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Gang Wu, PhD
Gang Wu, PhD

Gang Wu, PhD

Associate Member, St. Jude Faculty

  • Director, Center for Applied Bioinformatics



Postdoctoral Fellow in Bioinformatics - Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
PhD - University of Maryland Baltimore County, Baltimore, Maryland, USA
MS - Wuhan University, Wuhan, Hubei Province, China
BS - Wuhan University, Wuhan, Hubei Province, China

Research Interests

  • Understanding the complexity of transcriptomes and epigenomes in normal brain cells and the aberrant events in brain tumor cells, as well as in motor neurons of Amyotrophic Lateral Sclerosis patients.
  • Identifying germline risk variants and novel risk genes for brain tumors and neurodegenerative diseases.
  • Modeling complex chromosomal re-arrangements through novel technology and innovative methods.
  • Bioinformatics method evaluation and optimization.

Selected Publications

Chen W, Wang S, Tithi SS, Ellison DW, Schaid DJ, Wu G. A rare variant analysis framework using public genotype summary counts to prioritize disease- predisposition genes. Nat Commun. May 11, 2022;13(1):2592. PMID: 35545612; Corresponding author.

Rampersaud E, Kang G, Palmer LE, Rashkin SR, Wang S, Bi W, Alberts NM, Anghelescu D, Barton M, Birch K, Boulos N, Brandow AM, Brooke RJ, Chang TC, Chen W, Cheng Y, Ding J, Easton J, Hodges JR, Kanne CK, Levy S, Mulder H, Patel AP, Puri L, Rosencrance C, Rusch M, Sapkota Y, Sioson E, Sharma A, Tang X, Thrasher A, Wang W, Yao Y, Yasui Y, Yergeau D, Hankins JS, Sheehan VA, Downing JR, Estepp JH, Zhang J, DeBaun M, Wu G#, Weiss MJ#. A polygenic score for acute vaso-occlusive pain in pediatric sickle cell disease. Blood Adv. Jul 27, 2021;5(14):2839-2851. PMID: 34283174 #Co-corresponding author.

Pinto EM, Figueiredo BC, Chen W, Galvao HCR, Formiga MN, Fragoso MCBV, Ashton-Prolla P, Ribeiro EMSF, Felix G, Costa TEB, Savage SA, Yeager M, PalmeroEI, Volc S, Salvador H, Fuster-Soler JL, Lavarino C, Chantada G, Vaur D, Odone-Filho V, Brugières L, Else T, Stoffel EM, Maxwell KN, Achatz MI, Kowalski L, deAndrade KC, Pappo A, Letouze E, Latronico AC, Mendonca BB, Almeida MQ, BrondaniVB, Bittar CM, Soares EWS, Mathias C, Ramos CRN, Machado M, Zhou W, Jones K,Vogt A, Klincha PP, Santiago KM, Komechen H, Paraizo MM, Parise IZS, HamiltonKV, Wang J, Rampersaud E, Clay MR, Murphy AJ, Lalli E, Nichols KE, Ribeiro RC,Rodriguez-Galindo C, Korbonits M, Zhang J, Thomas MG, Connelly JP, Pruett-MillerS, Diekmann Y, Neale G, Wu G, Zambetti GP. XAF1 as a modifier of p53 functionand cancer susceptibility. Sci Adv Jun 24;6(26):eaba3231, 2020. doi:10.1126/sciadv.aba3231. PMID: 32637605

Chen W, Zhang S, Williams J, Ju B, Shaner B, Easton J, Wu G, Chen X. A comparison of methods accounting for batch effects in differential expression analysis of UMI count based single cell RNA sequencing. Comput Struct Biotechnol J 30(18):861-873, 2020. doi: 10.1016/j.csbj.2020.03.026. PMID: 32322368

Smith KS*, Xu K*, Mercer KS, Boop F, Klimo P, DeCupyere M, Grenet J, Robinson S, Dunphy P, Baker SJ, Ellison DW, Merchant TE, Upadayaya SA, Gajjar A, Wu G, Orr BA, Robinson GW, Northcott PA, Roussel MF. 2020. Patient-derived orthotopic xenografts of pediatric brain tumors: a St. Jude resource. Acta Neuropathologica Jun 10, 2020. doi: 10.1007/s00401-020-02171-5. PMID: 32519082

Rampersaud E, Ziegler DS, Iacobucci I, Payne-Turner D, Churchman ML, Schrader KA, Joseph V, Offit K, Tucker K, Sutton R, Warby M, Chenevix-Trench G, Huntsman DG, Tsoli M, Mead RS, Qu C, Leventaki V, Wu G, Mullighan CG. Germline deletion of ETV6 in familial acute lymphoblastic leukemia. Blood Adv Apr 9;3(7):1039-1046, 2019. PMID: 30940639

