{"id":253,"date":"2016-11-17T23:23:47","date_gmt":"2016-11-17T23:23:47","guid":{"rendered":"http:\/\/www.tianhonglab.org\/WordPress\/?page_id=253"},"modified":"2025-12-04T04:19:12","modified_gmt":"2025-12-04T04:19:12","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.tianhonglab.org\/WordPress\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Underline<\/a> : Graduate trainee. Double-underline<\/a> : Undergraduate trainee. Bold<\/a> : Lab member.<\/p>\r\n\r\n

 <\/p>\r\n\r\n

2025<\/p>\r\n\r\n\r\n\r\n

Wen, H<\/a>, Carpenter S, McGinnis K, Nelson A, Smith K, Hong T *<\/strong>. EssSubgraph improves performance and generalizability of mammalian essential gene prediction with large networks.. GigaScience <\/em>2025; giaf136 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Lopez D<\/a>, Tyson DR, Hong T *<\/strong>. Intercellular signaling reinforces single-cell level phenotypic transitions and facilitates robust re-equilibrium of heterogeneous cancer cell populations. Cell Commun Signal <\/em>2025; 23(1):386 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n\r\n\r\n\r\n

Hong T *<\/strong>. Mathematical Modeling for Oscillations Driven by Noncoding RNAs (book chapter) In: Lai X, Gupta S, Gonzalez JV (eds) Computational Biology of Non-Coding RNA. Methods and Protocols. Springer Nature<\/em> 2025, pp 155-165 (* corresponding author)
[Link]<\/a> [Draft]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

 <\/p>\r\n\r\n

2024<\/p>\r\n\r\n\r\n\r\n

Paul S, Adetunji J, <\/a>Hong T *<\/a>. Widespread biochemical reaction networks enable Turing patterns without imposed feedback. Nat Commun<\/em> 2024, 15: 8380 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Hong T *<\/a>, Xing J*. Data\u2010and theory\u2010driven approaches for understanding paths of epithelial\u2013mesenchymal transition. genesis<\/em> 2024, 62(2), p.e23591 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

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

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

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2023<\/p>\r\n\r\n

Gross LJ, McCord RP, LoRe S, Ganusov VV, Hong T<\/strong>, 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<\/em> 2023 18(4), p.e0284982
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n

Mykins M, Layo-Carris D, Dunn LR, Skinner DW, McBryar AH, Perez S, Shultz TR, Willems A<\/a>, Lau BY, Hong T<\/strong>, Krishnan K. Wild-type MECP2 expression coincides with age-dependent sensory phenotypes in a female mouse model for Rett syndrome. J Neurosci Res<\/em> 2023;00:1\u201323
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n

Groves SM, Panchy N<\/strong>, Tyson DR, Harris LA, Quaranta V, Hong T *<\/strong>. Involvement of epithelial-mesenchymal transition genes in small cell lung cancer phenotypic plasticity. Cancers<\/em> 2023, 15(5):1477 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n

Willems A<\/a>, Panchy N<\/strong>, Hong T *<\/strong>. Using single-cell RNA sequencing and microRNA targeting data to improve colorectal cancer survival prediction. Cells<\/em> 2023, 12(2):228 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n

 <\/p>\r\n

2022<\/p>\r\n\r\n\r\n\r\n

Nordick B<\/a>, Park MCY<\/a>, Quaranta V, Hong T *<\/strong>. Cooperative RNA degradation stabilizes intermediate epithelial-mesenchymal states and supports a phenotypic continuum. iScience<\/em> 2022, 25(10):105224 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Panchy N<\/a>, Watanabe K, Takahashi M, Willems A<\/a>, Hong T *<\/strong>. Comparative single-cell transcriptomes of dose and time dependent epithelial\u2013mesenchymal spectrums. NAR Genom Bioinform<\/em> 2022, 4(3):lqac072 (Editor’s choice) (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Nordick B<\/a>, Yu PY, Liao G, Hong T *<\/strong>. Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression. Nucleic Acids Res<\/em> 2022, 50(7):3693 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

 <\/p>\r\n

2021<\/p>\r\n\r\n\r\n\r\n

Willems A<\/a>, Hong T *<\/strong>. Fate decisions of CD4+ T Cells (book chapter) In: Kraikivski P. (eds) Case Studies in Systems Biology. Springer, Cham.<\/em> 2021, pp 149-162 (* corresponding author)
[Link]<\/a> [Draft]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Nordick B<\/a>, Hong T *<\/strong>. Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks. BMC Bioinform<\/em> 2021, 22:481 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Panchy N<\/a>, Watanabe K<\/a>, Hong T *<\/strong>. Interpretable, scalable, and transferrable functional projection of large-scale transcriptome data using constrained matrix decomposition. Front Genet<\/em> 2021, 12:719099
(* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Li C-J, Liau ES, Lee Y-H, Huang Y-Z, Liu Z<\/a>, Willems A<\/a>, Garside V, McGlinn E, Chen J-A *, Hong T<\/strong> *. MicroRNAs govern bistable cell differentiation and lineage segregation via noncanonical feedback. Mol Syst Biol<\/em> 2021, 17:e9945 (cover story) (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

 <\/p>\r\n

2020<\/p>\r\n\r\n\r\n\r\n

Liu Z<\/a>, Shpak ED<\/a>, Hong T<\/strong> *. A mathematical model for understanding synergistic regulations and paradoxical feedbacks in the shoot apical meristem. Comput Struct Biotechnol J<\/em> 2020, 18:1878 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n

