Tian Hong – Laboratory of Computational Systems Biology

Tian Hong

Associate Professor

Department of Biological Sciences, The University of Texas at Dallas

E-mail: hong@utdallas.edu

Joint Research Associate Professor
Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville

Education & Training

Postdoctoral Scholar Department of Mathematics, Center for Complex Biological Systems, UC Irvine
Ph.D. Genetics, Bioinformatics and Computational Biology, Virginia Tech
M.S. Bioinformatics, Nanyang Technological University, Singapore
B.S. Biological Sciences, Nanyang Technological University, Singapore

Research

Tian Hong is a computational biologist with a broad interest in understanding complex biological processes using systems approach. He has developed a series of models for T cell differentiation. He is currently focusing on plasticity and heterogeneity of epithelial cells and immune cells during development and cancer progression. He is also interested in identifying common performance objectives of biological circuits.

Theme: Plasticity and heterogeneity of cells in development and diseases. Gene regulatory networks.

Biological problems: Dynamical systems of development, immune response and cancer progression. Spatial patterning of tissues.

Approaches: Bioinformatic analysis. Mathematical modeling of biomolecules and cells.

Publications

Paul S, Adetunji J, Hong T *. Widespread biochemical reaction networks enable Turing patterns without imposed feedback. Nat Commun 2024, 15: 8380 (* corresponding author)
[Link] [Article]

Hong T *, Xing J*. Data‐and theory‐driven approaches for understanding paths of epithelial–mesenchymal transition. genesis 2024, 62(2), p.e23591 (* corresponding author)
[Link] [Article]

Uzair M, Urquidi Camacho RA, Liu Z, Overholt AM, DeGennaro D, Zhang L, Herron BS, Hong T, Shpak ED. An updated model of shoot apical meristem regulation by ERECTA family and CLAVATA3 signaling pathways in Arabidopsis. Development 2024, 151 (12) pp.dev-202870
[Link] [Article]

Harrell MA, Liu Z, Campbell BF, Chinsen O, Hong T, Das M. Arp2/3-dependent endocytosis ensures Cdc42 oscillations by removing Pak1-mediated negative feedback. J. Cell Biol. 2024, 223(10)
[Link] [Article]

Gross LJ, McCord RP, LoRe S, Ganusov VV, Hong T, Strickland WC, Talmy D, von Arnim AG, Wiggins G. Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science. PLoS ONE 2023 18(4), p.e0284982
[Link] [Article]

Mykins M, Layo-Carris D, Dunn LR, Skinner DW, McBryar AH, Perez S, Shultz TR, Willems A, Lau BY, Hong T, Krishnan K. Wild-type MECP2 expression coincides with age-dependent sensory phenotypes in a female mouse model for Rett syndrome. J Neurosci Res 2023;00:1–23
[Link] [Article]

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 (* corresponding author)
[Link] [Article]

Willems A, Panchy N, Hong T *. Using single-cell RNA sequencing and microRNA targeting data to improve colorectal cancer survival prediction. Cells 2023, 12(2):228 (* corresponding author)
[Link] [Article]

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 (* corresponding author)
[Link] [Article]

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 (Editor’s choice) (* corresponding author)
[Link] [Article]

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 (* corresponding author)
[Link] [Article]

Willems A, Hong T *. Fate decisions of CD4+ T Cells (book chapter) In: Kraikivski P. (eds) Case Studies in Systems Biology. Springer, Cham. 2021, pp 149-162 (* corresponding author)
[Link]

Nordick B, Hong T *. Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks. BMC Bioinform 2021, 22:481 (* corresponding author)
[Link] [Article]

Panchy N, Watanabe K, Hong T *. Interpretable, scalable, and transferrable functional projection of large-scale transcriptome data using constrained matrix decomposition. Front Genet 2021, 12:719099
(* corresponding author)
[Link] [Article]

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

Liu Z, Shpak ED, Hong T *. A mathematical model for understanding synergistic regulations and paradoxical feedbacks in the shoot apical meristem. Comput Struct Biotechnol J 2020, 18:1878 (* corresponding author)
[Link] [Article]

Panchy N, von Arnim A, Hong T *. Early Detection of Daylengths with a Feedforward Circuit Coregulated by Circadian and Diurnal Cycles. Biophys J 2020, 119(9):1878 (* corresponding author)
[Link] [Article]

