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Yiwen Chen - Publications

Affiliations: 
Bioinformatics & Comp Biology The University of Texas MD Anderson Cancer Center 
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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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