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Zhang Lab: Publications

2016

  • Qaddoumi I, Orisme W, Wen J, Santiago T, Gupta K, Dalton JD, Tang B, Haupfear K, Punchihewa C, Easton J, Mulder H, Boggs K, Shao Y, Rusch M, Becksfort J, Gupta P, Wang S, Lee RP, Brat D, Peter Collins V, Dahiya S, George D, Konomos W, Kurian KM, McFadden K, Serafini LN, Nickols H, Perry A, Shurtleff S, Gajjar A, Boop FA, Klimo PD Jr, Mardis ER, Wilson RK, Baker SJ, Zhang J, Wu G, Downing JR, Tatevossian RG, Ellison DW. Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology. Acta Neuropathol. 2016 Jun;131(6):833-45. doi: 10.1007/s00401-016-1539-z. Epub 2016 Jan 25. PubMed PMID: 26810070; PubMed Central PMCID: PMC4866893.

  • Li Y, Wang X, Cho JH, Shaw TI, Wu Z, Bai B, Wang H, Zhou S, Beach TG, Wu G, Zhang J, Peng J. JUMPg: an Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. J Proteome Res. 2016 May 26. [Epub ahead of print] PubMed PMID: 27225868.

  • Valentin-Vega YA, Wang YD, Parker M, Patmore DM, Kanagaraj A, Moore J, Rusch M, Finkelstein D, Ellison DW, Gilbertson RJ, Zhang J, Kim HJ, Taylor JP. Cancer-associated DDX3X mutations drive stress granule assembly and impair global translation. Sci Rep. 2016 May 16;6:25996. doi: 10.1038/srep25996. PubMed PMID: 27180681; PubMed Central PMCID: PMC4867597.

  • Matlawska-Wasowska K, Kang H, Devidas M, Wen J, Harvey RC, Nickl CK, Ness SA, Rusch M, Li Y, Onozawa M, Martinez C, Wood BL, Asselin BL, Chen IM, Roberts KG, Baruchel A, Soulier J, Dombret H, Zhang J, Larson RS, Raetz EA, Carroll WL, Winick NJ, Aplan PD, Loh ML, Mullighan CG, Hunger SP, Heerema NA, Carrol AJ, Dunsmore KP, Winter SS. MLL rearrangements impact outcome in HOXA-deregulated T-lineage acute lymphoblastic leukemia: A children’s oncology group study. Leukemia. 2016 Mar 8. doi: 10.1038/leu.2013.60. PMID: 26952838.

  • Bahrami A, Lee S, Wu G, Kerstetter J, Rahvar M, Li X, Easton J. Zhang J, Barnhill RL. Pigment-Synthesizing Melanocytic Neoplasm With Protein Kinase C Alpha (PRKCA) Fusion. JAMA Dermatol. 2016 Mar 1;152(3):318-22. doi 10.1001/jamadermatol. 2015.2524. PMID: 26676968.

  • Wu G, Barnhill RL, Lee S, Li Y, Shao Y, Easton J, Dalton J, Zhang J, Pappo A, Bahrami A. The landscape of fusion transcripts in spitzoid melanoma and biological indeterminate spitzoid tumors by RNA sequencing. Mod Pathol. 2016 Feb 19. Doi: 10.1038/modpathol.2016.37. PMID: 26892443.

2015

  • Iacobucci I, Li Y, Roberts KG, Dobson SM, Kim JC, Payne-Turner D, Harvey RC, Valentine M, McCastlain K, Easton J, Yergeau D, Janke LJ, Shao Y, Chen IM, Rusch M, Zandi S, Kornblau SM, Konopleva M, Jabbour E, Paietta EM, Rowe JM, Pui CH, Gastier-Foster J, Gu Z, Reshmi S, Loh ML, Racevskis J, Tallman MS, Wiernik PH, Litzow MR, Wilman CL, McPherson JD, Downing JR, Zhang J, Dick JE, Hunger SP, Mullighan CG. Truncating Erythropoietin Receptor Rearrangements in Acute Lymphoblastic Leukemia. Cancer Cell. 2016 Feb 8;29(2):186-200. doi: 10.1016/j.ccell.2015.12.013. PMID: 26859458.

  • 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. Nat Genet. 2015 Dec 29;48(1):4-6. doi: 10.1038/ng.3466. PubMed PMID: 26711108.

  • 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 JB, 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. N Engl J Med. 2015 Dec 10;373(24):2336-46. doi: 10.1056/NEJMoa1508054. Epub 2015 Nov 18. PMID: 26580448. PMCID: PMC4734119.

  • Jones CL, Gearheart CM, Fosmire S, Delgado-Martin C, Evensen NA, Bride K, Waanders AJ, Pais F, Wang J, Bhatla T, Bitterman DS, de Rijk SR, Bourgeois W, Dandekar S, Park E, Burleson TM, Madhusoodhan PP, Teachey DT, Raetz EA, Hermiston ML, Müschen M, Loh ML, Hunger SP, Zhang J, Garabedian MJ, Porter CC, Carroll WL. MAPK signaling cascades mediate distinct glucocorticoid resistance mechanisms in pediatric leukemia. Blood. 2015 Nov 5;126(19):2202-12. doi: 10.1182/blood-2015-04-639138. Epub 2015 Aug 31. PMID: 26324703. PMCID: PMC4635116.

  • Mullighan CG, Jeha S, Pei D, Payne-Turner D, Coustan-Smith E, Roberts KG, Waanders E, Choi JK, Ma X, Raimondi SC, Fan Y, Yang W, Song G, Yang JJ, Inaba H, Downing JR, Leung WH, Bowman WP, Relling MV, Evans WE, Zhang J, Campana D, Pui CH. Outcome of children with hypodiploid ALL treated with risk-directed therapy based on MRD levels. Blood. 2015 Nov 2. pii: blood-2015-09-671131. PMID: 26527677. PMCID: PMC4692147.

