Yiwen Chen, PhD

Peer-Reviewed Articles

1. Xu L, Peng F, Luo Q, Ding Y, Yuan F, Zheng L, He W, Zhang SS, Fu X, Liu J, Mutlu AS, Wang S, Nehring RB, Li X, Tang Q, Li C, Lv X, Dobrolecki LE, Zhang W, Han D, Zhao N, Jaehnig E, Wang J, Wu W, Graham DA, Li Y, Chen R, Peng W, Chen Y, Catic A, Zhang Z, Zhang B, Mustoe AM, Koong AC, Miles G, Lewis MT, Wang MC, Rosenberg SM, O'Malley BW, Westbrook TF, Xu H, Zhang XH, Osborne CK, Li JB, Ellis MJ, Rimawi MF, Rosen JM, Chen X. IRE1alpha silences dsRNA to prevent taxane-induced pyroptosis in triple-negative breast cancer. Cell 187(25):7248-7266.e34, 2024. e-Pub 2024. PMID: 39419025.
2. Hou J, Wei Y, Zou J, Jaffery R, Sun L, Liang S, Zheng N, Guerrero AM, Egan NA, Bohat R, Chen S, Zheng C, Mao X, Yi SS, Chen K, McGrail DJ, Sahni N, Shi PY, Chen Y, Xie X, Peng W. Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection. Nat Commun 15(1):109, 2024. e-Pub 2024. PMID: 38168026.
3. 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, Cao S, Diao Y, Meyer-Gauen S, Höök M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz S, Chen Y. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nat Struct Mol Biol 30(12):1878-1892, 2023. e-Pub 2023. PMID: 37932451.
4. 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 Res 51(18):9880-9893, 2023. e-Pub 2023. PMID: 37615574.
5. Lv X, Lu X, Cao J, Luo Q, Ding Y, Peng F, Pataer A, Lu D, Han D, Malmberg E, Chan DW, Wang X, Savage SR, Mao S, Yu J, Peng F, Yan L, Meng H, Maneix L, Han Y, Chen Y, Yao W, Chang EC, Catic A, Lin X, Miles G, Huang P, Sun Z, Burt B, Wang H, Wang J, Yao QC, Zhang B, Roth JA, O'Malley BW, Ellis MJ, Rimawi MF, Ying H, Chen X. Modulation of the proteostasis network promotes tumor resistance to oncogenic KRAS inhibitors. Science 381(6662):eabn4180, 2023. e-Pub 2023. PMID: 37676964.
6. 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, McGrail DJ, Zhang C, Huang S, Xu H, Chen J, Lang FF, Hu J, Chen Y. Multiomics analyses reveal DARS1-AS1/YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Sci Adv 9(31):eadf3984, 2023. e-Pub 2023. PMID: 37540752.
7. 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, Xu H, Sun M, Chen X, Chen Y. CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer. J Clin Invest 133(5), 2023. e-Pub 2023. PMID: 36856111.
8. Hou J, Liang S, Xu C, Wei Y, Wang Y, Tan Y, Sahni N, McGrail DJ, Bernatchez C, Davies M, Li Y, Chen R, Yi SS, Chen Y, Yee C, Chen K, Peng W. Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors. NAR Cancer 4(4):zcac038, 2022. e-Pub 2022. PMID: 36518525.
9. Li L, Zhou A, Wei Y, Liu F, Li P, Fang R, Ma L, Zhang S, Wang L, Liu J, Richard HT, Chen Y, Wang H, Huang S. Critical Role of LncEPAT in Coupling Dysregulated EGFR Pathway and Histone H2A Deubiquitination during Glioblastoma Tumorigenesis. Sci Adv 8(40):eabn2571, 2022. e-Pub 2022. PMID: 36197973.
10. 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. Nat Commun 13(1):474, 2022. e-Pub 2022. PMID: 35078987.
11. 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 Biol 22(1):240, 2021. e-Pub 2021. PMID: 34425866.
12. Zhou X, Shin S, He C, Zhang Q, Rasband MN, Ren J, Dai C, Zorrilla-Veloz RI, Shingu T, Yuan L, Wang Y, Chen Y, Lan F, Hu J. Qki regulates myelinogenesis through Srebp2-dependent cholesterol biosynthesis. Elife 10, 2021. e-Pub 2021. PMID: 33942715.
13. Shin S, Zhou H, He C, Wei Y, Wang Y, Shingu T, Zeng A, Wang S, Zhou X, Li H, Zhang Q, Mo Q, Long J, Lan F, Chen Y, Hu J. Qki activates Srebp2-mediated cholesterol biosynthesis for maintenance of eye lens transparency. Nat Commun 12(1):3005, 2021. e-Pub 2021. PMID: 34021134.
14. 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 37(1):134-136, 2021. e-Pub 2021. PMID: 33394026.
15. Hou J, Wang Y, Shi L, Chen Y, Xu C, Saeedi A, Pan K, Bohat R, Egan NA, McKenzie JA, Mbofung RM, Williams LJ, Yang Z, Sun M, Liang X, Rodon Ahnert J, Varadarajan N, Yee C, Chen Y, Hwu P, Peng W. Integrating genome-wide CRISPR immune screen with multi-omic clinical data reveals distinct classes of tumor intrinsic immune regulators. J Immunother Cancer 9(2), 2021. e-Pub 2021. PMID: 33589527.
16. Ren J, Dai C, Zhou X, Barnes JA, Chen X, Wang Y, Yuan L, Shingu T, Heimberger AB, Chen Y, Hu J. Qki is an essential regulator of microglial phagocytosis in demyelination. J Exp Med 218(1), 2021. e-Pub 2021. PMID: 33045062.
17. Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Group MC, working group PNSMCM, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, Consortium P. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11(1):4748, 2020. e-Pub 2020. PMID: 32958763.
18. Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, Subtypes PT, Translation C, Boutros PC, Consortium P. Sex differences in oncogenic mutational processes. Nat Commun 11(1):4330, 2020. e-Pub 2020. PMID: 32859912.
19. Zhou X, He C, Ren J, Dai C, Stevens SR, Wang Q, Zamler D, Shingu T, Yuan L, Chandregowda CR, Wang Y, Ravikumar V, Rao AU, Zhou F, Zheng H, Rasband MN, Chen Y, Lan F, Heimberger AB, Segal BM, Hu J. Mature myelin maintenance requires Qki to coactivate PPARβ-RXRα-mediated lipid metabolism. J Clin Invest 130(5):2220-2236, 2020. e-Pub 2020. PMID: 32202512.
20. Genomes Consortium IPAOW. Pan-cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
21. 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 Biolology 15(1):140-150, 2020. e-Pub 2020. PMID: 31846293.
22. Ma L, Lin K, Chang G, Chen Y, Yue C, Guo Q, Zhang S, Jia Z, Huang TT, Zhou A, Huang S. Aberrant Activation of β-Catenin Signaling Drives Glioma Tumorigenesis via USP1-Mediated Stabilization of EZH2. Cancer Res 79(1):72-85, 2019. e-Pub 2019. PMID: 30425057.