Silveira AB, Kasper LH, Fan Y, Jin H, Wu G, Shaw TI, Zhu X, Larson JD, Easton J, Shao Y, Yergeau DA, Rosencrance C, Boggs K, Rusch MC, Ding L, Zhang J, Finkelstein D, Noyes RM, Russell BL, Xu B, Broniscer A, Wetmore C, Pounds SB, Ellison DW, Zhang J, Baker SJ. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathol Apr;137(4):637-655, 2019. doi: 10.1007/s00401-019-01975-4. Epub 2019 Feb 15. PMID: 30770999

Larson JD, Kasper LH, Paugh BS, Jin H, Wu G, Kwon CH, Fan Y, Shaw TI, Silveira AB, Qu C, Xu R, Zhu X, Zhang J, Russell HR, Peters JL, Finkelstein D, Xu B, Lin T, Tinkle CL, Patay Z, Onar-Thomas A, Pounds SB, McKinnon PJ, Ellison DW, Zhang J, Baker SJ. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell Jan 14;35(1):140-155.e7, 2019. PMID: 30595505

Xu K, Ding L, Chang TC, Shao Y, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW#, Zhang J#, Baker SJ#, Wu G#. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol Jan;137(1):123-137, 2019. PMID: 30267146 Corresponding author

Walsh MF, Ritter DI, Kesserwan C, Sonkin D, Chakravarty D, Chao E, Ghosh R, Kemel Y, Wu G, Lee K, Kulkarni S, Hedges D, Mandelker D, Ceyhan-Birsoy O, Luo M, Drazer M, Zhang L, Offit K, Plon SE. Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes. Hum Mutat Nov;39(11):1542-1552, 2018. PMID: 30311369

Wu G, Fan L, Edmonson MN, Shaw T, Boggs K, Easton J, Rusch MC, Webb TR, Zhang J, Potter PM. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping. RNA Aug;24(8):1056-1066, 2018. PMID: 29844105 First author

Pottier C, Rampersaud E, Baker M, Wu G, Wuu J, McCauley JL, Zuchner S, Schule R, Bermudez C, Hussain S, Cooley A, Wallace M, Zhang J, Taylor JP, Benatar M, Rademakers R. Identification of compound heterozygous variants in OPTN in an ALS-FTD patient from the CReATe consortium: a case report. Amyotroph Lateral Scler Frontotemporal Degener Aug;19(5-6):469-471, 2018. doi: 10.1080/21678421.2018.1452947. Epub 2018 Mar 20. PMID: 29558868; PubMed Central PMCID: PMC6116528

Chen W, Li Y, Easton J, Finkelstein D, Wu G, Chen X. UMI-count modeling and differential expression analysis for single-cell RNA sequencing. Genome Biol May 31;19(1):70, 2018. PMID: 29855333

Wei L*, Murphy BL*, Wu G*, Parker M, Easton J, Gilbertson RJ, Zhang J, Roussel MF. Exome sequencing analysis of murine medulloblastoma models identifies WDR11 as a potential tumor suppressor in Group 3 tumors. Oncotarget Sep 12;8(39):64685-64697, 2017. PMID: 29029386 Co-first author

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 biologically indeterminate spitzoid tumors by RNA sequencing. Mod Pathol. 2016 Apr;29(4):359-69.  PMID: 26892443. First author

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 CH, Nichols KE, Downing JR. Germline Mutations in Predisposition Genes in Pediatric Cancer. N Engl J Med. 2015 Dec 10;373(24):2336-2346. PMID: 26580448. Co-first author

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 Dec;16(16):1659-66.  PMID: 26522332.  Co-first author

Koçer ZA, Fan Y, Huether R, Obenauer J, Webby RJ, Zhang J, Webster RG#, Wu G#. Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses. Sci Rep. 2014 Dec 12;4:7455. PMID: 25503687. Co-corresponding author

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. PMID: 24458951.

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.2014 May;46(5):444-450.  PMID: 24705251. Co-first author

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. 2013 Jun;45(6):602-12.  PMID: 23583981.

Kuhn E*, Wu RC*, Guan B*, Wu G*, Zhang J, Wang Y, Song L, Yuan X, Wei L, Roden RB, Kuo KT, Nakayama K, Clarke B, Shaw P, Olvera N, Kurman RJ, Levine DA, Wang TL, Shih IeM. Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analyses. J Natl Cancer Inst. 2012 Oct 3;104(19):1503-13.  PMID: 22923510. 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. 2012 Feb 21;109(8):3184-9.  PMID: 22308418.

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. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet. 2012 Jan 29;44(3):251-3.  PMID: 22286216. Co-first author

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.  PMID: 22237106.

Wu G, Zheng Y, Qureshi I, Zin HT, Beck T, Bulka B, Freeland SJ. SGDB: a database of synthetic genes re-designed for optimizing protein over-expression. Nucleic Acids Res. 2007 Jan;35(Database issue):D76-9.  PMID: 17062619. First author

Nie L, Wu G, Brockman FJ, Zhang W. Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins. Bioinformatics. 2006 Jul 1;22(13):1641-7.  PMID: 16675466

Last update: June 2022