  • Moriyama T, Metzger ML, Wu G, Nishii R, Qian M, Devidas M, Yang W, Cheng C, Cao X, Quinn E, Raimondi S, Gastier-Foster JM, Raetz E, Larsen E, Martin PL, Bowman WP, Winick N, Komada Y, Wang S, Edmonson M, Xu H, Mardis E, Fulton R, Pui CH, Mullighan C, Evans WE, Zhang J, Hunger SP, Relling MV, Nichols KE, Loh ML, Yang JJ. Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study. Lancet Oncol. 2015 Oct 27. pii: S1470-2045(15)00369-1. doi: 10.1016/S1470-2045(15)00369-1. PMID: 26522332. PMCID: PMC4684709.

  • Koçer, ZA, Carter R, Wu, G, Zhang J, Webster RG. The Genomic Contributions of Avian H1N1 Influenza A Viruses to the Evolution of Mammalian Strains. PLoS One. 2015 Jul 24; 0(7):e0133795. doi: 10.1371/journal.pone.0133795. eCollection 2015. PMID: 26208281.

  • Xu H, Zhang H, Yang W, Yadav R, Morrison AC, Qian M, Devidas M, Liu Y, Perez-Andreu V, Zhao X, Gastier-Foster JM, Lupo PJ, Neale G, Raetz E, Larsen E, Bowman WP, Carroll WL, Winick N, Williams R, Hansen T, Holm JC, Mardis E, Fulton R, Pui CH, Zhang J, Mullighan CG, Evans WE, Hunger SP, Gupta R, Schmiegelow K, Loh ML, Relling MV, Yang JJ. Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children. Nat Commun. 2015 Jun 24;6:7553. doi: 10.1038/ncomms8553. PMID: 26104880. PMCID: PMC4544058.

  • Dang J, Wei L, de Ridder J, Su X, Rust AG, Roberts KG, Payne-Turner D, Cheng J, Ma J, Qu C, Wu G, Song G, Huether RG, Schulman B, Janke L, Zhang J, Downing JR, van der Weyden L, Adams DJ, Mullighan CG. PAX5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia. Blood. 2015 Jun 4;125(23):3609-17. doi: 10.1182/blood-2015-02-626127. Epub 2015 Apr 8. PMID: 25855603; PMCID: PMC4458800.

  • Topka S, Vijai J, Walsh MF, Jacobs L, Maria A, Villano D, Gaddam P, Wu G, McGee RB, Quinn E, Inaba H, Hartford C, Pui CH, Pappo A, Edmonson M, Zhang MY, Stepensky P, Steinherz P, Schrader K, Lincoln A, Bussel J, Lipkin SM, Goldgur Y, Harit M, Stadler ZK, Mullighan C, Weintraub M, Shimamura A, Zhang J, Downing JR, Nichols KE, Offit K. Germline ETV6 Mutations Confer Susceptibility to Acute Lymphoblastic Leukemia and Thrombocytopenia. PLoS Genet. 2015 Jun 23;11(6):e1005262. doi: 10.1371/journal.pgen.1005262. eCollection 2015 Jun. PMID: 26102509. PMCID: PMC4477877.

  • Li B, Li H, Bai Y, Kirschner-Schwabe R, Yang JJ, Chen Y, Lu G, Tzoneva G, Ma X, Wu T, Li W, Lu H, Ding L, Liang H, Huang X, Yang M, Jin L, Kang H, Chen S, Du A, Shen S, Ding J, Chen H, Chen J, von Stackelberg A, Gu L, Zhang J, Ferrando A, Tang J, Wang S, Zhou BB. Negative feedback-defective PRPS1 mutants drive thiopurine resistance in relapsed childhood ALL. Nat Med. 2015 Jun;21(6):563-71. doi: 10.1038/nm.3840. Epub 2015 May 11. PMID: 25962120.

  • 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 S, Dyer M, Shurtleff S, Espy S, Pounds S, Downing J, Ellison D, Mullighan C, and Zhang J. CONSERTING: an accurate method for detecting somatic DNA copy number alterations in whole genome sequencing data. Nature Meth. 2015 Jun;12(6):527-30. doi: 10.1038/nmeth.3394. Epub 2015 May 4. PMID: 25938371; PMCID: PMC4591043.

  • Tong Y, Merino D, Nimmervoll B, Gupta K, Wang YD, Finkelstein D, Dalton J, Ellison DW, Ma X, Zhang J, Malkin D, Gilbertson RJ. Cross-Species Genomics Identifies TAF12, NFYC, and RAD54L as Choroid Plexus Carcinoma Oncogenes. Cancer Cell. 2015 May 11;27(5):712-27. doi: 10.1016/j.ccell.2015.04.005. PMID: 25965574. PMCID: PMC4458854.

  • Zaraket H, Baranovich T, Kaplan BS, Carter R, Song MS, Paulson JC, Rehg JE, Bahl J, Crumpton JC, Seiler J, Edmonson M, Wu G, Karlsson E, Fabrizio T, Zhu H, Guan Y, Husain M, Schultz-Cherry S, Krauss S, McBride R, Webster RG, Govorkova EA, Zhang J, Russell CJ, Webby RJ. Mammalian adaptation of influenza A(H7N9) virus is limited by a narrow genetic bottleneck. Nat Commun. 2015 Apr 8;6:6553. doi: 10.1038/ncomms7553. PMID: 25850788; PMCID: PMC4403340.

  • 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. 2015 Apr;47(4):330-7. doi: 10.1038/ng.3230. Epub 2015 Mar 2. PMID: 25730765; PMCID: PMC4553269.

