Jinghui Zhang, PhD

    Jinghui Zhang, PhD

    Member, St. Jude Faculty

    Departments

    Computational Biology

    Contact Information

    Jinghui Zhang, PhD
    Computational Biology
    MS 1160, Room I-6104
    St. Jude Children's Research Hospital
    262 Danny Thomas Place
    Memphis, TN 38105-3678
    Email: jinghui.zhang@stjude.org
    Phone: (901) 595-6829

    Education

    BS – Fu Dan University , Shanghai, China (1989)
    MS – The University of Connecticut, Storrs, Connecticut (1991)
    PhD – The University of Connecticut, Storrs, Connecticut (1994)


    Research Interests

    I am a computational biologist interested in understanding the effect of genetic alterations on cancer initiation, progression and prognosis through integrative analysis of large-scale, multi-dimensional genomic data. My research interest has been in the development of highly accurate and sensitive computational methods for analyzing large-scale genomic data derived from high-throughput sequencing, especially in the area of genetic and epigenetic alterations in cancer genome. Early in my career, I participated in the development of the widely used BLAST algorithm and led the genetic variation analysis of the first assembled human genome. For the last 10 years I have been working very closely with experimental cancer genomics researchers, which has made me keenly aware of the consequences of analytical errors on downstream functional research. Therefore, building a comprehensive error model for large-scale genomic analysis and developing cross-platform data integration methods have been my primary research interest. Development of visualization tools for viewing integrative genomic data is another key interest as these tools are indispensable for gaining understanding of the experimental data and for reviewing the accuracy of the computational results obtained from the astronomical volume of the genomic data generated with the current technology.

    By focusing on understanding genomic data error model, the tools we developed have contributed to the key discoveries made in the pilot phase of two major cancer genomic initiatives of the National Cancer Institute: Cancer Genome Atlas Project (TCGA) and the Therapeutically Applicable Research to Generate Effective Treatment (TARGET). Understanding the genetic and epigenetic landscape of pediatric cancer is currently the main focus of my research as my group leads the computational analysis of the next-generation sequencing data generated from the St. Jude Children’s Research Hospital - Washington University Pediatric Cancer Genome Project (PCGP). Developing novel approaches that integrate whole-genome sequencing data with RNA sequencing, copy number variation, structural variation, telomere content and gene expression is an ongoing effort. As of Jan. 2013, we have published key findings which unveil the genetic basis of several pediatric cancers including early T-cell precursor acute lymphoblastic leukaemia, retinoblastoma, medulloblastoma, neuroblastoma and high grade glioblastoma.

    Research Lab


    Selected Publications

    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 121(3):485-8, 2013. (co-first author)

    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 Published online, 2013.

    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 481(7381):329-34, 2012.

    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 481(7380):157-63, 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 data. Genome Biol 13(12):R113, 2012.

    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 R; for the St Jude Children’s Research Hospital - Washington University Pediatric Cancer Genome Project. Novel mutations target distinct subgroups of medulloblastoma. Nature 488(7409):43-8, 2012. (co-corresponding author).

    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 44(3):251-3, 2012. (co-corresponding author).

    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 307(10):1062-71, 2012. (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 U S A 109(8):3184-9, 2012.

    Downing JR, Wilson RK, Zhang J, Mardis ER, Pui C-H, Ding L, Ley TJ, Evans WE. The Pediatric Cancer Genome Project. Nature Genetics 44: 619-622, 2012.

    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 22: 153-166, 2012.

    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 22:683-97, 2012.

    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 U S A 109(36):14476-81, 2012.

    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, Zhang J. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nature Methods 8(8):652-4, 2011.

    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 118(11):3080-7, 2011.

    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 471(7337):235-9, 2011. (co-first author)

    Integrated Genomic Analyses of Ovarian Carcinoma (2011). The Cancer Genome Atlas Research Network. Nature 474(7353):609-15, 2011.

    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 27(6):865-6, 2011.

    Mullighan CG, Su X, Zhang J, Radtke I, Phillips LA, Miller CB, et al. Deletion of IKZF1 and Prognosis in Acute Lymphoblastic Leukemia. N Engl J Med 360:470-80, 2009.

    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 U S A 106:9414-8, 2009. (co-first author)

    Comprehensive genomic characterization defines human glioblastoma genes and core pathways. The Cancer Genome Atlas Research Network. Nature 455:1061-8, 2008.

    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 447:1087-93, 2007.

    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 Computational Biology (5):e53, 2005.

    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 73(6):1073-81, 2003.

    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 22(2):121-8, 2003.

    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 AY, 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 291: 1145-1434, 2001.

    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. Nucleic Acids Res. 25:3389-3402, 1997.

    Complete list of publications

    Last updated: January 2013