Xiang Chen, PhD
Xiang Chen, PhD

Xiang Chen, PhD

Assistant Member, St. Jude Faculty

Departments

Education

BS – Fu Dan University, Shanghai, China
MS – National University of Singapore, Singapore, Rep. of Singapore
MS – Carnegie Mellon University, Pittsburgh, Pennsylvania
PhD – Carnegie Mellon University, Pittsburgh, Pennsylvania
Postdoctoral Training – Yale University, New Haven, Connecticut

Research Interests

  • Algorithm development for assessing the interplays between genetic alterations and epigenetic deregulations
  • Functional consequences of complex genetic alterations in pediatric solid tumors
  • Novel biological discovery from high throughput screening

Selected Publications

Hiler D, Chen X, Hazen J, Kupriyanov S, Carroll PA, Qu C, Xu B, Johnson D, Griffiths L, Frase S, Rodriguez AR, Martin G, Zhang J, Jeon J, Fan Y, Finkelstein D, Eisenman RN, Baldwin K, Dyer MA. Quantification of Retinogenesis in 3D Cultures Reveals Epigenetic Memory and Higher Efficiency in iPSCs Derived from Rod Photoreceptors. Cell Stem Cell Jul 2;17(1):101-15, 2015. doi: 10.1016/j.stem.2015.05.015. PMID: 26140606

Chen X, Gupta P, Wang J, Nakitandwe J, Roberts K, Dalton JD, Parker M, Patel S, Holmfeldt L, Payne D, Easton J, Ma J, Rusch M, Wu G, Patel A, Baker SJ, Dyer MA, Shurtleff S, Espy S, Pounds S, Downing JR, Ellison DW, Mullighan CG, Zhang J. CONSERTING: integrating copy-number analysis with structural-variation detection. Nat Methods  Jun;12(6):527-30, 2015. doi: 10.1038/nmeth.3394. Epub 2015 May 4. PMID: 2593837. PMCID: PMC4591043.

Pinto EM, Chen X, Easton J, Finkelstein D, Liu Z, Pounds S, Rodriguez-Galindo C, Lund TC, Mardis ER, Wilson RK, Boggs K, Yergeau D, Cheng J, Mulder HL, Manne J, Jenkins J, Mastellaro MJ, Figueiredo BC, Dyer MA, Pappo A, Zhang J, Downing JR, Ribeiro RC, Zambetti GP. Genomic landscape of paediatric adrenocortical tumours. Nat Commun Mar 6;6:6302, 2015. doi: 10.1038/ncomms7302. PMID: 25743702. PMCID: PMC4352712

Andersson AK, Ma J, Wang J, Chen X, Gedman AL, Dang J, Nakitandwe J, Holmfeldt L, Parker M, Easton J, Huether R, Kriwacki R, Rusch M, Wu G, Li Y, Mulder H, Raimondi S, Pounds S, Kang G, Shi L, Becksfort J, Gupta P, Payne-Turner D, Vadodaria B, Boggs K, Yergeau D, Manne J, Song G, Edmonson M, Nagahawatte P, Wei L, Cheng C, Pei D, Sutton R, Venn NC, Chetcuti A, Rush A, Catchpoole D, Heldrup J, Fioretos T, Lu C, Ding L, Pui CH, Shurtleff S, Mullighan CG, Mardis ER, Wilson RK, Gruber TA, Zhang J, Downing JR; St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat Genet Apr;47(4):330-7, 2015. doi: 10.1038/ng.3230. Epub 2015 Mar 2. PMID: 25730765

Chen X, Pappo A, Dyer MA. Pediatric solid tumor genomics and developmental pliancy. Oncogene Feb 2, 2015. doi: 10.1038/onc.2014.474. PMID: 25639868

Chen X, Bahrami A, Pappo A, Easton J, Dalton J, Hedlund E, Ellison D, Shurtleff S, Wu G, Wei L, Parker M, Rusch M, Nagahawatte P, Wu J, Mao S, Boggs K, Mulder H, Yergeau D, Lu C, Ding L, Edmonson M, Qu C, Wang J, Li Y, Navid F, Daw NC, Mardis ER, Wilson RK, Downing JR, Zhang J, Dyer MA. Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Rep Apr 10;7(1):104-12, 2014. doi: 10.1016/j.celrep.2014.03.003. Epub 2014 Apr 3. PMID: 24703847. PMCID: PMC4096827