  • Ma X, Edmonson M, Yergeau D, Muzny DM, Hampton, OA, Rusch M, Song G, Easton J, Harvey RC, Wheeler DA, Ma J, Doddapaneni HV, Vadodaria B, Wu G, Nagahawatte P, Carroll WL, Chen, I-M Chen, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Guidry Auvil JM, Downing JR, Loh ML, Willman CL, Gerhard DS, Mullighan CG, Hunger SP, Zhang J. Rise and Fall of Subclones from Diagnosis to Relapse in Pediatric B-Acute Lymphoblastic Leukemia. Nat Commun. 2015 Mar 19;6:6604. doi: 10.1038/ncomms7604. PMID: 25790293; PMCID: PMC4377644.

  • 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. 2015 Mar 6;6:6302. doi: 10.1038/ncomms7302. PMID: 25743702. PMCID: PMC4352712.

  • Lu C, Zhang J*, Nagahawatte P, Easton J, Lee S, Liu Z, Ding L, Wyczalkowski MA, Valentine M, Navid F, Mulder H, Tatevossian RG, Dalton J, Davenport J, Yin Z, Edmonson M, Rusch M, Wu G, Li Y, Parker M, Hedlund E, Shurtleff S, Raimondi S, Bhavin V, Donald Y, Mardis ER, Wilson RK, Evans WE, Ellison DW, Pounds S, Dyer M, Downing JR, Pappo A, Bahrami A. The Genomic Landscape of Childhood and Adolescent Melanoma. J Invest Dermatol. 2015 Mar;135(3):816-23. doi: 10.1038/jid.2014.425. Epub 2014 Sep 30. PMID: 25268584; PMCID: PMC4340976.

  • Ma C, Chen Y, Wilkins D, Chen X, Zhang J. An unsupervised learning approach to find ovarian cancer genes through integration of biological data. BMC Genomics. 2015;16 Suppl 9:S3. doi: 10.1186/1471-2164-16-S9-S3. Epub 2015 Aug 17. PMID: 26328548. PMCID: PMC4547402.

  • Koçer ZA, Carter R, Wu G, Zhang J, Webster RG. The Genomic Contributions of Avian H1N1 Influenza A Viruses to the Evolution of Mammalian Strains. PLoS One. 2015 Jul 24;10(7):e0133795. doi: 10.1371/journal.pone.0133795. eCollection 2015. PMID: 26208281. PMCID: PMC4514870.

2014

  • 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 C. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014 Sep 11;371(11):1005-15. doi: 10.1056/NEJMoa1403088. PMID: 25207766; PMCID: PMC4191900 (Co-corresponding author).

  • 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. 2014 Nov;4(11):1342-53. doi: 10.1158/2159-8290.CD-14-0622. Epub 2014 Sep 15. PMID: 25223734; PMCID: PMC4264969. (Co-corresponding author).

  • Roberts KG, Pei D, Campana D, Payne-Turner D, Li Y, Cheng C, Sandlund JT, Jeha S, Easton J, Becksfort J, Zhang J, Coustan-Smith E, Raimondi SC, Leung WH, Relling MV, Evans WE, Downing JR, Mullighan CG, Pui CH. Outcomes of Children With BCR-ABL1-Like Acute Lymphoblastic Leukemia Treated With Risk-Directed Therapy Based on the Levels of Minimal Residual Disease. J Clin Oncol. 2014 Sep 20;32(27):3012-20. PMID: 25049327; PMCID: PMC4162497.

  • Philip NH, Dillon CP, Snyder AG, Fitzgerald P, Wynosky-Dolfi MA, Zwack EE, Hu B, Fitzgerald L, Mauldin EA, Copenhaver AM, Shin S, Wei L, Parker M, Zhang J, Oberst A, Green DR, Brodsky IE. Caspase-8 mediates caspase-1 processing and innate immune defense in response to bacterial blockade of NF-κB and MAPK signaling. Proc Natl Acad Sci USA. 2014 May 20;111(20):7385-90. doi: 10.1073/pnas.1403252111. Epub 2014 May 5. PMID: 24799700; PMCID: PMC4034241.

  • Pawlikowska I, Wu G, Edmonson M, Liu Z, Gruber T, Zhang J, Pounds S. The Most Informative Spacing Test Effectively Discovers Biologically Relevant Outliers or Multiple Modes in Expression. Bioinformatics. 2014 May 15;30(10):1400-8. doi: 10.1093/bioinformatics/btu039. Epub 2014 Jan 22. PMID: 24458951; PMCID: PMC4068004.

  • 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 RC, 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* and Baker SJ. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet. 2014 May;46(5):444-50. doi: 10.1038/ng.2938. Epub 2014 Apr 6. PMID: 24705251; PMCID: PMC4056452. (Co-corresponding author).

  • 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; St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project. Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Rep. 2014 Apr 10;7(1):104-12. doi: 10.1016/j.celrep.2014.03.003. Epub 2014 Apr 3. PMID: 24703847; PMCID: PMC4096827. (Co-corresponding author).

  • 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. 2014 Apr 8;5:3630. 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. 2014 Feb 27;506(7489):451-5. doi: 10.1038/nature13109. Epub 2014 Feb 19. Erratum in: Nature. 2014 Apr 24;508(7497):554. PMID: 24553141; PMCID: PMC4050669. (Co-corresponding author).

  • Faraji F, Hu Y, Wu G, Goldberger NE, Walker RC, Zhang J, Hunter KW. An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease. Genome Res. 2014 Feb;24(2):227-40. doi: 10.1101/gr.166223.113. Epub 2013 Dec 9. PMID: 24322557; PMCID: PMC3912413.

  • 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. 2014 Jan 30;5(2):438-50. PMID: 24509483; PMCID: PMC3964219.

