Yao, L., Shah, S. R., Ozer, A., Zhang, J., Pan, X., Xia, T., Fangal, V. D., Leung, A. K.-Y., Wei, M., Lis, J., & Yu, H. (2025). High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples. bioRxiv.
Zhang, J., Leung, A. K.-Y., Zhu, Y., Yao, L., Willis, A., Pan, X., Ozer, A., Zhou, Z., Silklenka, K., Berrera, A., Liang, J., Tippens, N. D., Reddy, T. E., Lis, J. T., & Yu, H. (2025). Comprehensive Evaluation of Diverse Massively Parallel Reporter Assays to Functionally Characterize Human Enhancers Genome-wide. bioRxiv.
Paramo, M. I., Leung, A. K.-Y., Shah, S. R., Zhang, J., Tippens, N. D., Liang, J., Yao, L., Jin, Y., Pan, X., Ozer, A., Lis, J. T., & Yu, H. (2025). Simultaneous measurement of intrinsic promoter and enhancer potential reveals principles of functional duality and regulatory reciprocity. bioRxiv.
Wang, N., Pachai, M. R., Li, D., Lee, C. J., Warda, S., Khudoynazarova, M. N., Cho, W. H., Xie, G., Shah, S. R., Yao, L., Qian, C., Wong, E. W. P., Yan, J., Tomas, F. V., Hu, W., Kuo, F., Gao, S. P., Luo, J., Smith, A. E., Han, M., Gao, D., Ge, K., Yu, H., Chandarlapaty, S., Lyer, G.V., Rosenberg, J.E., Solit, D.B., Al-Ahmadie, H.A., Chi, P. & Chen, Y. (2025). Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A-menin to bivalent promoters. Nature Genetics.
Chen, Y., Paramo, M. I., Zhang, Y., Yao, L., Shah, S. R., Jin, Y., Zhang, J., Pan, X., & Yu, H. (2023). Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants. Annual Review of Genetics, 1(57),
201-222.
Yao, L., Liang, J., Ozer, A., Leung, A. K.-Y., Lis, J. T., & Yu, H. (2022). A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers. Nature Biotechnology, 40(7),
1056-1065.
Cotter, K. A., Shah, S. R., Paramo, M. I., Lou, S., Yao, L., Rubin, P. D., Chen, Y., Gerstein, M., Rubin, M. A., & Yu, H. (2022). Capped nascent RNA sequencing reveals novel therapy-responsive enhancers in prostate cancer. bioRxiv.
Yan, R., Li, J., Zhou, Y., Yao, L., Sun, R., Xu, Y., Ge, Y., & An, G. (2020). Inhibition of DCLK1 down-regulates PD-L1 expression through Hippo pathway in human pancreatic cancer. Life Sciences, 241,
117150.
Fragoza, R., Das, J., Wierbowski, S. D., Liang, J., Tran, T. N., Liang, S., Beltran, J. F., Rivera-Erick, C. A., Ye, K., Wang, T.-Y., Yao, L., Mort, M., Stenson, P. D., Cooper, D. N., Wei, X., Keinan, A., Schimenti, J. C., Clark, A. G., & Yu, H. (2019). Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nature Communications, 10(1),
1-15.
Babaian, A., Ebou, A., Fegen, A., Kam, H. Y., Novakovsky, G. E., Wong, J., Aïssi D., Yao, L. (2018). bioSyntax: syntax highlighting for computational biology. BMC Bioinformatics, 19(1),
303.
Yao, L., Wang, H., Song, Y., Dai, Z., Yu, H., Yin, M., Wang, D., Yang, X., Wang, J., Wang, T., Cao, N., Zhu, J., Shen, X., Song, G., & Zhao, Y. (2019). Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing. Briefings in Bioinformatics, 20(1),
102-109.
Zhao, Y., Song, Y., Yao, L., Song, G., & Teng, C. (2017). Circulating microRNAs: Promising Biomarkers Involved in Several Cancers and Other Diseases. DNA and Cell Biology, 36(2),
77-94.
Total publications: 15 : co-first author : corresponding author