Huether R, Dong L, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun Apr 8;5:3630, 2014. doi: 10.1038/ncomms4630. PMID: 24710217. PMCID: PMC4119022

Chen X, Stewart E, Shelat A, Qu C, Bahrami A, Hatley M, Wu G, Bradley C, McEvoy J, Pappo A, Spunt S, Valentine M, Valentine V, Krafcik F, Lang W, Wierdl M, Tsurkan L, Tolleman V, Federico S, Morton C, Lu C, Ding L, Easton J, Rusch M, Nagahawatte P, Wang J, Parker M, Wei L, Hedlund E, Finkelstein D, Edmonson M, Shurtleff S, Boggs K, Mulder H, Yergeau D, Skapek S, Hawkins D, Ramirez N, Potter PM, Sandoval J, Davidoff AM, Mardis ER, Wilson RK, Zhang J, Downing JR, Dyer MA. Targeting oxidative stress in embryonal rhabdomyosarcoma. Cancer Cell Dec 9;24(6):710-24, 2013. doi: 10.1016/j.ccr.2013.11.002. PMID: 24332040. PMCID: PMC3904731

Parker M, Chen X, Bahrami A, Dalton J, Rusch M, Wu G, Easton J, Cheung NK, Dyer M, Mardis ER, Wilson RK, Mullighan C, Gilbertson R, Baker SJ, Zambetti G, Ellison DW, Downing JR, Zhang J. Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing. Genome Biol Dec 11;13(12):R113, 2012. doi: 10.1186/gb-2012-13-12-r113. PMID: 23232254. PMCID: PMC3580411

Robinson G, Parker M, Kranenburg TA, Lu C, Chen X, Ding L, Phoenix TN, Hedlund E, Wei L, Zhu X, Chalhoub N, Baker SJ, Huether R, Kriwacki R, Curley N, Thiruvenkatam R, Wang J, Wu G, Rusch M, Hong X, Beckford J, Gupta P, Ma J, Easton J, Vadodaria B, Pounds S, Zhao D, Gajjar A, Kawauchi D, Roussel MF, Finkelstein D, Elliso DW, Lau CC, Bouffet E, Hassall T, Gururangan S, Cohn R, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Mardis ER, Wilson RK, Downing JR, Zhang J, Gilbertson RJ. Novel mutations target distinct subgroups of medulloblastoma. Nature Aug 2;488(7409):43-8, 2012. doi: 10.1038/nature11213. PMID: 22722829. PMCID: PMC3412905

Cheung NV, Zhang J, Lu C, Parker M, Bahrami A, Tickoo SK, Heguy A, Pappo AS, Federico S, Dalton J, Cheung IY, Ding L, Fulton B, Wang J, Chen X, Becksfort J, Wu J, Billups CA, Ellison D, Mardis ER, Wilson RK, Downing JR, Dyer MA. Association of Age at Diagnosis and Genetic Mutations in Patients With Neuroblastoma. JAMA Mar 14;307(10):1062-71, 2012. doi: 10.1001/jama.2012.228. PMID: 22416102 [PubMed - indexed for MEDLINE] PMCID: PMC3527076

Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu G, Wilson M, Wang J, Brennan R, Rusch M, Manning AL, Ma J, Easton J, Shurtleff S, Mullighan C, Pounds S, Mukatira S, Gupta P, Neale G, Zhao D, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Naeve C, Dyson NJ, Mardis ER, Bahrami A, Ellison D, Wilson RK, Downing JR, Dyer MA. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature Jan 11;481(7381):329-34, 2012. doi: 10.1038/nature10733. PMID: 22237022. PMCID: PMC3289956

Chen X, Wang M, Zhang H. The use of classification trees for bioinformatics.  Wiley Interdiscip Rev Data Min Knowl Discov Jan;1(1):55-63, 2011. Epub 2011 Jan 6. PMID: 22523608 [PubMed] PMCID: PMC3329156

Chen X, Liu CT, Zhang M, Zhang H. A forest-based approach to identifying gene and gene–gene interactions.  Proc Natl Acad Sci U S A Dec 4;104(49):19199-203, 2007. Epub 2007 Nov 28. PMID: 18048322. PMCID: PMC2148267

Chen X, Velliste M, Murphy RF. Automated Interpretation of Subcellular Patterns in Fluorescence Microscope Images for Location Proteomics. Cytometry A Jul;69(7):631-40, 2006. PMID: 16752421. PMCID: PMC2901544

Last update: January 2016