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Gang Wu
Bioinformatics Research Scientist
Group Lead - DNA analysis group
Department of Computational Biology
St Jude Children's Research Hospital
262 Danny Thomas Place
Memphis, TN 38105
Email: wug1 @ umbc.edu
Gang.Wu @ stjude.org
Website: http://userpages.umbc.edu/~wug1/


My current research

   I am now a bioinformatics scientist in Dr. Jinghui Zhang's research team at St. Jude Children's Research Hospital. I am actively involved in the analysis of next-generation sequencing data in the Pediatric Cancer Genome Project (Downing et al 2012).

My publications (* co- first author)

  1. Gang Wu*, Alexander K Diaz, et al. The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nature Genetics (2014) published online on April 7th, 2014

  2. 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, Gang Wu, 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.

  3. Pawlikowska I, Gang Wu, Edmonson M, Liu Z, Gruber T, Zhang J and Pounds S. The Most Informative Spacing Test Effectively Discovers Biologically Relevant Outliers or Multiple Modes in Expression. Bioinformatics (2014) First published online: January 22, 2014

  4. Chen X, Stewart E, Shelat AA, Qu C,Bahrami A, Hatley M, Gang Wu, et al. Targeting Oxidative Stress in Embryonal Rhabdomyosarcoma. Cancer Cell (2013) Volume 24, Issue 6, 9 December 2013, Pages 710-724.

  5. Faraji F, Hu Y, Gang Wu, Goldberger NE, Walker RC, Zhang J, Hunter KW. An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease. Genome Research (2013) Dec 9 doi: 10.1101/gr.166223.113.

  6. Shah S, Schrader KA, Waanders E, Timms AE, Vijai J, Miething C, Wechsler J, Yang J, Hayes J, Klein RJ, Zhang J, Wei L, Gang Wu, Rusch M, Nagahawatte P, Ma J, Chen SC, Song G, Cheng J, Meyers 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, Raimondi SC, Kuiper RP, Simons A, Schiffman JD, Onel K, Plon SE, Wheeler DA, Ritter D, Ziegler DS, Tucker K, Sutton R, Chenevix-Trench G, Li J, Huntsman DG, Hansford S, Senz J, Walsh T, Lee M, Hahn CN, Roberts KG, King MC, Lo SM, Levine RL, Viale A, Socci ND, Nathanson KL, Scott HS, Daly M, Lipkin SM, Lowe SW, Downing JR, Altshuler D, Sandlund JT, Horwitz MS, Mullighan CG, Offit K. A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia. Nat Genet. (2013) Oct, 45(10):1226-31.

  7. Zhang J, Gang Wu, 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) Apr 14. doi:10.1038/ng.2611

  8. Wang J, Gang Wu, Chen L, Zhang W. Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria. BMC Genomics (2013) Feb 19;14:112. doi: 10.1186/1471-2164-14-112

  9. Qiao J, Shao M, Chen L, Wang J, Gang Wu, Tian X, Liu J, Huang S, Zhang W. Systematic characterization of hypothetical proteins in Synechocystis sp. PCC 6803 reveals proteins functionally relevant to stress responses. Gene (2013) Jan 1;512(1):6-15. doi: 10.1016/j.gene.2012.10.004.

  10. 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, Gang Wu, 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) 45, 242-252.

  11. Mignon L. Loh, Jinghui Zhang, Richard C. Harvey, Kathryn Roberts, Debbie Payne-Turner, Huining Kang, Gang Wu, Xiang Chen, Jared Becksfort, Michael Edmonson, Kenneth H. Buetow, William L. Carroll, I-Ming Chen, Brent Wood, Michael J. Borowitz, Meenakshi Devidas, Daniela S. Gerhard1, Paul Bowman1, Eric Larsen1, Naomi Winick1, Elizabeth Raetz, Malcolm Smith1, James R. Downing, Cheryl L. Willman, Charles G. Mullighan, and Stephen P. Hunger. Tyrosine kinome sequencing of pediatric acute lymphoblastic leukemia: a report from The Children's Oncology Group TARGET Project. Blood. 121 (2013) (3):485-8.

