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Xiang Chen Lab: Publications

2015

  • Aldiri I, Ajioka I, Xu B, Zhang J, Chen X, Benavente, Finkelstein D, Johnson D, Akiyama J, Pennacchio L, Dyer M. Brg1 Coordinates Multiple Processes During Retinogenesis and is a Tumor Suppressor in Retinoblastoma. Development 2015 Dec 1;142(23):4092-106. Doi:10.1242/dev. 124800. PMID: 26628093. PMCID: PMC4712833

  • Stewart E, Shelat A, Bradley C, Chen X, Federico S, Thiagarajan S, Shirinifard A, Bahrami A, Pappo A, Qu C, Finkelstein D, Sablauer A, Dyer D. Development and characterization of a human orthotopic neuroblastoma xenograft. Developmental Biology 2015Nov 15;407(2):344-55. Doi:1016/j.ydbio.2015.02.002 PMID: 25863122

  • 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

2014

  • 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

  • Tirode F, Surdez D, Ma X, Parker M, Le Deley MC, Bahrami A, Zhang Z, Lapouble E, Grossetête-Lalami S, Rusch M, Reynaud S, Rio-Frio T, Hedlund E, Wu G, Chen X, Pierron G, Oberlin O, Zaidi S, Lemmon G, Gupta P, Vadodaria B, Easton J, Gut M, Ding L, Mardis ER, Wilson RK, Shurtleff S, Laurence V, Michon J, Marec-Bérard P, Gut I, Downing J, Dyer M, Zhang J, Delattre O. Genomic Landscape of Ewing Sarcoma Defines an Aggressive Subtype with Co-Association of STAG2 and TP53 Mutations. Cancer Discov 4(11):1342–1353, 2014. doi: 10.1158/2159-8290.CD-14-0622.Epub 2014 Sep 15. PMID: 25223734. PMCID: PMC4264969

  • Roberts KG, Li Y, Payne-Turner D, Harvey RC, Yang YL, Pei D, McCastlain K, Ding L, Lu C, Song G, Ma J, Becksfort J, Rusch M, Chen SC, Easton J, Cheng J, Boggs K, Santiago-Morales N, Iacobucci I, Fulton RS, Wen J, Valentine M, Cheng C, Paugh SW, Devidas M, Chen IM, Reshmi S, Smith A, Hedlund E, Gupta P, Nagahawatte P, Wu G, Chen X, Yergeau D, Vadodaria B, Mulder H, Winick NJ, Larsen EC, Carroll WL, Heerema NA, Carroll AJ, Grayson G, Tasian SK, Moore AS, Keller F, Frei-Jones M, Whitlock JA, Raetz EA, White DL, Hughes TP, Guidry Auvil JM, Smith MA, Marcucci G, Bloomfield CD, Mrózek K, Kohlschmidt J, Stock W, Kornblau SM, Konopleva M, Paietta E, Pui CH, Jeha S, Relling MV, Evans WE, Gerhard DS, Gastier-Foster JM, Mardis E, Wilson RK, Loh ML, Downing JR, Hunger SP, Willman CL, Zhang J, Mullighan CG. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med Sep 11;371(11):1005-15, 2014. doi: 10.1056/NEJMoa1403088. PMID: 25207766. PMCID: PMC4191900

  • Wu G, Diaz AK, Paugh BS, Rankin SL, Ju B, Li Y, Zhu X, Qu C, Chen X, Zhang J, Easton J, Edmonson M, Ma X, Lu C, Nagahawatte P, Hedlund E, Rusch M, Pounds S, Lin T, Onar-Thomas A, Huether R, Kriwacki R, Parker M, Gupta P, Becksfort J, Wei L, Mulder HL, Boggs K, Vadodaria B, Yergeau D, Russell JC, Ochoa K, Fulton RS, Fulton LL, Jones C, Boop FA, Broniscer A, Wetmore C, Gajjar A, Ding L, Mardis ER, Wilson RK, Taylor MR, Downing JR, Ellison DW, Zhang J, Baker SJ. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet May;46(5):444-50, 2014. doi: 10.1038/ng.2938. Epub 2014 Apr 6. PMID: 24705251. PMCID: PMC4056452

