Ph.D. Genetics Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University

Dynamic and plastic cellular behaviors are the key features of many complex biological processes such as development and disease progression. Rigorous description and theoretical analysis of the cellular dynamics are critical to elucidate these processes. We use systems approach to understand cellular plasticity arising from intrinsic dynamics of gene regulatory networks and intercellular communications. We are interested in a wide spectrum of biological problems including T cell differentiation, epithelial plasticity during development and cancer progression, and specialization of motor neurons in early embryos. We build general theoretical frameworks and specific models to evaluate conflicting hypotheses in silico, to make predictions at gene and cellular levels, and to improve the intuitive understanding of complex biological systems.

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Groves SM, Panchy N, Tyson DR, Harris LA, Quaranta V, Hong T. Involvement of epithelial-mesenchymal transition genes in small cell lung cancer phenotypic plasticity. Cancers 2023, 15(5):1477 [Link]

Nordick B, Yu PY, Liao G, Hong T. Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression. Nucleic Acids Res 2022, 50(7):3693 [Link]

Nordick B, Park MCY, Quaranta V, Hong T. Cooperative RNA degradation stabilizes intermediate epithelial-mesenchymal states and supports a phenotypic continuum. iScience 2022, 25(10):105224 [Link]

Panchy N, Watanabe K, Takahashi M, Willems A, Hong T. Comparative single-cell transcriptomes of dose and time dependent epithelial–mesenchymal spectrums. NAR Genom Bioinform 2022, 4(3):lqac072 [Link]

Li C-J, Liau ES, Lee Y-H, Haung Y-Z, Liu Z, Willems A, Garside V, McClinn E, Chen J-A, Hong T. MicroRNAs govern bistable cell differentiation and lineage segregation via noncanonical feedback. Mol Syst Biol 2021, 17:e9945 [Link]

Liu Z, Shpak E, Hong T. A mathematical model for understanding synergy and tradeoff in gene expression patterns of the shoot apical meristem. Comput Struct Biotechnol J 2020, 18:1878 [Link]

Panchy N, von Arnim AG, Hong T. Early detection of daylengths with a feedforward circuit coregulated by circadian and diurnal cycles. Biophys J 2020, 119 (9), 1878-1895 [Link]

Panchy N, Azeredo-Tseng C, Luo M, Randall N and Hong T. Integrative transcriptomic analysis reveals a multiphasic epithelial–mesenchymal spectrum in cancer and non-tumorigenic cells. Front Oncol 2020 9:1479 [Link]

Watanabe K*, Panchy N*, Noguchi S, Suzuki H, Hong T. Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition. npj Syst Biol Appl 2019, 5 (21) [Link]

Ye Y, Kang X, Bailey J, Li C, Hong T. An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. PLoS Comput Biol 2019, 15 (3), e1006855 [Link]