Selected Publications
Zhou X*, Wang J, Patel J, Valentine M, Shao Y, Newman S, Sioson E, Tian L, Liu Y, Brady SW, Flasch D, Ma X, Liu Y, Paul R, Edmonson MN, Rusch MC, Li C, Baker SJ, Easton J, Zhang J*. Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint. Cancer Cell Jan 11;39(1):83-95.e4, 2021. doi: 10.1016/j.ccell.2020.12.011. PMID: 33434514. (* Co-corresponding authors)
McLeod C, Gout AM, Zhou X, Thrasher A, Rahbarinia D, Brady SW, Macias M, Birch K, Finkelstein D, Sunny J, Mudunuri R, Orr BA, Treadway M, Davidson B, Ard TK, Chiao A, Swistak A, Wiggins S, Foy S, Wang J, Sioson E, Wang S, Michael JR, Liu Y, Ma X, Patel A, Edmonson MN, Wilkinson MR, Frantz AM, Chang TC, Tian L, Lei S, Islam SMA, Meyer C, Thangaraj N, Tater P, Kandali V, Ma S, Nguyen T, Serang OA, McGuire I, Robison N, Gentry D, Tang X, Palmer LE, Wu G, Suh E, Tanner L, McMurry J, Lear M, Pappo AS, Wang Z, Wilson CL, Cheng Y, Meshinchi S, Alexandrov LB, Weiss MJ, Armstrong GT, Robison LL, Yasui Y, Nichols KE, Ellison DW, Bangur C, Mullighan CG, Baker SJ, Dyer MA, Miller G, Newman S, Rusch M, Daly R, Perry K, Downing JR, Zhang J. St. Jude Cloud-a Pediatric Cancer Genomic Data Sharing Ecosystem. Cancer Discov Jan 6:CD-20-1230, 2021. doi: 10.1158/2159-8290.CD-20-1230. Epub ahead of print. PMID: 33408242.
Tian L, Li Y, Edmonson MN, Zhou X, Newman S, McLeod C, Thrasher A, Liu Y, Tang B, Rusch MC, Easton J, Ma J, Davis E, Trull A, Michael JR, Szlachta K, Mullighan C, Baker SJ, Downing JR, Ellison DW, Zhang J. CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data. Genome Biology 21:1-18, 2020.
Brady SW, Liu Y, Ma X, Gout AM, Hagiwara K, Zhou X, Wang J, Macias M, Chen X, Easton J, Mulder HL, Rusch M, Wang L, Nakitandwe J, Lei S, Davis EM, Naranjo A, Cheng C, Maris JM, Downing JR, Cheung NKV, Hogarty MD, Dyer MA, Zhang J. Pan-neuroblastoma analysis reveals age-and signature-associated driver alterations. Nature communications 11:1-13, 2020.
Qin N, Li Z, Song N, Wilson CL, Easton J, Mulder H, Plyler E, Neale G, Walker E, Zhou X, Pan H, Hudson MM, Yasui Y, Robison LL, Zhang J, Ness KK, Wang Z. Epigenetic Age Acceleration and Chronic Health Conditions among Adult Survivors of Childhood Cancer. JNCI: Journal of the National Cancer Institute May 4;113(5):597-605, 2021.
Waanders E, Gu Z, Dobson SM, Antić Ž, Crawford JC, Ma X, Edmonson MN, Payne-Turner D, van der Vorst M, Jongmans MCJ, McGuire I, Zhou X, Wang J, Shi L, Pounds S, Pei D, Cheng C, Song G, Fan Y, Shao Y, Rusch M, McCastlain K, Yu J, van Boxtel R, Blokzijl F, Iacobucci I, Roberts KG, Wen J, Wu G, Ma J, Easton J, Neale G, Olsen SR, Nichols KE, Pui C-H, Zhang J, Evans WE, Relling MV, Yang JJ, Thomas PG, Dick JE, Kuiper RP, Mullighan CG. Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia. Blood cancer discovery 1:96, 2020.
