• 809 Citations

Research output per year

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Personal profile

Research interests

My research interests include computational biology and bioinformatics as they apply to cancer genomics and radiation oncology. My doctoral work focused on developing structural variation discovery tools using next-generation sequencing data, including SVseq 1 & 2. I also worked on algorithmic problems in haplotype inference, recombination, rare variants, etc. My postdoctoral work focused on developing algorithms analyzing whole transcriptome sequencing data to discover RNA specific aberrations and their applications in cancers. We designed and implemented the state-of-the-art gene fusion discovery tool, INTEGRATE, leading to his discoveries of novel biomarkers in breast cancer, liver cancer, leukemia, etc. We implemented the first tool in cancer immunology, INTEGRATE-Neo, to predict neo-antigens from tumor specific gene fusion peptides. We discovered a single-gene biomarker, lncRNA PCAT-14, in prostate cancer metastasis, and novel mid-sized small RNAs in acute myeloid leukemia. I am currently working on creating and integrating advanced computational approaches using high-throughput sequencing data and imaging data into the development of novel diagnostic, prognostic, and therapeutic strategies in cancer.

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Research Output

  • 809 Citations
  • 18 Article
  • 5 Conference contribution
  • 2 Chapter
  • 1 Comment/debate

Gene Fusion Discovery with INTEGRATE

Zhang, J. & Maher, C. A., Jan 1 2020, Methods in Molecular Biology. Humana Press Inc., p. 41-68 28 p. (Methods in Molecular Biology; vol. 2079).

Research output: Chapter in Book/Report/Conference proceedingChapter

  • HPV-EM: an accurate HPV detection and genotyping EM algorithm

    Inkman, M. J., Jayachandran, K., Ellis, T. M., Ruiz, F., McLellan, M. D., Miller, C. A., Wu, Y., Ojesina, A. I., Schwarz, J. K. & Zhang, J., Dec 1 2020, In : Scientific reports. 10, 1, 14340.

    Research output: Contribution to journalArticle

    Open Access
  • The clonal evolution of metastatic colorectal cancer

    Dang, H. X., Krasnick, B. A., White, B. S., Grossman, J. G., Strand, M. S., Zhang, J., Cabanski, C. R., Miller, C. A., Fulton, R. S., Goedegebuure, S. P., Fronick, C. C., Griffith, M., Larson, D. E., Goetz, B. D., Walker, J. R., Hawkins, W. G., Strasberg, S. M., Linehan, D. C., Lim, K. H., Lockhart, A. C. & 5 others, Mardis, E. R., Wilson, R. K., Ley, T. J., Maher, C. A. & Fields, R. C., Jun 2020, In : Science Advances. 6, 24, eaay9691.

    Research output: Contribution to journalArticle

    Open Access
  • Neutrophils promote tumor resistance to radiation therapy

    Wisdom, A. J., Hong, C. S., Lin, A. J., Xiang, Y., Cooper, D. E., Zhang, J., Xu, E. S., Kuo, H. C., Mowery, Y. M., Carpenter, D. J., Kadakia, K. T., Himes, J. E., Luo, L., Ma, Y., Williams, N., Cardona, D. M., Haldar, M., Diao, Y., Markovina, S., Schwarz, J. K. & 1 others, Kirsch, D. G., Sep 10 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 37, p. 18584-18589 6 p.

    Research output: Contribution to journalArticle

    Open Access
  • 11 Scopus citations

    Erratum: Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer (Cell (2018) 174(3) (758–769.e9), (S0092867418308420) (10.1016/j.cell.2018.06.039))

    Quigley, D. A., Dang, H. X., Zhao, S. G., Lloyd, P., Aggarwal, R., Alumkal, J. J., Foye, A., Kothari, V., Perry, M. D., Bailey, A. M., Playdle, D., Barnard, T. J., Zhang, L., Zhang, J., Youngren, J. F., Cieslik, M. P., Parolia, A., Beer, T. M., Thomas, G., Chi, K. N. & 43 others, Gleave, M., Lack, N. A., Zoubeidi, A., Reiter, R. E., Rettig, M. B., Witte, O., Ryan, C. J., Fong, L., Kim, W., Friedlander, T., Chou, J., Li, H., Das, R., Li, H., Moussavi-Baygi, R., Goodarzi, H., Gilbert, L. A., Lara, P. N., Evans, C. P., Goldstein, T. C., Stuart, J. M., Tomlins, S. A., Spratt, D. E., Cheetham, R. K., Cheng, D. T., Farh, K., Gehring, J. S., Hakenberg, J., Liao, A., Febbo, P. G., Shon, J., Sickler, B., Batzoglou, S., Knudsen, K. E., He, H. H., Huang, J., Wyatt, A. W., Dehm, S. M., Ashworth, A., Chinnaiyan, A. M., Maher, C., Small, E. J. & Feng, F. Y., Oct 18 2018, In : Cell. 175, 3, p. 889 1 p.

    Research output: Contribution to journalComment/debate

  • 9 Scopus citations