  • Meerzaman DM, Yan C, Chen QR, Edmonson MN, Schaefer CF, Clifford RJ, Dunn BK, Dong L, Finney RP, Cultraro CM, Hu Y, Yang Z, Nguyen CV, Kelley JM, Cai S, Zhang H, Zhang J, Wilson R, Messmer L, Chung YH, Kim JA, Park NH, Lyu MS, Song IH, Komatsoulis G, Buetow KH. Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma. Cancer Genomics Proteomics. 2014 Jan-Feb;11(1):1-12. PMID: 24633315.

2013

  • Chen X, Stewart E, Shelat AA, Qu C, Bahrami A, Hatley M, Wu G, Bradley C, McEvoy J, Pappo A, Spunt S, Valentine MB, Valentine V, Krafcik F, Lang WH, Wierdl M, Tsurkan L, Tolleman V, Federico SM, 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 DS, Ramirez N, Potter PM, Sandoval JA, Davidoff AM, Mardis ER, Wilson RK, Zhang J, Downing JR,Dyer MA. Targeting oxidative stress in embryonal rhabdomyosarcoma. Cancer Cell. 2013 Dec 9;24(6):710-24. doi: 10.1016/j.ccr.2013.11.002. PMID: 24332040; PMCID: PMC3904731.

  • Koçer ZA, Obenauer J, Zaraket H, Zhang J, Rehg JE, Russell CJ, Webster RG. Fecal influenza in mammals: selection of novel variants. J Virol. 2013 Nov;87(21):11476-86. doi: 10.1128/JVI.01544-13. Epub 2013 Aug 21. PMID: 23966381; PMCID: PMC3807347.

  • Jaffe JD, Wang Y, Chan HM, Zhang J, Huether R, Kryukov GV, Bhang HE, Taylor JE, Hu M, Englund NP, Yan F, Wang Z, Robert McDonald E 3rd, Wei L, Ma J, Easton J, Yu Z, Debeaumount R, Gibaja V, Venkatesan K, Schlegel R, Sellers WR, Keen N, Liu J, Caponigro G, Barretina J, Cooke VG, Mullighan C, Carr SA, Downing JR, Garraway LA, Stegmeier F. Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia. Nat Genet. 2013 Nov;45(11):1386-91. doi: 10.1038/ng.2777. Epub 2013 Sep 29. PMID: 24076604; PMCID: PMC4262138.

  • Paugh BS, Zhu X, Qu C, Endersby R, Diaz AK, Zhang J, Bax DA, Carvalho D, Reis RM, Onar-Thomas A, Broniscer A, Wetmore C, Zhang J, Jones C, Ellison DW, Baker SJ. Novel oncogenic PDGFRA mutations in pediatric high-grade gliomas. Cancer Res. 2013 Oct 15;73(20):6219-29. doi: 10.1158/0008-5472.CAN-13-1491. Epub 2013 Aug 22. PMID: 23970477; PMCID: PMC3800209.

  • Shah S, Schrader KA, Waanders E, Timms AE, Vijai J, Miething C, Wechsler J, Yang J, Hayes J, Klein RJ, Zhang J, Wei L, Wu G, Rusch M, Nagahawatte P, Ma J, Chen S-C, Song G, Cheng Jinjun, Myers P, Bhojwani D, Jhanwar S, Maslak P, Fleisher M, Littman J, Offit L, Rau-Murthy R, Fleischut MH, Corines M, Murali R, Gao X, Manschreck C, Kitzing T, Murty VV, Raimond S, Kuiper RP, Simons A, Schiffman JD, Onel K, Plon SE, Wheeler D, Ritter D, Ziegler DS, Tucker K, Sutton R, Chenevix-Trench G, Li J, Huntsman DG, Hansford S, Senz J, Walsh, Lee M, Hahn CN, Roberts K, King M-C, Lo SM, Levine RL, Viale A, Socci N, Nathanson KL, Scott HS, Daly M, Lkpkin SM, Lowe SW, Downing JR, Altshuler D, Sandlund JT, Horwitz MS, Mullighan CG, and Offit KG. Identification of a recurrent germline PAX5 mutation and susceptibility to pre-B cell acute lymphoblastic leukemia. Nat Genet. 2013 Oct;45(10):1226-31. doi: 10.1038/ng.2754. Epub 2013 Sep 8. PMID: 24013638; PMCID: PMC3919799.

  • Pounds S, Cheng C, Li S, Liu Z, Zhang J, and Mullighan CG. A Genomic Random Interval Model for Statistical Analysis of Genomic Lesion Data. Bioinformatics. 2013 Sep 1;29(17):2088-95. doi: 10.1093/bioinformatics/btt372. Epub 2013 Jul 10. PMID: 23842812; PMCID: PMC3740633.

  • Benavente CA, McEvoy JD, Finkelstein D, Wei L, Kang G, Wang YD, Neale G, Ragsdale S, Valentine V, Bahrami A, Temirov J, Pounds S, Zhang J, Dyer MA. Cross-species genomic and epigenomic landscape of retinoblastoma. Oncotarget. 2013 Jun;4(6):844-59. PMID: 23765217; PMCID: PMC3757242.

  • Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Parker M, 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 novel genetic alterations in pediatric low-grade gliomas. Nat Genet. 2013 Jun;45(6):602-12. 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 genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet 2013 Mar;45(3):242-52. doi: 10.1038/ng.2532. Epub 2013 Jan 20. PMID: 23334668; PMCID: PMC3919793.

2012

  • Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, Healy J, Grenier JC, de Malliard T, Busche S, Spinella JF, Larivière M, Gibson G, Andersson A, Holmfeldt L, Ma J, Wei L, Zhang J, Andelfinger G, Downing JR, Mullighan CG, Awadalla P. Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Res 2013 Mar;23(3):419-30. doi: 10.1101/gr.144188.112. Epub 2012 Dec 5. PMID: 23222848; PMCID: PMC3589531.

