Yiwen Chen, PhD
Department of Bioinformatics and Computational Biology, Division of Discovery Science
Present Title & Affiliation
Primary Appointment
Associate Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX
Research Interests
By utilizing integrative computational and multi-omic (genomic, epigenomic, transcriptomic, and proteomic) approaches, the long-term goal of my group is to decipher the cell signaling, epigenetic/epitranscriptomic and RNA-based regulation mechanism underlying pathogenesis in cancer with a focus on the signaling and RNA-based gene regulation in both tumor (e.g. cancer stem cells) and immune cells.
On the translational research side, my group aims at identifying RNAs that may serve as predictive biomarkers for both targeted- and immuno-therapy and developing targeted- and immuno-therapy for treating difficult-to-treat cancer types such as glioblastoma multiform (GBM),
non-small cell lung cancer (NSCLC) and triple negative breast cancer (TNBC).
Education & Training
Degree-Granting Education
| 2007 | University of North Carolina at Chapel Hill, Chapel Hill, NC, USA, PHD, Physics/Biophysics |
| 2000 | Fudan University, Shanghai, CHN, BS, Physics |
Postgraduate Training
| 2009-2015 | Research Fellowship, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA |
| 2007-2009 | Research Fellowship, Harvard Medical School, Boston, MA |
Experience & Service
Other Appointments/Responsibilities
Member, Quantitative Sciences program admissions sub-committee, Houston, TX, 2019 - Present
Regular Faculty Member, Graduate School of Biomedical Sciences, The University of Texas Health Sciences Center at Houston & The University of Texas MD Anderson Cancer Center, Houston, TX, 2017 - Present
Institutional Committee Activities
Member, Molecular Testing Evaluation Committee, 2018 - Present
Honors & Awards
| 2019 | Bristol-Myers Squibb - MRA Young Investigator Award in Immunotherapy, Melanoma Research Alliance |
| 2015 | Texas rising STAR award, The University of Texas System |
| 2014 | CPRIT Recruitment of First-Time Tenure-Track Faculty Members Award, CPRIT |
| 2013 | NIH (NCI) K99/R00 Pathway to Independence Award, NIH (NCI) |
Selected Publications
Peer-Reviewed Articles
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. PMID: 33589527.
- 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. e-Pub 2021. PMID: 33394026.
- 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. PMID: 33045062.
- 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. PMID: 32202512.
- ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
- 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.
- 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.
- 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.
- Fei T*, Chen Y*(co-first author), 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.
- 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 2016. PMID: 27841882.
- Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y#(co-corresponding author), Kantoff PW#, Liu XS#. 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.
- 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.
- 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.
- 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.
- Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Chen Y#(co-corresponding author), Liu XS#. 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.
- 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.
- 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. PMID: 22955991.
- 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.
- 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.
- Ni M*, Chen Y* (co-first author), 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. PMID: 21741601.
- 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.
- 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.
- 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 2008. PMID: 18838738.
- 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.
- 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.
- 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.
- 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.
- Dixon RD*, Chen Y*(co-first author), 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. PMID: 15576030.
Invited Articles
- 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.
Patient Reviews
CV information above last modified January 10, 2025