Panchy N<\/a>, von Arnim A<\/a>, Hong T *<\/strong>. Early Detection of Daylengths with a Feedforward Circuit Coregulated by Circadian and Diurnal Cycles. Biophys J<\/em> 2020, 119(9):1878 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Pattarawat P, Hong T <\/strong>, 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<\/em> 2020, 1-14
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Panchy N<\/a>, Azeredo-Tseng C<\/a>, Luo M<\/a>, Randall N<\/a>, Hong T *<\/strong>. Integrative transcriptomic analysis reveals a multiphasic epithelial\u2013mesenchymal spectrum in cancer and non-tumorigenic cells. Front Oncol<\/em> 2020, 9:1479
(* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

 <\/p>\r\n

2019<\/p>\r\n\r\n\r\n\r\n

Watanabe K *, Panchy N *<\/a>, Noguchi S, Suzuki H, Hong T **<\/strong>. Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition. npj Syst Biol Appl<\/em> 2019, 5: 1
(* Co-first author, ** corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n

Mukherjee T, Elmas M, Vo L, Alexiades L, Hong T<\/strong>, Alexandre G. Multiple CheY homologs control swimming reversals and transient pauses in Azospirillum brasilense. Biophys J<\/em> 2019, 116(8): 1257
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Ye Y<\/a>, Kang X, Bailey J,<\/a> Li C, Hong T *<\/strong>. An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. PLoS Comput Biol<\/em> 2019, 15(3): e1006855 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

 <\/p>\r\n

2018<\/strong><\/p>\r\n\r\n\r\n\r\n

MacLean A*, Hong T *, <\/strong>Nie Q. Exploring intermediate cell states through the lens of single cells. Curr Opin Sys Biol <\/em>2018, 2: 009 (* equal contributions)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

 <\/p>\r\n

2017<\/strong><\/p>\r\n\r\n\r\n\r\n

Peterlin B, Liu P, Wang X, Cary D, Shao W, Leoz M, Hong T<\/strong>, Pan T, Fujinaga K. Hili inhibits HIV replication in activated T cells. J Virol <\/em>2017 pii: JVI.00237-17
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Li C *, Hong T *<\/strong>, 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 <\/em>2017, 8: 14685 (* equal contributions)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

 <\/p>\r\n

Before 2017<\/strong><\/p>\r\n\r\n\r\n\r\n

Li C, Hong T<\/strong>, Webb C, Karner H, Sun S, Nie Q. A self-enhanced transport feedback mechanism for X chromosome inactivation. Sci Rep<\/em> 2016, 6:31517
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Ta CH, Nie Q, Hong T *<\/strong>. Controlling stochasticity in epithelial-mesenchymal transition through multiple intermediate cellular states. Discrete Continuous Dyn Syst Ser B<\/em> 2016, 21(7): 2275-2291 (* corresponding author)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Li C, Hong T<\/strong>, Nie Q. Quantifying the landscape and kinetic paths for epithelial\u2013mesenchymal transition from a core circuit. Phys Chem Chem Phys<\/em> 2016, 18: 17949-17956
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Hong T *<\/strong>, Watanabe K *<\/strong>, 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<\/em> 2015, 11(11): e1004569 (* equal contributions)
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Hong T<\/strong>, Fung ES, Zhang L, Huynh G, Monuki ES, Nie Q. Semi-adaptive response and noise attenuation in BMP signaling. J R Soc Interface <\/em>2015, 12 (107): 20150258
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Hong T<\/strong>, Oguz C, Tyson JJ. A mathematical framework for understanding four-dimensional heterogeneous differentiation of CD4+<\/sup> T cells. Bull Math Biol<\/em> 2015, 77 (6): 1046-1064
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

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<\/strong>, 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<\/em> 2013, 39(2):272-85
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Jensen RV, DePasquale, SM, Harbolick EA, Hong T<\/strong>, Kernell AL, Kruchko DH, Modise T, Smith CE, McCarter LL, Stevens AM. Complete Genome Sequence of Pre-pandemic Vibrio parahaemolyticus <\/em>BB22OP. Genome Announcements<\/em> 2013, 1
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Hong T<\/strong>, Xing J, Li L, Tyson JJ. A simple theoretical framework for understanding heterogeneous differentiation of CD4+<\/sup> T cells. BMC Syst Biol<\/em> 2012, 6: 66
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Lin X, Hong T<\/strong>, Mu Y, Torres J. Identification of residues involved in water versus glycerol selectivity in aquaporins by differential residue pair co-evolution. Biochim Biophys Acta<\/em> 2012, 1818(3):907-14
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n\r\n\r\n\r\n

Hong T<\/strong>, 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 <\/em>2011, 7(7):e1002122
[Link]<\/a> [Article]<\/a><\/span><\/p>\r\n","protected":false},"excerpt":{"rendered":"

Underline : Graduate trainee. Double-underline : Undergraduate trainee. Bold : Lab member.   2025 Wen, H, Carpenter S, McGinnis K, Nelson A, Smith K, Hong T *. EssSubgraph improves performance and generalizability of mammalian essential gene prediction with large networks.. GigaScience 2025; giaf136 (* corresponding author)[Link] [Article] Lopez D, Tyson DR, Hong T *. Intercellular […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"custom-templates\/full-wdith.php","meta":{"footnotes":""},"class_list":["post-253","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages\/253","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/comments?post=253"}],"version-history":[{"count":75,"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages\/253\/revisions"}],"predecessor-version":[{"id":792,"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages\/253\/revisions\/792"}],"wp:attachment":[{"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/media?parent=253"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}