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Personal profile

Research interests

Our research interests include developing innovative computational tools/methods and utilizing single-cell (epi)genomic techniques to gain a comprehensive understanding of gene regulation in mammalian models and human diseases, particularly in brain tumors and neuropsychiatric disorders. 

Available to Mentor:

  • PhD/MSTP Students
  • Postdocs
  • Residents and Fellows


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Collaborations and top research areas from the last five years

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  • A deep population reference panel of tandem repeat variation

    Ziaei Jam, H., Li, Y., DeVito, R., Mousavi, N., Ma, N., Lujumba, I., Adam, Y., Maksimov, M., Huang, B., Dolzhenko, E., Qiu, Y., Kakembo, F. E., Joseph, H., Onyido, B., Adeyemi, J., Bakhtiari, M., Park, J., Javadzadeh, S., Jjingo, D., Adebiyi, E., & 2 othersBafna, V. & Gymrek, M., Dec 2023, In: Nature communications. 14, 1, 6711.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    3 Scopus citations
  • A guide to the BRAIN Initiative Cell Census Network data ecosystem

    Hawrylycz, M., Martone, M. E., Ascoli, G. A., Bjaalie, J. G., Dong, H. W., Ghosh, S. S., Gillis, J., Hertzano, R., Haynor, D. R., Hof, P. R., Kim, Y., Lein, E., Liu, Y., Miller, J. A., Mitra, P. P., Mukamel, E., Ng, L., Osumi-Sutherland, D., Peng, H., Ray, P. L., & 83 othersSanchez, R., Regev, A., Ropelewski, A., Scheuermann, R. H., Tan, S. Z. K., Thompson, C. L., Tickle, T., Tilgner, H., Varghese, M., Wester, B., White, O., Zeng, H., Aevermann, B., Allemang, D., Ament, S., Athey, T. L., Baker, C., Baker, K. S., Baker, P. M., Bandrowski, A., Banerjee, S., Bishwakarma, P., Carr, A., Chen, M., Choudhury, R., Cool, J., Creasy, H., D'Orazi, F., Degatano, K., Dichter, B., Ding, S. L., Dolbeare, T., Ecker, J. R., Fang, R., Fillion-Robin, J. C., Fliss, T. P., Gee, J., Gillespie, T., Gouwens, N., Zhang, G. Q., Halchenko, Y. O., Harris, N. L., Herb, B. R., Hintiryan, H., Hood, G., Horvath, S., Huo, B., Jarecka, D., Jiang, S., Khajouei, F., Kiernan, E. A., Kir, H., Kruse, L., Lee, C., Lelieveldt, B., Li, Y., Liu, H., Liu, L., Markuhar, A., Mathews, J., Mathews, K. L., Mezias, C., Miller, M. I., Mollenkopf, T., Mufti, S., Mungall, C. J., Orvis, J., Puchades, M. A., Qu, L., Receveur, J. P., Ren, B., Sjoquist, N., Staats, Tward, D., van Velthoven, C. T. J., Wang, Q., Xie, F., Xu, H., Yao, Z., Yun, Z., Zhang, Y. R., Zheng, W. J. & Zingg, B., Jun 2023, In: PLoS biology. 21, 6, e3002133.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    3 Scopus citations
  • Droplet-based single-cell joint profiling of histone modifications and transcriptomes

    Xie, Y., Zhu, C., Wang, Z., Tastemel, M., Chang, L., Li, Y. E. & Ren, B., Oct 2023, In: Nature Structural and Molecular Biology. 30, 10, p. 1428-1433 6 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    5 Scopus citations
  • Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity

    Raviram, R., Raman, A., Preissl, S., Ning, J., Wu, S., Koga, T., Zhang, K., Brennan, C. W., Zhu, C., Luebeck, J., Van Deynze, K., Han, J. Y., Hou, X., Ye, Z., Mischel, A. K., Li, Y. E., Fang, R., Baback, T., Mugford, J., Han, C. Z., & 7 othersGlass, C. K., Barr, C. L., Mischel, P. S., Bafna, V., Escoubet, L., Ren, B. & Chen, C. C., May 16 2023, In: Proceedings of the National Academy of Sciences of the United States of America. 120, 20, e2210991120.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1 Scopus citations
  • Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

    Xie, F., Armand, E. J., Yao, Z., Liu, H., Bartlett, A., Behrens, M. M., Li, Y. E., Lucero, J. D., Luo, C., Nery, J. R., Pinto-Duarte, A., Poirion, O. B., Preissl, S., Rivkin, A. C., Tasic, B., Zeng, H., Ren, B., Ecker, J. R. & Mukamel, E. A., Jul 12 2023, In: Cell Genomics. 3, 7, 100342.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    2 Scopus citations