23. 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, Ellis MJ, Rosen JM. FGFR1-Activated Translation of WNT Pathway Components with Structured 5' UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation. Cancer Res 78(15):4229-4240, 2018. e-Pub 2018. PMID: 29844125.
24. 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, Jiang Y, Li M, Gong Y, Sun Z, Ying H, Yuan B, Lin X, Feng XH, Hartig SM, Li F, Shen H, Chen Y, Han L, Zeng Q, Patterson JB, Kaipparettu BA, Putluri N, Sicheri F, Rosen JM, Lewis MT, Chen X. Pharmacological targeting of MYC-regulated IRE1/XBP1 pathway suppresses MYC-driven breast cancer. J Clin Invest 128(4):1283-1299, 2018. e-Pub 2018. PMID: 29480818.
25. 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, Shao C, Lim DH, Liu X, Li N, Wang W, He M, Liu YL, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang YG, Wang Y, Qin B, Anko ML, Hutchins AP, Sun H, Wang H, Fu XD, Zhang B, Esteban MA. Capturing the interactome of newly transcribed RNA. Nat Methods 15(3):213-220, 2018. e-Pub 2018. PMID: 29431736.
26. 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, Rosen JM, Hawke DH, Ji Z, Chen Y. Genome-wide identification and differential analysis of translational initiation. Nat Commun 8(1):1749, 2017. e-Pub 2017. PMID: 29170441.
27. 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, Brown M. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proc Natl Acad Sci U S A 114(26):E5207-E5215, 2017. e-Pub 2017. PMID: 28611215.
28. 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, Wang J, Liu JS, Liu XS. Exploring genetic associations with ceRNA regulation in the human genome. Nucleic Acids Res 45(10):5653-5665, 2017. e-Pub 2017. PMID: 28472449.
29. Shingu T, Ho AL, Yuan L, Zhou X, Dai C, Zheng S, Wang Q, Zhong Y, Chang Q, Horner JW, Liebelt BD, Yao Y, Hu B, Chen Y, Fuller GN, Verhaak RG, Heimberger AB, Hu J. Qki deficiency maintains stemness of glioma stem cells in suboptimal environment by downregulating endolysosomal degradation. Nat Genet 49(1), 2017. e-Pub 2017. PMID: 27841882.
30. Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Y# C, PW# K, XS# L. Integrative analyses reveal a long non-coding-RNA mediated sponge regulatory network in prostate cancer. Nat Commun 7:10982, 2016. e-Pub 2016. PMID: 26975529.
31. 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. Mol Cancer Res 14(2):163-72, 2016. e-Pub 2016. PMID: 26659825.
32. 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. Proc Natl Acad Sci U S A 111(20):7319-24, 2014. e-Pub 2014. PMID: 24778216.
33. 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, Song M, Tan C, Landis MD, Ferrari M, Shin SJ, Brown M, Chang JC, Liu XS, Glimcher LH. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway. Nature 508(7494):103-7, 2014. e-Pub 2014. PMID: 24670641.
34. 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(7493):448-54, 2014. e-Pub 2014. PMID: 24670762.
35. Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Y# C, XS# L. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol 20(7):908-13, 2013. e-Pub 2013. PMID: 23728290.
36. Ni M, Chen Y, Fei T, Li D, Lim E, Liu XS, Brown M. Amplitude modulation of androgen signaling by c-MYC. Genes Dev 27(7):734-48, 2013. e-Pub 2013. PMID: 23530127.
37. 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, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22(9):1813-31, 2012. e-Pub 2012. PMID: 22955991.
38. 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, Lieb JD, Liu XS. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods 9(6):609-14, 2012. e-Pub 2012. PMID: 22522655.
39. 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 Res 71(22):6940-7, 2011. e-Pub 2011. PMID: 21940749.
40. 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(1):119-31, 2011. e-Pub 2011. PMID: 21741601.
41. 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 Biol 12(2):R11, 2011. e-Pub 2011. PMID: 21284836.
42. 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, Turpaz Y, Liu XS. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 12(8):R83, 2011. e-Pub 2011. PMID: 21859476.
43. Petrotchenko EV, Xiao K, Cable J, Chen Y, Dokholyan NV, Borchers CH. BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics. Mol Cell Proteomics 8(2):273-86, 2009. e-Pub 2009. PMID: 18838738.
44. Chen Y, Dokholyan NV. Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. Mol Biol Evol 25(8):1530-3, 2008. e-Pub 2008. PMID: 18503047.
45. Chen Y, Ding F, Nie H, Serohijos AW, Sharma S, Wilcox KC, Yin S, Dokholyan NV. Protein folding: then and now. Arch Biochem Biophys 469(1):4-19, 2008. e-Pub 2008. PMID: 17585870.
46. Chen Y, Campbell SL, Dokholyan NV. Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys J 93(7):2300-6, 2007. e-Pub 2007. PMID: 17557784.
47. Chen Y, Ding F, Dokholyan NV. Fidelity of the protein structure reconstruction from inter-residue proximity constraints. J Phys Chem B 111(25):7432-8, 2007. e-Pub 2007. PMID: 17542631.
48. Serohijos AW, Chen Y, Ding F, Elston TC, Dokholyan NV. A structural model reveals energy transduction in dynein. Proc Natl Acad Sci U S A 103(49):18540-5, 2006. e-Pub 2006. PMID: 17121997.
49. Chen Y, Dokholyan NV. Insights into allosteric control of vinculin function from its large scale conformational dynamics. J Biol Chem 281(39):29148-54, 2006. e-Pub 2006. PMID: 16891659.
50. Chen Y, Dokholyan NV. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet 22(8):416-9, 2006. e-Pub 2006. PMID: 16797778.
51. Chen Y, Dokholyan NV. A single disulfide bond differentiates aggregation pathways of beta2-microglobulin. J Mol Biol 354(2):473-82, 2005. e-Pub 2005. PMID: 16242719.
52. Dixon RD, Chen Y, Ding F, Khare SD, Prutzman KC, Schaller MD, Campbell SL, Dokholyan NV. New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure 12(12):2161-71, 2004. e-Pub 2004. PMID: 15576030.