  • Loh ML, Zhang J*, Harvey RC, Roberts K, Payne-Turner D, Kang H, Wu G, Chen X, Becksfort J, Edmonson M, Buetow KH, Carroll WL, Chen IM, Wood B, Borowitz MJ, Devidas M, Gerhard DS, Bowman P, Larsen E, Winick N, Raetz E, Smith M, Downing JR, Willman CL, Mullighan CG, Hunger SP. Tyrosine kinome sequencing of pediatric acute lymphoblastic leukemia: a report from The Children's Oncology Group TARGET Project. Blood. Jan 17;121(3):485-8. doi: 10.1182/blood-2012-04-422691. Epub 2012 Dec 4. PMID: 23212523; PMCID: PMC3548168. (co-first author).

  • 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 data. Genome Biol. 2012 Dec 11;13(12):R113. doi: 10.1186/gb-2012-13-12-r113. PMID: 23232254; PMCID: PMC3580411.

  • Gruber TA, Larson Gedman A, Zhang J, Koss CS, Marada S, Ta HQ, Chen SC, Su X, Ogden SK, Dang J, Wu G, Gupta V, Andersson AK, Pounds S, Shi L, Easton J, Barbato MI, Mulder HL, Manne J, Wang J, Rusch M, Ranade S, Ganti R, Parker M, Ma J, Radtke I, Ding L, Cazzaniga G, Biondi A, Kornblau SM, Ravandi F, Kantarjian H, Nimer SD, Döhner K, Döhner H, Ley TJ, Ballerini P, Shurtleff S, Tomizawa D, Adachi S, Hayashi Y, Tawa A, Shih LY, Liang DC, Rubnitz JE, Pui CH, Mardis ER, Wilson RK, Downing JR. An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer Cell. 2012 Nov 13;22(5):683-97. doi: 10.1016/j.ccr.2012.10.007. PMID: 23153540; PMCID: PMC3547667.

  • Kuhn E, Wu R-C, Wu G, Guan B, Zhang J, Wang Y, Song L, Yuan X, Wei L, Roden R, Kuo K-T, Nakayama K, Clarke B, Shaw P, Olvera N, Levine D, Kurman R, Wang T-L, Shih I-M. Genome-wide analyses of uterine serous carcinoma identify pathway aberrations involving cyclinE-Fbxw7, PI3K and p53. J Natl Cancer Inst. 2012 Oct 3;104(19):1503-13. doi: 10.1093/jnci/djs345. Epub 2012 Aug 23. PMID: 22923510; PMCID: PMC3692380.

  • Greulich H, Kaplan B, Mertins P, Chen TH, Tanaka KE, Yun CH, Zhang X, Lee SH, Cho J, Ambrogio L, Liao R, Imielinski M, Banerji S, Berger AH, Lawrence MS, Zhang J, Pho NH, Walker SR, Winckler W, Getz G, Frank D, Hahn WC, Eck MJ, Mani DR, Jaffe JD, Carr SA, Wong KK, Meyerson M. Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2. Proc Natl Acad Sci USA. 2012 Sep 4;109(36):14476-81. doi: 10.1073/pnas.1203201109. Epub 2012 Aug 20. PMID: 22908275; PMCID: PMC3437859.

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

  • Robinson G, Parker M, Kranenburg TA, Lu C, Chen X, Ding L, Eden T, Hedlund E, Lei W, Wang J, Wu G, Rusch M, Hong X, Beckford J, Gupta P, Ma J, Easton J, Pounds S, Zhao D, Gajjar A, Roussel MF, Ellison DW, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Mardis ER, Wilson RK, Downing J, Zhang J*, Gilbertson RJ for the St Jude Children’s Research Hospital - Washington University Pediatric Cancer Genome Project. Novel mutations target distinct subgroups of medulloblastoma, Nature. 2012 Aug 2;488(7409):43-8. doi: 10.1038/nature11213. PMID: 22722829; PMCID: PMC3412905. (co-corresponding author).

  • Downing JR, Wilson RK, Zhang J, Mardis ER, Pui C-H, Ding L, Ley TJ, Evans WE. The Pediatric Cancer Genome Project. Nat Genet. 2012 May 29;44(6):619-22. doi: 10.1038/ng.2287. Erratum in: Nat Genet. 2012 Sep;44(9):1072. PMID: 22641210; PMCID: PMC3619412.

  • Gegonne A, Tai X, Zhang J, Wu G, Zhu J, Yoshimoto A, Hanson J, Cultraro C, Chen QR, Guinter T, Yang Z, Hathcock K, Singer A, Rodriguez-Canales J, Tessarollo L, Mackem S, Meerzaman D, Buetow K, Singer DS. The general transcription factor TAF7 is essential for embryonic development but not essential for the survival or differentiation of mature T cells. Mol Cell Biol. 2012 May;32(10):1984-97. doi: 10.1128/MCB.06305-11. Epub 2012 Mar 12. PMID: 22411629; PMCID: PMC3347399.

  • Cheung NK, Zhang J*, Lu C, Parker M, Bahrami A, Tickoo SK, Heguy A, Pappo AS, Federico S, Dalton J, Cheung IY, Ding L, Fulton R, Wang J, Chen X, Becksfort J, Wu J, Billups CA, Ellison D, Mardis ER, Wilson RK, Downing JR, Dyer MA; St Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project. Association of age at diagnosis and genetic mutations in patients with neuroblastoma. JAMA. 2012 Mar 14;307(10):1062-71. doi: 10.1001/jama.2012.228. PMID: 22416102; PMCID: PMC3527076. (co-first author).

  • Hu Y, Wu G, Rusch M, Lukes L, Buetow KH, Zhang J, Hunter KW. Integrated cross-species transcriptional network analysis of metastatic susceptibility. Proc Natl Acad Sci USA. 2012 Feb 21;109(8):3184-9. doi: 10.1073/pnas.1117872109. Epub 2012 Jan 30. PMID: 22308418; PMCID: PMC3286991.