Zeineldin M, Federico S, Chen X, Fan Y, Xu B, Stewart E, Zhou X, Jeon J, Griffiths L, Nguyen R, Norrie J, Easton J, Mulder H, Yergeau D, Liu Y, Wu J, Van Ryn C, Naranjo A, Hogarty MD, Kamiński MM, Valentine M, Pruett-Miller SM, Pappo A, Zhang J, Clay MR, Bahrami A, Vogel P, Lee S, Shelat A, Sarthy JF, Meers MP, George RE, Mardis ER, Wilson RK, Henikoff S, Downing JR, Dyer MA. MYCN amplification and ATRX mutations are incompatible in neuroblastoma. Nature communications Feb 14;11(1):913, 2020.
Li B, Brady SW, Ma X, Shen S, Zhang Y, Li Y, Szlachta K, Dong L, Liu Y, Yang F, Wang N, Flasch DA, Myers MA, Mulder HL, Ding L, Liu Y, Tian L, Hagiwara K, Xu K, Zhou X, Sioson E, Wang T, Yang L, Zhao J, Zhang H, Shao Y, Sun H, Sun L, Cai J, Sun H-Y, Lin T-N, Du L, Li H, Rusch M, Edmonson MN, Easton J, Zhu X, Zhang J, Cheng C, Raphael BJ, Tang J, Downing JR, Alexandrov LB, Zhou B-BS, Pui C-H, Yang JJ, Zhang J. Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia. Blood 135:41-55, 2020.
Norrie JL, Lupo MS, Xu B, Al Diri I, Valentine M, Putnam D, Griffiths L, Zhang J, Johnson D, Easton J, Shao Y, Honnell V, Frase S, Miller S, Stewart V, Zhou X, Chen X, Dyer MA. Nucleome dynamics during retinal development. Neuron 104:512-528, 2019.
Edmonson MN, Patel AN, Hedges DJ, Wang Z, Rampersaud E, Kesserwan CA, Zhou X, Liu Y, Newman S, Rusch MC, McLeod CL, Wilkinson MR, Rice SV, Soussi T, Taylor JP, Benatar M, Becksfort JB, Nichols KE, Robison LL, Downing JR, Zhang J. Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants. Genome Research 29(9):1555-1565, 2019.
Tian L, Shao Y, Nance S, Dang J, Xu B, Ma X, Li Y, Ju B, Dong L, Newman S, Zhou X, Schreiner P, Tseng E, Hon T, Ashby M, Li C, Easton J, Gruber TA, Zhang J. Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia. Nature Communications 10(1):1-10, 2019.
Iacobucci I, Wen J, Meggendorfer M, Choi JK, Shi L, Pounds SB, Carmichael CL, Masih KE, Morris SM, Lindsley RC, Janke LJ, Alexander TB, Song G, Qu C, Li Y, Payne-Turner D, Tomizawa D, Kiyokawa N, Valentine M, Valentine V, Basso G, Locatelli F, Enemark EJ, Kham SKY, Yeoh AEJ, Ma X, Zhou X, Sioson E, Rusch M, Ries RE, Stieglitz E, Hunger SP, Wei AH, To LB, Lewis ID, D’Andrea RJ, Kile BT, Brown AL, Scott HS, Hahn CN, Marlton P, Pei D, Cheng C, Loh ML, Ebert BL, Meshinchi S, Haferlach T, Mullighan CG. Genomic subtyping and therapeutic targeting of acute erythroleukemia. Nature Genetics 51(4):694-704, 2019.
Newman S, Fan L, Pribnow A, Silkov A, Rice SV, Lee S, Shao Y, Shaner B, Mulder H, Nakitandwe J, Shurtleff S, Azzato EM, Wu G, Zhou X, Barnhill R, Easton J, Nichols KE, Ellison DW, Downing JR, Pappo A, Potter PM, Zhang J, Bahrami A. Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas. Nature Medicine 25(4):597-602, 2019.