  • 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

  • Parker M, Mohankumar KM, Punchihewa C, Weinlich R, Dalton JD, Li Y, Lee R, Tatevossian RG, Phoenix TN, Thiruvenkatam R, White E, Tang B, Orisme W, Gupta K, Rusch M, Chen X, Li Y, Nagahawhatte P, Hedlund E, Finkelstein D, Wu G, Shurtleff S, Easton J, Boggs K, Yergeau D, Vadodaria B, Mulder HL, Becksford J, Gupta P, Huether R, Ma J, Song G, Gajjar A, Merchant T, Boop F, Smith AA, Ding L, Lu C, Ochoa K, Zhao D, Fulton RS, Fulton LL, Mardis ER, Wilson RK, Downing JR, Green DR, Zhang J, Ellison DW, Gilbertson RJ. C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma. Nature Feb 27;506(7489):451-5, 2014. doi: 10.1038/nature13109. Epub 2014 Feb 19. PMID: 24553141. PMCID: PMC4050669

  • McEvoy J, Nagahawatte P, Finkelstein D, Richards-Yutz J, Valentine M, Ma J, Mullighan C, Song G, Chen X, Wilson M, Brennan R, Pounds S, Becksfort J, Huether R, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Mardis ER, Wilson RK, Easton J, Zhang J, Downing JR, Ganguly A, Dyer MA. RB1 gene inactivation by chromothripsis in human retinoblastoma. Oncotarget Jan 30;5(2):438-50, 2014. PMID: 24509483. PMCID: PMC3964219

2013

  • 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

  • Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet Jun;45(6):602-12, 2013. doi: 10.1038/ng.2611. Epub 2013 Apr 14. PMID: 23583981 PMCID: PMC3727232

  • Holmfeldt L, Wei L, Diaz-Flores E, Walsh M, Zhang J, Ding L, Payne-Turner D, Churchman M, Andersson A, Chen SC, McCastlain K, Becksfort J, Ma J, Wu G, Patel SN, Heatley SL, Phillips LA, Song G, Easton J, Parker M, Chen X, Rusch M, Boggs K, Vadodaria B, Hedlund E, Drenberg C, Baker S, Pei D, Cheng C, Huether R, Lu C, Fulton RS, Fulton LL, Tabib Y, Dooling DJ, Ochoa K, Minden M, Lewis ID, To LB, Marlton P, Roberts AW, Raca G, Stock W, Neale G, Drexler HG, Dickins RA, Ellison DW, Shurtleff SA, Pui CH, Ribeiro RC, Devidas M, Carroll AJ, Heerema NA, Wood B, Borowitz MJ, Gastier-Foster JM, Raimondi SC, Mardis ER, Wilson RK, Downing JR, Hunger SP, Loh ML, Mullighan CG. The genetic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet Mar;45(3):242-52, 2013. doi: 10.1038/ng.2532. Epub 2013 Jan 20. PMID: 23334668. PMCID: PMC3919793

2012

  • 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

  • Roberts KG, Morin R, Zhang J, Hirst M, Zhao Y, Su X, Chen S, Payne-Turner D, Churchman M, Chen X, Harvey R, Kasap C, Yan C, Becksfort J, Finney R, Teachey D, Maude S, Tse K, Moore R, Jones S, Mungall K, Birol I, Edmonson M, Hu Y, Buetow K, Chen IM, Carol W, Wei L, Ma J, Kleppe M, Levine R, Garcia-Manero G; Larsen E, Shah N, Devidas M, Reaman G, Smith M, Paugh S, Evans W, Grupp S, Jeha S, Pui CH, Gerhard D, Downing J, Willman C, Loh M, Hunger S, Marra M, Mullighan CG. Genetic alterations activating kinase and cytokine receptor signaling in high risk acute lymphoblastic leukemia.  Cancer Cell Aug 14;22(2):153-66, 2012. doi: 10.1016/j.ccr.2012.06.005. PMID: 22897847. PMCID: PMC3422513

  • 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

  • Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature Jan 11;481(7380):157-63, 2012. doi: 10.1038/nature10725. PMID: 22237106.  PMCID: PMC3267575

2011

  • 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, Cho K, Singer BH, Zhang H. The nuclear transcription factor PKNOX2 is a candidate gene for substance dependence in European-origin women.  PLoS One Jan 27;6(1):e16002, 2011. doi: 10.1371/journal.pone.0016002. PMID: 21298047. PMCID: PMC3029286

  • Zhang J, Mullighan CG, Harvey RC, Wu G, Chen X, Edmonson M, Buetow KH, Carroll WL, Chen IM, Devidas M, Devidas M, Gerhard DS, Loh ML, Reaman GH, Relling MV, Camitta BM, Bowman WP, Smith MA, Willman CL, Downing JR, Hunger SP. Key pathways are frequently mutated in high risk childhood acute lymphoblastic leukemia: a report from the Children's Oncology Group. Blood Sep 15;118(11):3080-7, 2011. doi: 10.1182/blood-2011-03-341412. Epub 2011 Jun 16. PMID: 21680795. PMCID: PMC3175785