Invited Articles

1. Wang Y, Hou J, He D, Sun M, Zhang P, Yu Y, Chen Y. The Emerging Function and Mechanism of ceRNAs in Cancer. Trends Genet 32(4):211-24, 2016. e-Pub 2016. PMID: 26922301.

Review Articles

1. Loughran G, Andreev DE, Terenin IM, Namy O, Mikl M, Yordanova MM, McManus CJ, Firth AE, Atkins JF, Fraser CS, Ignatova Z, Iwasaki S, Kufel J, Larsson O, Leidel SA, Mankin AS, Mariotti M, Tanenbaum ME, Topisirovic I, Vazquez-Laslop N, Viero G, Caliskan N, Chen Y, Clark PL, Dinman JD, Farabaugh PJ, Gilbert WV, Ivanov P, Kieft JS, Muhlemann O, Sachs MS, Shatsky IN, Sonenberg N, Steckelberg AL, Willis AE, Woodside MT, Valasek LS, Dmitriev SE, Baranov PV. Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). Nat Struct Mol Biol 32(3):418-430, 2025. e-Pub 2025. PMID: 40033152.

Book Chapters

1. Du Z, Fei T, Brown M, Liu XS, Chen Y. Integrating omics data: statistical and computational methods. In: Data integration on non-coding RNA studies. Cambridge University Press, 2015.