  • Wu G, Broniscer A, McEachron TA, Lu C, Paugh BS, Becksfort J, Qu C, Ding L, Huether R, Parker M, Zhang J, Gajjar A, Dyer MA, Mullighan CG, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Ellison DW, Zhang J*, Baker SJ; St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet. 2012 Jan 29;44(3):251-3. doi: 10.1038/ng.1102. PMID: 22286216; PMCID: PMC3288377. (co-corresponding author).

  • 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. 2012 Jan 11;481(7381):329-34. 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. 2012 Jan 11;481(7380):157-63. doi: 10.1038/nature10725. PMID: 22237106; PMCID: PMC3267575.

  • McEvoy J, Ulyanov A, Brennan R, Wu G, Pounds S, Zhang J, Dyer MA. Analysis of MDM2 and MDM4 single nucleotide polymorphisms, mRNA splicing and protein expression in retinoblastoma. PLoS One. 2012;7(8):e42739. doi: 10.1371/journal.pone.0042739. Epub 2012 Aug 20. PMID: 22916154; PMCID: PMC3423419.

  • Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. Erratum in: Nature. 2012 Oct 11;490(7419):298. PMID: 21720365; PMCID: PMC3163504.

2011

  • Andersson AK, Miller DW, Lynch JA, Lemoff AS, Cai Z, Pounds SB, Radtke I, Yan B, Schuetz JD, Rubnitz JE, Ribeiro RC, Raimondi SC, Zhang J, Mullighan CG, Shurtleff SA, Schulman BA, Downing JR. IDH1 and IDH2 mutations in pediatric acute leukemia. Leukemia. 2011 Oct;25(10):1570-7. doi: 10.1038/leu.2011.133. Epub 2011 Jun 7. PMID: 21647154; PMCID: PMC3883450.

  • Zhang J, Mullighan CG, Harvey RC, Wu G, Chen X, Edmonson M, Buetow KH, Carroll WL, Chen I-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. 2011 Sep 15;118(11):3080-7. doi: 10.1182/blood-2011-03-341412. Epub 2011 Jun 16. PMID: 21680795; PMCID: PMC3175785.

  • Gill RK, Yang SH, Meerzaman D, Mechanic LE, Bowman ED, Jeon HS, Roy Chowdhuri S, Shakoori A, Dracheva T, Hong KM, Fukuoka J, Zhang JH, Harris CC, Jen J. Frequent homozygous deletion of the LKB1/STK11 gene in non-small cell lung. Cancer Oncogene. 2011 Sep 1;30(35):3784-91. doi: 10.1038/onc.2011.98. Epub 2011 May 2. PMID: 21532627; PMCID: PMC3616488.

  • Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR and Zhang J. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nature Meth. 2011 Jun 12;8(8):652-4. doi: 10.1038/nmeth.1628. PMID: 21666668; PMCID: PMC3527068.

  • Shih IM, Nakayama K, Wu G, Nakayama N, Zhang J, Wang TL. Amplification of the ch19p13.2 NACC1 locus in ovarian high-grade serous carcinoma. Mod Pathol. 2011 May;24(5):638-45. doi: 10.1038/modpathol.2010.230. Epub 2011 Jan 14. PMID: 21240255; PMCID: PMC3085564.

  • Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH. Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics. 2011 Mar 15;27(6):865-6. doi: 10.1093/bioinformatics/btr032. Epub 2011 Jan 28. PMID: 21278191; PMCID: PMC3051333.

  • Mullighan CG, Zhang J*, Kasper LH, Lerach S, Payne-Turner D, Phillips LA, Heatley SL, Holmfeldt L, Collins-Underwood JR, Ma J, Buetow KH, Pui CH, Baker SD, Brindle PK, Downing JR. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature. 2011 Mar 10;471(7337):235-9. doi: 10.1038/nature09727. PMID: 21390130; PMCID: PMC3076610. (co-first author).

2010

  • Clifford RJ, Zhang J, Meerzaman DM, Lyu MS, Hu Y, Cultraro CM, Finney RP, Kelley JM, Efroni S, Greenblum SI, Nguyen CV, Rowe WL, Sharma S, Wu G, Yan C, Zhang H, Chung YH, Kim JA, Park NH, Song IH, Buetow KH. Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma. Hepatology. 2010 Dec;52(6):2034-43. doi: 10.1002/hep.23943. PMID: 21105107.

2009

  • Braun R, Rowe W, Schaefer C, Zhang J, Buetow K. Needles in the haystack: identifying individuals present in pooled genomic data. PLoS Genet. 2009 Oct 2. PMID: 19798441; PMCID: PMC2747273.

  • Mullighan CG, Zhang J*, Harvey RC, Collins-Underwood JR, Schulman BA, Phillips LA, et al. JAK mutations in high-risk childhood acute lymphoblastic leukemia. Proc Natl Acad Sci USA. 2009 Jun 9;106(23):9414-8. doi: 10.1073/pnas.0811761106. Epub 2009 May 22. PMID: 19470474; PMCID: PMC2695045. (co-first author).

  • Franceschini N, North KE, Arnett D, Pankow JS, Chung JH, Baird L, Leppert MF, Eckfeldt JH, Boerwinkle E, Gu CC, Lewis CE, Myers RH, Turner ST, Weder A, Kao WH, Mosley TH, Chakravarti A, Kramer H, Zhang J, Hunt SC. The association of cell cycle checkpoint 2 variants and kidney function: findings of the Family Blood Pressure Program and the Atherosclerosis Risk In Communities study. Am J Hypertens. 2009 May;22(5):552-8. doi: 10.1038/ajh.2009.41. Epub 2009 Mar 5. PMID: 19265784; PMCID: PMC2727134.