  12. Tanja A. Gruber, Amanda Larson Gedman, Jinghui Zhang, Cary S. Koss, Suresh Marada, Huy Q. Ta, Shann-Ching Chen, Xiaoping Su, Stacey K. Ogden, Jinjun Dang, Gang Wu, Vedant Gupta, Anna K. Andersson, Stanley Pounds, Lei Shi, John Easton, Michael I. Barbato, Heather L. Mulder, Jayanthi Manne, Jianmin Wang, Michael Rusch, Swati Ranade, Ramapriya Ganti, Matthew Parker, Jing Ma, Ina Radtke, Li Ding, Giovanni Cazzaniga, Andrea Biondi, Steven M. Kornblau, Farhad Ravandi, Hagop Kantarjian, Stephen D. Nimer, Konstanze D?hner, Hartmut D?hner, Timothy J. Ley, Paola Ballerini, Sheila Shurtleff, Daisuke Tomizawa, Souichi Adachi, Yasuhide Hayashi, Akio Tawa, Lee-Yung Shih, Der-Cherng Liang, Jeffrey E. Rubnitz, Ching-Hon Pui, Elaine R. Mardis, Richard K. Wilson, James R. Downing. An Inv(16)(p13.3q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein Defines an Aggressive Subtype of Pediatric Acute Megakaryoblastic Leukemia. Cancer Cell. (2012) 22:683-697.

  13. McEvoy J, Ulyanov A, Brennan R, Gang Wu, 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

  14. Parker M, Chen X, Bahrami A, Dalton J, Rusch M, Gang Wu, 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

  15. E. Kuhn*, R.C. Wu*, B. Guan*, Gang Wu*, J. Zhang, Y. Wang, L. Song, X. Yuan, L. Wei, R. B.S. Roden, K.T. Kuo, K. Nakayama, B. Clarke, P. Shaw, N. Olvera, D. A. Levine, R. J. Kurman, T. L. Wang, I.M. Shih. Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analyses. Journal of the National Cancer Institute, 2012 Aug 23.

  16. G. Robinson, M. Parker, T.A. Kranenburg, C. Lu, X. Chen, L. Ding, T.N. Phoenix, E. Hedlund, L. Wei, X. Zhu, N. Chalhoub, S. J. Baker, R. Huether, R. Kriwacki, N. Curley, R. Thiruvenkatam, J. Wang, Gang Wu, M. Rusch, X. Hong, J. Becksfort, P. Gupta, J. Ma, J. Easton, B. Vadodaria, A. Onar-Thomas, T. Lin, S. Li, S. Pounds, S. Paugh, D.Zhao, D. Kawauchi, M. F. Roussel, D. Finkelstein, D. W. Ellison, C. C. Lau, E. Bouffet, T. Hassall, S. Gururangan, R. Cohn, R. S. Fulton, L. L. Fulton, D. J. Dooling, K. Ochoa, A. Gajjar, E. R. Mardis, R. K. Wilson, J. R. Downing, J. Zhang & R. J. Gilbertson. Novel mutations target distinct subgroups of medulloblastoma. Nature 488 (2012) 43-48.

  17. Gang Wu*, A. Broniscer*, T.A. McEachron*, C. Lu, B.S. Paugh, J. Becksfort, C. Qu, L. Ding, R. Huether, M. Parker, J. Zhang, A. Gajjar, M.A. Dyer, C.G. Mullighan, R.J. Gilbertson, E.R. Mardis, R.K. Wilson, J.R. Downing, D.W. Ellison, and S.J. Baker, Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet 44 (2012) 251-3.

