract A22: Functional long noncoding RNAs in castration-resistant prostate cancer Cancer Research. 76. DOI: 10.1158/1538-7445.Nonrna15-A22 |
0.41 |
|
2015 |
Xu H, Xu K, He HH, Zang C, Chen CH, Chen Y, Qin Q, Wang S, Wang C, Hu S, Li F, Long H, Brown M, Liu XS. Integrative analysis reveals the transcriptional collaboration between EZH2 and E2F1 in the regulation of cancer-related gene expression. Molecular Cancer Research : McR. PMID 26659825 DOI: 10.1158/1541-7786.Mcr-15-0313 |
0.725 |
|
2015 |
Sun T, Du Z, Fei T, Brown M, Lee GM, Chen Y, Liu XS, Kantoff PW. Long non-coding RNA-mediated PTEN regulation in prostate cancer. Journal of Clinical Oncology. 33: e16081-e16081. DOI: 10.1200/Jco.2015.33.15_Suppl.E16081 |
0.623 |
|
2014 |
Hsieh CL, Fei T, Chen Y, Li T, Gao Y, Wang X, Sun T, Sweeney CJ, Lee GS, Chen S, Balk SP, Liu XS, Brown M, Kantoff PW. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proceedings of the National Academy of Sciences of the United States of America. 111: 7319-24. PMID 24778216 DOI: 10.1073/Pnas.1324151111 |
0.599 |
|
2014 |
Lu T, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang TH, Kim HM, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA. REST and stress resistance in ageing and Alzheimer's disease. Nature. 507: 448-54. PMID 24670762 DOI: 10.1038/Nature13163 |
0.531 |
|
2014 |
Chen X, Iliopoulos D, Zhang Q, Tang Q, Greenblatt MB, Hatziapostolou M, Lim E, Tam WL, Ni M, Chen Y, Mai J, Shen H, Hu DZ, Adoro S, Hu B, et al. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway. Nature. 508: 103-7. PMID 24670641 DOI: 10.1038/Nature13119 |
0.594 |
|
2014 |
Fei T, Chen Y, Du Z, Liu XS, Brown M. Abstract 5238: Integrative analysis of functional long noncoding RNAs during prostate cancer progression Cancer Research. 74: 5238-5238. DOI: 10.1158/1538-7445.Am2014-5238 |
0.419 |
|
2013 |
Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Chen Y, Liu XS. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nature Structural & Molecular Biology. 20: 908-13. PMID 23728290 DOI: 10.1038/Nsmb.2591 |
0.607 |
|
2013 |
Ni M, Chen Y, Fei T, Li D, Lim E, Liu XS, Brown M. Amplitude modulation of androgen signaling by c-MYC. Genes & Development. 27: 734-48. PMID 23530127 DOI: 10.1101/Gad.209569.112 |
0.593 |
|
2012 |
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111 |
0.399 |
|
2012 |
Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods. 9: 609-14. PMID 22522655 DOI: 10.1038/Nmeth.1985 |
0.587 |
|
2011 |
Tang Q, Chen Y, Meyer C, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M, Liu XS. A comprehensive view of nuclear receptor cancer cistromes. Cancer Research. 71: 6940-7. PMID 21940749 DOI: 10.1158/0008-5472.Can-11-2091 |
0.621 |
|
2011 |
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology. 12: R83. PMID 21859476 DOI: 10.1186/Gb-2011-12-8-R83 |
0.599 |
|
2011 |
Ni M, Chen Y, Lim E, Wimberly H, Bailey ST, Imai Y, Rimm DL, Liu XS, Brown M. Targeting androgen receptor in estrogen receptor-negative breast cancer. Cancer Cell. 20: 119-31. PMID 21741601 DOI: 10.1016/J.Ccr.2011.05.026 |
0.556 |
|
2011 |
Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS. MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biology. 12: R11. PMID 21284836 DOI: 10.1186/Gb-2011-12-2-R11 |
0.586 |
|
2011 |
Ni M, Chen Y, Bailey ST, Imai Y, Liu XS, Brown M. Abstract 941: Targeting androgen receptor in estrogen receptor-negative breast cancer Cancer Research. 71: 941-941. DOI: 10.1158/1538-7445.Am2011-941 |
0.358 |
|
2006 |
Chen Y, Dokholyan NV. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends in Genetics : Tig. 22: 416-9. PMID 16797778 DOI: 10.1016/J.Tig.2006.06.008 |
0.306 |
|
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