Pattarawat P, Hong T , Wallace S, Hu Y, Donnell R, Wang TH, Tsai CL, Wang J, Wang HC. Compensatory combination of romidepsin with gemcitabine and cisplatin to effectively and safely control urothelial carcinoma. British Journal of Cancer 2020, 1-14
[Link] [Article]

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

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: 1
(* Co-first author, ** corresponding author)
[Link] [Article]

Mukherjee T, Elmas M, Vo L, Alexiades L, Hong T, Alexandre G. Multiple CheY homologs control swimming reversals and transient pauses in Azospirillum brasilense. Biophys J 2019, 116(8): 1257
[Link] [Article]

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 (* corresponding author)
[Link] [Article]

MacLean A*, Hong T *, Nie Q. Exploring intermediate cell states through the lens of single cells. Curr Opin Sys Biol 2018, 2: 009 (* equal contributions)
[Link] [Article]

Peterlin B, Liu P, Wang X, Cary D, Shao W, Leoz M, Hong T, Pan T, Fujinaga K. Hili inhibits HIV replication in activated T cells. J Virol 2017 pii: JVI.00237-17
[Link] [Article]

Li C *, Hong T *, Yen Y, Lu Y, Chang M, Nie Q, Chen J. MicroRNA filters hox transcription noise and confers robust boundary formation in the spinal cord. Nat Commun 2017, 8: 14685 (* equal contributions)
[Link] [Article]

Li C, Hong T, Webb C, Karner H, Sun S, Nie Q. A self-enhanced transport feedback mechanism for X chromosome inactivation. Sci Rep 2016, 6:31517
[Link] [Article]

Ta CH, Nie Q, Hong T *. Controlling stochasticity in epithelial-mesenchymal transition through multiple intermediate cellular states. Discrete Continuous Dyn Syst Ser B 2016, 21(7): 2275-2291 (* corresponding author)
[Link] [Article]

Li C, Hong T, Nie Q. Quantifying the landscape and kinetic paths for epithelial–mesenchymal transition from a core circuit. Phys Chem Chem Phys 2016, 18: 17949-17956
[Link] [Article]

Hong T *, Watanabe K *, Ta CH, Villarreal-Ponce A, Nie Q, Dai X. An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States. PLoS Comput Biol 2015, 11(11): e1004569 (* equal contributions)
[Link] [Article]

Hong T, Fung ES, Zhang L, Huynh G, Monuki ES, Nie Q. Semi-adaptive response and noise attenuation in BMP signaling. J R Soc Interface 2015, 12 (107): 20150258
[Link] [Article]

Hong T, Oguz C, Tyson JJ. A mathematical framework for understanding four-dimensional heterogeneous differentiation of CD4⁺ T cells. Bull Math Biol 2015, 77 (6): 1046-1064
[Link] [Article]

Chen Z, Barbi J, Bu S, Yang HY, Li Z, Gao Y, Jinasena D, Fu J, Lin F, Chen C, Zhang J, Yu N, Li X, Shan Z, Nie J, Gao Z, Hong T, Li Y, Yao Z, Zheng Y, Park BV, Pan Z, Zhang J, Dang E, Li Z, Wang H, Luo W, Li L, Semenza GL, Zheng SG, Loser K, Tsun A, Greene MI, Pardoll DM, Pan F, Li B. The ubiquitin ligase Stub1 negatively modulates regulatory T cell suppressive activity by promoting degradation of the transcription factor Foxp3. Immunity 2013, 39(2):272-85
[Link] [Article]

Jensen RV, DePasquale, SM, Harbolick EA, Hong T, Kernell AL, Kruchko DH, Modise T, Smith CE, McCarter LL, Stevens AM. Complete Genome Sequence of Pre-pandemic Vibrio parahaemolyticus BB22OP. Genome Announcements 2013, 1
[Link] [Article]

Hong T, Xing J, Li L, Tyson JJ. A simple theoretical framework for understanding heterogeneous differentiation of CD4⁺ T cells. BMC Syst Biol 2012, 6: 66
[Link] [Article]

Lin X, Hong T, Mu Y, Torres J. Identification of residues involved in water versus glycerol selectivity in aquaporins by differential residue pair co-evolution. Biochim Biophys Acta 2012, 1818(3):907-14
[Link] [Article]

Hong T, Xing J, Li L, Tyson JJ. A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Comput Biol 2011, 7(7):e1002122
[Link] [Article]