  18. J. Zhang*, L. Ding*, L. Holmfeldt*, Gang Wu, S.L. Heatley, D. Payne-Turner, J. Easton, X. Chen, J. Wang, M. Rusch, C. Lu, S.C. Chen, L. Wei, J.R. Collins-Underwood, J. Ma, K.G. Roberts, S.B. Pounds, A. Ulyanov, J. Becksfort, P. Gupta, R. Huether, R.W. Kriwacki, M. Parker, D.J. McGoldrick, D. Zhao, D. Alford, S. Espy, K.C. Bobba, G. Song, D. Pei, C. Cheng, S. Roberts, M.I. Barbato, D. Campana, E. Coustan-Smith, S.A. Shurtleff, S.C. Raimondi, M. Kleppe, J. Cools, K.A. Shimano, M.L. Hermiston, S. Doulatov, K. Eppert, E. Laurenti, F. Notta, J.E. Dick, G. Basso, S.P. Hunger, M.L. Loh, M. Devidas, B. Wood, S. Winter, K.P. Dunsmore, R.S. Fulton, L.L. Fulton, X. Hong, C.C. Harris, D.J. Dooling, K. Ochoa, K.J. Johnson, J.C. Obenauer, W.E. Evans, C.H. Pui, C.W. Naeve, T.J. Ley, E.R. Mardis, R.K. Wilson, J.R. Downing, and C.G. Mullighan, The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481 (2012) 157-63.

  19. J. Zhang*, C.A. Benavente*, J. McEvoy*, J. Flores-Otero, L. Ding, X. Chen, A. Ulyanov, Gang Wu, M. Wilson, J. Wang, R. Brennan, M. Rusch, A.L. Manning, J. Ma, J. Easton, S. Shurtleff, C. Mullighan, S. Pounds, S. Mukatira, P. Gupta, G. Neale, D. Zhao, C. Lu, R.S. Fulton, L.L. Fulton, X. Hong, D.J. Dooling, K. Ochoa, C. Naeve, N.J. Dyson, E.R. Mardis, A. Bahrami, D. Ellison, R.K. Wilson, J.R. Downing, and M.A. Dyer, A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature 481 (2012) 329-34.

  20. Y. Hu, Gang Wu, M. Rusch, L. Lukes, K.H. Buetow, J. Zhang, and K.W. Hunter, Integrated cross-species transcriptional network analysis of metastatic susceptibility. Proc Natl Acad Sci U S A 109 (2012) 3184-9.

  21. A. Gegonne, X. Tai, J. Zhang, Gang Wu, J. Zhu, A. Yoshimoto, J. Hanson, C. Cultraro, Q.R. Chen, T. Guinter, Z. Yang, K. Hathcock, A. Singer, J. Rodriguez-Canales, L. Tessarollo, S. Mackem, D. Meerzaman, K. Buetow, and D.S. Singer, 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).

  22. J. Zhang*, C.G. Mullighan*, R.C. Harvey, Gang Wu, X. Chen, M. Edmonson, K.H. Buetow, W.L. Carroll, I.M. Chen, M. Devidas, D.S. Gerhard, M.L. Loh, G.H. Reaman, M.V. Relling, B.M. Camitta, W.P. Bowman, M.A. Smith, C.L. Willman, J.R. Downing, and S.P. Hunger, Key pathways are frequently mutated in high-risk childhood acute lymphoblastic leukemia: a report from the Children's Oncology Group. Blood 118 (2011) 3080-7.

  23. I.M. Shih, K. Nakayama, Gang Wu, N. Nakayama, J. Zhang, and T.L. Wang, Amplification of the ch19p13.2 NACC1 locus in ovarian high-grade serous carcinoma. Mod Pathol (2011).

  24. F. Li, L. Nie, Gang Wu, J. Qiao, and W. Zhang, Prediction and Characterization of Missing Proteomic Data in Desulfovibrio vulgaris. Comp Funct Genomics 2011 (2011) 780973.

  25. R.J. Clifford, J. Zhang, D.M. Meerzaman, M.S. Lyu, Y. Hu, C.M. Cultraro, R.P. Finney, J.M. Kelley, S. Efroni, S.I. Greenblum, C.V. Nguyen, W.L. Rowe, S. Sharma, Gang Wu, C. Yan, H. Zhang, Y.H. Chung, J.A. Kim, N.H. Park, I.H. Song, and K.H. Buetow, Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma. Hepatology 52 (2010) 2034-43.

