Yiwen Chen, PhD
Department of Bioinformatics and Computational Biology, Division of VP, Research
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 mechanism of RNA-mediated pathogenesis in cancer with a focus on the 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
RNA-based 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
- 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.
Grant & Contract Support
| Title: | An Integrated Approach to Dissect the Functional Network of Large Non-coding RNA |
| Funding Source: | NIH/NCI |
| Role: | Principal Investigator |
| Title: | Activating PPARβ/QKI signaling in macrophage/microglia to sensitize brain cancer to immunotherapy |
| Funding Source: | NIH/NCI |
| Role: | Advisor |