Student Publications

  • 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, 57(1). https://doi.org/10.1146/annurev-genet-030723-120717
  • Leung, A. K.-Y., Yao, L., & Yu, H. (2022). Functional genomic assays to annotate enhancer–promoter interactions genome wide. Human Molecular Genetics, 31(R1), R97–R104. https://doi.org/10.1093/hmg/ddac204
  • 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), Article 7. https://doi.org/10.1038/s41587-022-01211-7
  • Meyer, M. J., Beltrán, J. F., Liang, S., Fragoza, R., Rumack, A., Liang, J., ... & Yu, H. (2018). Interactome INSIDER: a structural interactome browser for genomic studies. Nature methods15(2), 107.
  • Wierbowski, S. D., Fragoza, R., Liang, S., & Yu, H. (2018). Extracting Complementary Insights from Molecular Phenotypes for Prioritization of Disease-Associated Mutations. Current Opinion in Systems Biology.
  • Duneau D., Sun H., Revah J., San Miguel K., Kunerth H.D., Caldas I.V., Messer P.W., Scott J.G., and Buchon, N. (2018). Signatures of Insecticide Selection in the Genome of Drosophila melanogaster. G3: Genes, Genomes, Genetics, Early online September 6, 2018.
  • Wei K.H.-C., Lower S.E., Caldas I.V., Sless T.J., Barbash D.A., and Clark, A.G. (2018). Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny. Molecular Biology and Evolution, 35(4) pp. 925-941.
  • Jackson Champer, Jingxian Liu, Suh Yeon Oh, Riona Reeves, Anisha Luthra, Nathan Oakes, Andrew G. Clark, and Philipp W. Messer (2018). Reducing resistance allele formation in CRISPR gene drive. Proceedings of the National Academy of Sciences (PNAS).
  • Tinyi Chu, Edward J. Rice, Gregory T. Booth, H. Hans Salamanca, hong Wang, Leighton J. Core, Sharon L. Longo, Robert J. Corona, Lawrence S. Chin, John T. Lis, Hojoong Kwak, Charles G. Danko, Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme, Nature Genetics (2018).
  • Jacob M. Tome, Nathaniel D. Tippens, John T. Lis, Single-Molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers, Nature Genetics (2018).
  • Saikia, M., Burnham, P., Keshavjee, S. H., Wang, M. F. Z., Heyang, M., Moral-Lopez, P., Hinchman, M. M., Danko, C. G., Parker, J. S. L. and De Vlaminck, I. (2018). Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells. Nature Methods. doi: 10.1038/s41592-018-0259-9, Nature (2018)
  • Borthakur, Ayon, Cleland, Thomas A., A Spike Time-Dependent Online Learning Algorithm Derived From Biological Olfaction, Frontiers in Neuroscience, 2019
  • Borthakur, Ayon, Cleland, Thomas A., Signal Conditioning for Learning in the Wild, DL Association for Computing Machinery, 2019