  • Udler MS, Meyer KB, Pooley KA, Karlins E, Struewing JP, Zhang J, Doody DR, MacArthur S, Tyrer J, Pharoah PD, Luben R, Bernstein L, Kolonel LN, Henderson BE, Le Marchand L, Ursin G, Press MF, Brennan P, Sangrajrang S, Gaborieau V, Odefrey F, Shen CY, Wu PE, Wang HC, Kang D, Yoo KY, Noh DY, Ahn SH, Ponder BA, Haiman CA, Malone KE, Dunning AM, Ostrander EA, Easton DF; SEARCH Collaborators. FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation. Hum Mol Genet. 2009 May 1;18(9):1692-703. doi: 10.1093/hmg/ddp078. Epub 2009 Feb 17. PMID: 19223389; PMCID: PMC2733817.

  • Mullighan CG, Su X, Zhang J, Radtke I, Phillips LA, Miller CB, Ma J, Liu W, Cheng C, Schulman BA, Harvey RC, Chen IM, Clifford RJ, Carroll WL, Reaman G, Bowman WP, Devidas M, Gerhard DS, Yang W, Relling MV, Shurtleff SA, Campana D, Borowitz MJ, Pui CH, Smith M, Hunger SP, Willman CL, Downing JR; Children's Oncology Group. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med. 2009 Jan 29;360(5):470-80. doi: 10.1056/NEJMoa0808253. Epub 2009 Jan 7. PMID: 19129520; PMCID: PMC2674612.

2008

  • Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8. doi: 10.1038/nature07385. Epub 2008 Sep 4. Erratum in: Nature. 2013 Feb 28;494(7438):506. PMID: 18772890; PMCID: PMC2671642.

2007

  • Crawford NP, Qian X, Ziogas A, Papageorge AG, Boersma BJ, Walker RC, Lukes L, Rowe WL, Zhang J, Ambs S, Lowy DR, Anton-Culver H, Hunter KW. Rrp1b, a new candidate susceptibility gene for breast cancer progression and metastasis. PLoS Genet. 2007 Nov;3(11):e214. Epub 2007 Oct 16. PMID: 18081427; PMCID: PMC2098807.

  • Pereira LH, Pineda MA, Rowe WH, Fonseca LR, Greene MH, Offit K, Ellis NA, Zhang J, Collins A, Struewing JP. The BRCA1 Ashkenazi founder mutations occur on common haplotypes and are not highly correlated with anonymous single nucleotide polymorphisms likely to be used in genome-wide case-control association studies. BMC Genet. 2007 Oct 4;8:68. PMID: 17916242; PMCID: PMC2093936.

  • Zhang J*, Finney R, Rowe W, Edmonson M, Yang SH, Dracheva T, Jen J, Struewing JP, Buetow KH. Systematic analysis of genetic alterations in tumors using cancer genome WorkBench (CGWB). Genome Res. 2007 Jul;17(7):1111-7. Epub 2007 May 24. PubMed PMID: 17525135; PubMed Central PMCID: PMC1899122. (Corresponding author).

  • Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R, Wareham N, Ahmed S, Healey CS, Bowman R; SEARCH collaborators, Meyer KB, Haiman CA, Kolonel LK, Henderson BE, Le Marchand L, Brennan P, Sangrajrang S, Gaborieau V, Odefrey F, Shen CY, Wu PE, Wang HC, Eccles D, Evans DG, Peto J, Fletcher O, Johnson N, Seal S, Stratton MR, Rahman N, Chenevix-Trench G, Bojesen SE, Nordestgaard BG, Axelsson CK, Garcia-Closas M, Brinton L, Chanock S, Lissowska J, Peplonska B, Nevanlinna H, Fagerholm R, Eerola H, Kang D, Yoo KY, Noh DY, Ahn SH, Hunter DJ, Hankinson SE, Cox DG, Hall P, Wedren S, Liu J, Low YL, Bogdanova N, Schürmann P, Dörk T, Tollenaar RA, Jacobi CE, Devilee P, Klijn JG, Sigurdson AJ, Doody MM, Alexander BH, Zhang J, Cox A, Brock IW, MacPherson G, Reed MW, Couch FJ, Goode EL, Olson JE, Meijers-Heijboer H, van den Ouweland A, Uitterlinden A, Rivadeneira F, Milne RL, Ribas G, Gonzalez-Neira A, Benitez J, Hopper JL, McCredie M, Southey M, Giles GG, Schroen C, Justenhoven C, Brauch H, Hamann U, Ko YD, Spurdle AB, Beesley J, Chen X; kConFab; AOCS Management Group, Mannermaa A, Kosma VM, Kataja V, Hartikainen J, Day NE, Cox DR, Ponder BA. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007 Jun 28;447(7148):1087-93. PMID: 17529967; PMCID: PMC2714974.

2006

  • Sood R, English MA, Jones M, Mullikin J, Wang DM, Anderson M, Wu D, Chandrasekharappa SC, Yu J, Zhang J, Paul Liu P. Methods for reverse genetic screening in zebrafish by resequencing and TILLING. Methods. 2006 Jul;39(3):220-7. PMID: 16828311.

  • Zhang P, Zhang J, Sheng H, Osborne B, Buetow K. Gene functional similarity search tool (GFSST). BMC Bioinformatics. 2006 Mar 14;7:135. PMID: 16536867; PMCID: PMC1421445.

2005

  • Zhang, J*, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, Liu P, Gibbs RA, Kenneth H. Buetow KH. SNPdetector: A software tool for sensitive and accurate SNP detection. PLOS Comput Biol. 2005 Oct;1(5):e53. Epub 2005 Oct 28. PMID: 16261194; PMCID: PMC1274293. (Corresponding author).

  • Zhang J*, Finney R, Clifford R, Buetow KH. Detecting false expression signals in high-density oligonucleotide arrays by an in-silico approach. Genomics. 2005 Mar;85(3):297-308. PMID: 15718097. (Corresponding author).