Gu Z, Churchman ML, Roberts KG, Moore I, Zhou X, Nakitandwe J, Hagiwara K, Pelletier S, Gingras S, Berns H, Payne-Turner D, Hill A, Iacobucci I, Shi L, Pounds S, Cheng C, Pei D, Qu C, Newman S, Devidas M, Dai Y, Reshmi SC, Gastier-Foster J, Raetz EA, Borowitz MJ, Wood BL, Carroll WL, Zweidler-McKay PA, Rabin KR, Mattano LA, Maloney KW, Rambaldi A, Spinelli O, Radich JP, Minden MD, Rowe JM, Luger S, Litzow MR, Tallman MS, Racevskis J, Zhang Y, Bhatia R, Kohlschmidt J, Mrózek K, Bloomfield CD, Stock W, Kornblau S, Kantarjian HM, Konopleva M, Evans WE, Jeha S, Pui C-H, Yang J, Paietta E, Downing JR, Relling MV, Zhang J, Loh ML, Hunger SP, Mullighan CG. PAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia. Nature Genetics 51(2):296-307, 2019.
Wang Z, Wilson CL, Easton J, Thrasher A, Mulder H, Liu Q, Hedges DJ, Wang S, Rusch MC, Edmonson MN, Levy S, Lanctot JQ, Caron E, Shelton K, Currie K, Lear M, Patel A, Rosencrance C, Shao Y, Vadodaria B, Yergeau D, Sapkota Y, Brooke RJ, Moon W, Rampersaud E, Ma X, Chang T-C, Rice SV, Pepper C, Zhou X, Chen X, Chen W, Jones A, Boone B, Ehrhardt MJ, Krasin MJ, Howell RM, Phillips NS, Lewis C, Srivastava D, Pui C-H, Kesserwan CA, Wu G, Nichols KE, Downing JR, Hudson MM, Yasui Y, Robison LL, Zhang J. Genetic risk for subsequent neoplasms among long-term survivors of childhood cancer. Journal of Clinical Oncology 36(20):2078, 2018.
Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho J-H, Wang X, Xu B, Gupta P, Fan Y, Liu Y, Rusch M, Griffiths L, Jeon J, Freeman III BB, Clay MR, Pappo A, Easton J, Shurtleff S, Shelat A, Zhou X, Boggs K, Mulder H, Yergeau D, Bahrami A, Mardis ER, Wilson RK, Zhang J, Peng J, Downing JR, Dyer MA, St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project. Identification of therapeutic targets in rhabdomyosarcoma through integrated genomic, epigenomic, and proteomic analyses. Cancer Cell 34(3):411-426, 2018.
Waszak SM, Northcott PA, Buchhalter I, Robinson GW, Sutter C, Groebner S, Grund KB, Brugières L, Jones DTW, Pajtler KW, Morrissy AS, Kool M, Sturm D, Chavez L, Ernst A, Brabetz S, Hain M, Zichner T, Segura-Wang M, Weischenfeldt J, Rausch T, Mardin BR, Zhou X, Baciu C, Lawerenz C, Chan JA, Varlet P, Guerrini-Rousseau L, Fults DW, Grajkowska W, Hauser P, Jabado N, Ra Y-S, Zitterbart K, Shringarpure SS, De La Vega FM, Bustamante CD, Ng H-K, Perry A, MacDonald TJ, Driever PH, Bendel AE, Bowers DC, McCowage G, Chintagumpala MM, Cohn R, Hassall T, Fleischhack G, Eggen T, Wesenberg F, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Kjaerheim K, Monoranu CM, Archer TC, Duke E, Pomeroy SL, Shelagh R, Frank S, Sumerauer D, Scheurlen W, Ryzhova MV, Milde T, Kratz CP, Samuel D, Zhang J, Solomon DA, Marra M, Eils R, Bartram CR, von Hoff K, Rutkowski S, Ramaswamy V, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Malkin D, Gajjar A, Korbel JO, Pfister SM. Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. The Lancet Oncology 19(6):785-798, 2018.
Wang L, Hiler D, Xu B, AlDiri I, Chen X, Zhou X, Griffiths L, Valentine M, Shirinifard A, Sablauer A, Thiagarajan S, Barabas M-E, Zhang J, Johnson D, Frase S, Dyer MA. Retinal cell type DNA methylation and histone modifications predict reprogramming efficiency and retinogenesis in 3D organoid cultures. Cell Reports 22(10):2601-2614, 2018.
Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Auvil JMG, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature 555:371-376, 2018.