  26. L. Nie*, Gang Wu*, and W. Zhang, Statistical application and challenges in global gel-free proteomic analysis by mass spectrometry. Crit Rev Biotechnol 28 (2008) 297-307.

  27. Gang Wu, Y. Zheng, I. Qureshi, H.T. Zin, T. Beck, B. Bulka, and S.J. Freeland, SGDB: a database of synthetic genes re-designed for optimizing protein over-expression. Nucleic Acids Res 35 (2007) D76-9.

  28. Gang Wu*, L. Nie*, and S.J. Freeland, The effects of differential gene expression on coding sequence features: analysis by one-way ANOVA. Biochem Biophys Res Commun 358 (2007) 1108-13.

  29. Gang Wu, L. Dress, and S.J. Freeland, Optimal encoding rules for synthetic genes: the need for a community effort. Mol Syst Biol 3 (2007) 134.

  30. J.C. Scholten, D.E. Culley, F.J. Brockman, Gang Wu, and W. Zhang, Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: Involvement of an ancient horizontal gene transfer. Biochem Biophys Res Commun 352 (2007) 48-54.

  31. L. Nie, Gang Wu, D.E. Culley, J.C. Scholten, and W. Zhang, Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications. Crit Rev Biotechnol 27 (2007) 63-75.

  32. W. Zhang, D.E. Culley, Gang Wu, and F.J. Brockman, Two-component signal transduction systems of Desulfovibrio vulgaris: structural and phylogenetic analysis and deduction of putative cognate pairs. J Mol Evol 62 (2006) 473-87.

  33. Gang Wu*, J.B. Wolf*, A.F. Ibrahim, S. Vadasz, M. Gunasinghe, and S.J. Freeland, Simplified gene synthesis: a one-step approach to PCR-based gene construction. J Biotechnol 124 (2006) 496-503.

  34. Gang Wu, L. Nie, and W. Zhang, Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. Antonie Van Leeuwenhoek 89 (2006) 135-46.

  35. Gang Wu, L. Nie, and W. Zhang, Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance. Biochem Biophys Res Commun 344 (2006) 114-21.

  36. Gang Wu, N. Bashir-Bello, and S.J. Freeland, The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression. Protein Expr Purif 47 (2006) 441-5.

  37. L. Nie, Gang Wu, and W. Zhang, Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations. Biochem Biophys Res Commun 339 (2006) 603-10.

  38. L. Nie*, Gang Wu*, and W. Zhang, Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis. Genetics 174 (2006) 2229-43.

  39. L. Nie, Gang Wu, F.J. Brockman, and W. Zhang, Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins. Bioinformatics 22 (2006) 1641-7.

  40. Gang Wu, D.E. Culley, and W. Zhang, Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. Microbiology 151 (2005) 2175-87.

  41. C. Xu*, Gang Wu*, Y. Zohar, and S.J. Du, Analysis of myostatin gene structure, expression and function in zebrafish. J Exp Biol 206 (2003) 4067-79.

  42. Gang Wu*, Yu D, Tu M, Xia S, Chong Y, Kang H. Growth and population ecology of Ranunculus sceleratus in Donghu Lake,Wuhan. Acta Hydrobiologica Sinica (Shui Sheng Sheng wu Hsueh bao) 23 (1999) 211-216.

  43. G.A. Yan, J.W. Jiang, Gang Wu, and X. Yan, Disappearance of linear alkylbenzene sulfonate from different cultures with Anabaena sp. HB 1017. Bull Environ Contam Toxicol 60 (1998) 329-34.

Research Interests at UMBC

   Heterologous gene expression is a process to express a gene in a non-native host. The goal of my Ph. D. study was to improve heterologous gene expression level by redesigning nucleotide sequence.

   I developed a web application Synthetic Gene Designer to optimize codon usage for boosting protein expression. If the link above is not working, try here . The Synthetic Gene Database has been moved to here as well. Please update your bookmark.

Last update: July, 2012.