  • Zhang J*, Hunter KW, Gandolph M, Rowe WL, Kelley JM, Edmonson M, Buetow KH. A high-resolution multi-strain haplotype analysis of laboratory mouse genome reveals three distinctive genetic variation patterns. Genome Res. 2005 Feb;15(2):241-9. PMID: 15687287; PMCID: PMC546525. (Corresponding author).

2003

  • Zhang J*, Rowe WL, Clark AG, Buetow KH. Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations. Am J Hum Genet. 2003 Nov;73(5):1073-81. Epub 2003 Oct 14. PMID: 14560401; PubMed Central PMCID: PMC1180487. (Corresponding author).

  • Rutter JL, Smith AM, Davila MR, Sigurdson AJ, Giusti RM, Pineda MA, Doody MM, Tucker MA, Greene MH, Zhang J, Struewing JP. Mutational analysis of the BRCA1-interacting genes ZNF350/ZBRK1 and BRIP1/BACH1 among BRCA1 and BRCA2-negative probands from breast-ovarian cancer families and among early-onset breast cancer cases and reference individuals. Hum Mutat. 2003 Aug; 22(2):121-8. PMID: 12872252.

2002

  • Zhang J*, Rowe WL, Struewing JP, Buetow KH. HapScope: A software system for automated and visual analysis of functionally annotated haplotypes. Nucl Acids Res. 2002 Dec 1;30(23):5213-21. PMID: 12466546; PMCID: PMC137968. (Corresponding author).

  • Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, Mayberry F, Mural R, Nodell M, Yandell M, Zhang J, Thomas P. The Celera discovery system. Nucl Acids Res. 2002 Jan 1;30(1):129-36. PMID: 11752274; PMCID: PMC99167.

2001

  • Venter JC, Adams MD, Myers EW, Li P, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson D, Wortman JR, Zhang Q, Kodira C, Zheng X, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL1, Nelson C2, Broder S, Clark AG11, Nadeau J5, McKusick VA7, Zinder N8, Levine AJ8, Roberts R9, Simon M10, Hunkapiller M6, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TA, Higgins ME, Ji R-R, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S3, Shao W, Shue B, Sun J, Wang ZY, Wang A, Wang X, Wang J, Wei M-H, Wides R12, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu SC, Zhao S3, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers Y-H, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF4, Guigó R4, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang Y-H, Coyne M, Dahlke C, Mays AD, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. The sequence of the human genome. Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838. PMID: 11181995.

2000

  • Yan WL, Guan XY, Green ED, Nicolson R, Yap TK, Zhang J, Jacobsen LK, Krasnewich DM, Kumra S, Lenane MC, Gochman P, Damschroder-Williams PJ, Esterling LE, Long RT, Martin BM, Sidransky E, Rapoport JL, Ginns EI. Childhood-onset schizophrenia/autistic disorder and t(1;7) reciprocal translocation: identification of a BAC contig spanning the translocation breakpoint at 7q21. Am J Med Genet. 2000 Dec 4;96(6):749-53. PMID: 11121174.

  • Slentz-Kesler K, Moore JT, Lombard M, Zhang J, Hollingsworth R and Weiner MP. Identification of the human mnk2 gene (MKNK2) through protein interaction with estrogen receptor beta. Genomics. 2000 Oct 1;69(1):63-71. PMID: 11013076.

1999

  • Zhang J*, Shen-Ong G, Ostell J. "KARIBIN", a KAryotypic RegIon-Based INtegrated information resource for identifying disease genes through multiple approaches. Genome Res. 1999 Jan;9(1):91-8. Review. PMID: 9927488; PMCID: PMC310702. (Corresponding author).

1997

  • Hwang DM, Dempsey AA, Wang RX, Rezvani M, Barrans JD, Dai KS, Wang HY, Ma H, Cukerman E, Liu YQ, Gu JR, Zhang, JH, Tsui SK, Waye MM, Fung KP, Lee CY, Liew CC. A genome-based resource for molecular cardiovascular medicine: toward acompendium of cardiovascular genes. Circulation. 1997 Dec 16;96(12):4146-203. PMID: 9416882.

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl Acids Res. 1997 Sep 1;25(17):3389-402. Review. PMID: 9254694. PMCID: PMC146917.

  • Zhang J*, Madden TL. PowerBlast: A network application for automated analysis of large genomic sequences. Genome Res. 1997 Sep 1;25(17):3389-402. Review. PMID: 9254694; PMCID: PMC146917.

  • Chao K-M, Zhang J, Ostell J, Miller W. A tool for aligning very similar DNA sequences. Comput Applic Biosci 1997 Feb;13(1):75-80. PMID: 9088712.

1996

  • Huang X, Zhang J. Methods for comparing a DNA sequence with a protein sequence. Comput Applic Biosci. 1996 Dec;12(6):497-506. PMID: 9021268.

  • Makalowski W, Zhang J, Boguski M. Comparative analysis of 1,196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res. 1996 Sep;6(9):846-57. PMID: 8889551.

  • Madden TL, Tatusov RL, Zhang J. Applications of Network BLAST Server. Meth Enzymol. 1996;266:131-41. PMID: 8743682.

1994

  • Chao K-M, Zhang J, Ostell J, Miller W. A local alignment tool for very long DNA sequences. Comput Applic Biosci 11:147-153, 1994.

  • Zhang J, Ostell J, Rudd KE. ChromoScope: A graphic interactive browser for E. coli data expressed in the NCBI data model. Proceedings of the Twenty-Seventh Annual Hawaii International Conference on System Sciences V. 58-67, 1994.

1992

  • Shin D-G, Lee C, Zhang J, Rudd KE, Berg CM. Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system. Comput Applic Biosci. 1992 Jun;8(3):227-38. PMID: 1633564.