Stewart E, Federico SM, Chen X, Shelat AA, Bradley C, Gordon B, Karlstrom A, Twarog NR, Clay MR, Bahrami A, Freeman III BB, Xu B, Zhou X, Wu J, Honnell V, Ocarz M, Blankenship K, Dapper J, Mardis ER, Wilson RK, Downing J, Zhang J, Easton J, Pappo A, Dyer MA. Orthotopic patient-derived xenografts of paediatric solid tumours. Nature 549:96-100, 2017.
Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz H-J, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, Waszak SM, Erkek S, Jones DTW, Worst BC, Kool M, Zapatka M, Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z, Ishaque N, Jäger-Schmidt C, Imbusch CD, Jugold A, Hübschmann D, Risch T, Amstislavskiy V, Gonzalez FGR, Weber UD, Wolf S, Robinson GW, Zhou X, Wu G, Finkelstein D, Liu Y, Cavalli FMG, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho Y-J, Pomeroy SL, Herold-Mende C, Schuhmann M, Ebinger M, Liau LM, Mora J, McLendon RE, Jabado N, Kumabe T, Chuah E, Ma Y, Moore RA, Mungall AJ, Mungall KL, Thiessen N, Tse K, Wong T, Jones SJM, Witt O, Milde T, Von Deimling A, Capper D, Korshunov A, Yaspo M-L, RKriwacki R, Gajjar A, Zhang J, Beroukhim R, Fraenkel E, Korbel JO, Brors B, Schlesner M, Eils R, Marra MA, Pfister SM, Taylor MD, Lichter P. The whole-genome landscape of medulloblastoma subtypes. Nature 547(7663):311-317, 2017.
Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, McCastlain K, Edmonson M, Pounds SB, Shi L, Zhou X, Ma X, Sioson E, Li Y, Rusch M, Gupta P, Pei D, Cheng C, Smith MA, Auvil JG, Gerhard DS, Relling MV, Winick NJ, Carroll AJ, Heerema NA, Raetz E, Devidas M, Willman CL, Harvey RC, Carroll WL, Dunsmore KP, Winter SS, Wood BL, Sorrentino BP, Downing JR, Loh ML, Hunger SP, Zhang J, Mullighan CG. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nature Genetics 49:1211-1218, 2017.
Aldiri I, Xu B, Wang L, Chen X, Hiler D, Griffiths L, Valentine M, Shirinifard A, Thiagarajan S, Sablauer A, Barabas M-E, Zhang J, Johnson D, Frase S, Zhou X, Easton J, Zhang J, Mardis ER, Wilson RK, Downing JR, Dyer MA. The dynamic epigenetic landscape of the retina during development, reprogramming, and tumorigenesis. Neuron 94(3):550-568, 2017.
Zhou X, Edmonson MN, Wilkinson MR, Patel A, Wu G, Liu Y, Li Y, Zhang Z, Rusch MC, Parker M, Becksfort J, Downing JR, Zhang J. Exploring genomic alteration in pediatric cancer using ProteinPaint. Nature Genetics 48:4-6, 2016.
Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort J, Wang S, Weaver MS, Ding L, Mardis ER, Wilson RK, Gajjar A, Ellison DW, Pappo AS, Pui C-H, Nichols KE, Downing JR. Germline Mutations in Predisposition Genes in Pediatric Cancer. New England Journal of Medicine 373:2336-2346, 2015.
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu Y-C, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh K-H, Feizi S, Karlic R, Kim A-R, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJM, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai L-H, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature 518(7539):317-330, 2015.
Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PAF, Smirnov I, Costello JF, Wang T. Epigenetic annotation to genetic variants using Roadmap EpiGenome Browser. Nature Biotechnology 33(4):345-346, 2015.
Zhou X, Li D, Lowdon RF, Costello JF, Wang T. methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. Bioinformatics 2014. doi:10.1093/bioinformatics/btu19
Zhou X, Lowdon RF, Li D, Lawson HA, Madden PAF, Costello JF, Wang T. Exploring long-range genome interaction data using WashU Epigenome Browser. Nature Methods 10:375-376, 2013.
Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PAF, Costello JF, Wang T. The Human Epigenome Browser at Washington University. Nature Methods 8:989-990, 2011.
Last update: July 2021