Li, B. I., Alvarez, M. J., Zhao, H., Chirathivat, N., Califano, A., & Shen, M. M. (2025). The regulatory architecture of the primed pluripotent cell state. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57894-4

Jin, C., Wang, X., Yang, J., Kim, S., Hudgins, A. D., Gamliel, A., Pei, M., Contreras, D., Devos, M., Guo, Q., Vijg, J., Conti, M., Hoeijmakers, J., Campisi, J., Lobo, R., Williams, Z., Rosenfeld, M. G., & Suh, Y. (2024). Molecular and genetic insights into human ovarian aging from single-nuclei multi-omics analyses. Nature Aging. https://doi.org/10.1038/s43587-024-00762-5

Mellis, I. A., Melzer, M. E., Bodkin, N., & Goyal, Y. (2024). Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03351-2

Buschur, K. L., Riley, C., Saferali, A., Castaldi, P., Zhang, G., Aguet, F., Ardlie, K. G., Durda, P., Craig Johnson, W., Kasela, S., Liu, Y., Manichaikul, A., Rich, S. S., Rotter, J. I., Smith, J., Taylor, K. D., Tracy, R. P., Lappalainen, T., Graham Barr, R., … Benos, P. V. (2023). Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis. Respiratory Research, 24(1). https://doi.org/10.1186/s12931-023-02316-6

Zhang, R., Tai, J., & Pei, S. (2023). Ensemble inference of unobserved infections in networks using partial observations. PLOS Computational Biology, 19(8), e1011355. https://doi.org/10.1371/journal.pcbi.1011355

He, B., Wang, K., Xiang, J., Bing, P., Tang, M., Tian, G., Guo, C., Xu, M., & Yang, J. (2022). DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network. Briefings in Bioinformatics, 23(6). https://doi.org/10.1093/bib/bbac405

Pahl, M. C., Doege, C. A., Hodge, K. M., Littleton, S. H., Leonard, M. E., Lu, S., Rausch, R., Pippin, J. A., De Rosa, M. C., Basak, A., Bradfield, J. P., Hammond, R. K., Boehm, K., Berkowitz, R. I., Lasconi, C., Su, C., Chesi, A., Johnson, M. E., Wells, A. D., … Grant, S. F. A. (2021). Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-27001-4

Hayward, S. B., & Ciccia, A. (2021). Towards a CRISPeR understanding of homologous recombination with high-throughput functional genomics. Current Opinion in Genetics & Development, 71, 171–181. https://doi.org/10.1016/j.gde.2021.08.006