{"id":32,"date":"2016-05-20T03:06:57","date_gmt":"2016-05-20T03:06:57","guid":{"rendered":"http:\/\/www.tianhonglab.org\/WordPress\/?page_id=32"},"modified":"2025-09-03T14:14:50","modified_gmt":"2025-09-03T14:14:50","slug":"tian-hong","status":"publish","type":"page","link":"https:\/\/www.tianhonglab.org\/WordPress\/people\/tian-hong\/","title":{"rendered":"Tian Hong"},"content":{"rendered":"\r\n<div class='content-column one_third'><div style=\"padding:45px 20px 20px 60px;\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-92 aligncenter\" src=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/portrait2-300x300.jpg\" alt=\"portrait2\" width=\"200\" height=\"200\" srcset=\"https:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/portrait2-300x300.jpg 300w, https:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/portrait2-150x150.jpg 150w, https:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/portrait2-768x768.jpg 768w, https:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/portrait2.jpg 942w\" sizes=\"auto, (max-width: 200px) 100vw, 200px\" \/><br \/><\/div><\/div>\r\n<div class='content-column one_third last_column'><div style=\"padding:20px 20px 20px 20px;\"><p style=\"font-size: 20px; font-weight: bold;\">Tian Hong<\/p>\r\n<p>Associate Professor<\/p>\r\n<p>Department of Biological Sciences, The University of Texas at Dallas<\/p>\r\n<p>E-mail: hong@utdallas.edu<\/p>\r\n<p>Joint Research Associate Professor\r\n<br \/>Department of Biochemistry &#038; Cellular and Molecular Biology, The University of Tennessee, Knoxville<\/p><\/div><\/div><div class='clear_column'><\/div><div class='content-column full_width'><div style=\"padding:0px 20px 20px 30px;\"><p style=\"font-size: 20px; font-weight: bold;\">Education &amp; Training<\/p>\r\n<p style=\"font-size: 16px; line-height: 1.4;\">Postdoctoral Scholar\u00a0 Department of Mathematics, Center for Complex Biological Systems, UC Irvine<br \/>Ph.D.\u2003\u2002Genetics, Bioinformatics and Computational Biology, Virginia Tech<br \/>M.S.\u2003\u2003Bioinformatics, Nanyang Technological University, Singapore<br \/>B.S.\u2003\u2003\u200aBiological Sciences, Nanyang Technological University, Singapore<\/p>\r\n<p style=\"font-size: 20px; font-weight: bold;\"><br class=\"nc\" \/>Research<\/p>\r\n<div class='content-column two_third'><div style=\"padding:0px 30px 0px 0px;\">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.<\/p>\r\n<p><strong>Theme:<\/strong> Plasticity and heterogeneity of cells in development and diseases. Gene regulatory networks.<\/p>\r\n<p><strong>Biological problems:<\/strong> Dynamical systems of development, immune response and cancer progression. Spatial patterning of tissues.<\/p>\r\n<p><strong>Approaches:<\/strong> Bioinformatic analysis. Mathematical modeling of biomolecules and cells.<\/div><\/div>\r\n<div class='content-column one_third last_column'><script type=\"text\/javascript\">\r\ndocument.addEventListener(\"DOMContentLoaded\", function(event) { \r\n\tjQuery( '#slider-pro-3-117' ).sliderPro({\r\n\t\t\/\/width\r\n\t\t\t\twidth: 1000,\r\n\t\t\t\t\r\n\t\t\/\/height\r\n\t\t\t\theight: 500,\r\n\t\t\t\t\r\n\t\t\/\/auto play\r\n\t\t\t\tautoplay:  true,\r\n\t\tautoplayOnHover: 'none',\r\n\t\t\t\t\t\t\t\tautoplayDelay: 5000,\r\n\t\t\r\n\t\t\r\n\t\tarrows: true,\r\n\t\tbuttons: true,\r\n\t\tsmallSize: 500,\r\n\t\tmediumSize: 1000,\r\n\t\tlargeSize: 3000,\r\n\t\tfade: true,\r\n\t\t\r\n\t\t\/\/thumbnail\r\n\t\tthumbnailArrows: true,\r\n\t\tthumbnailWidth: 120,\r\n\t\tthumbnailHeight: 120,\r\n\t\t\t\t\t\tthumbnailsPosition: 'bottom',\r\n\t\t\t\t\t\tcenterImage: true,\r\n\t\timageScaleMode: 'cover',\r\n\t\tallowScaleUp: true,\r\n\t\t\t\tstartSlide: 0,\r\n\t\tloop: true,\r\n\t\tslideDistance: 5,\r\n\t\tautoplayDirection: 'normal',\r\n\t\ttouchSwipe: true,\r\n\t\tfullScreen: true,\r\n\t});\r\n});\r\n<\/script>\r\n<style>\r\n\/* Layout 3 *\/\r\n\/* border *\/\r\n#slider-pro-3-117 .sp-selected-thumbnail {\r\n\tborder: 4px solid #000000;\r\n}\r\n\r\n\/* font + color *\/\r\n.title-in  {\r\n\tfont-family: Arial !important;\r\n\tcolor: #FFFFFF !important;\r\n\tbackground-color: #000000 !important;\r\n\topacity: 0.7 !important;\r\n}\r\n.desc-in  {\r\n\tfont-family: Arial !important;\r\n\tcolor: #FFFFFF !important;\r\n\tbackground-color: #00000 !important;\r\n\topacity: 0.7 !important;\r\n}\r\n\r\n\/* bullets color *\/\r\n.sp-button  {\r\n\tborder: 2px solid #000000 !important;\r\n}\r\n.sp-selected-button  {\r\n\tbackground-color: #000000 !important;\r\n}\r\n\r\n\/* pointer color - bottom *\/\r\n.sp-selected-thumbnail::before {\r\n\tborder-bottom: 5px solid #000000 !important;\r\n}\r\n.sp-selected-thumbnail::after {\r\n\tborder-bottom: 13px solid #000000 !important;\r\n}\r\n\r\n\/* pointer color - top *\/\r\n\r\n\/* full screen icon *\/\r\n.sp-full-screen-button::before {\r\n    color: #FFFFFF !important;\r\n}\r\n\r\n\/* hover navigation icon color *\/\r\n.sp-next-arrow::after, .sp-next-arrow::before {\r\n\tbackground-color: #FFFFFF !important;\r\n}\r\n.sp-previous-arrow::after, .sp-previous-arrow::before {\r\n\tbackground-color: #FFFFFF !important;\r\n}\r\n\r\n#slider-pro-3-117 .title-in {\r\n\tcolor: #FFFFFF !important;\r\n\tfont-weight: bolder;\r\n\ttext-align: center;\r\n}\r\n\r\n#slider-pro-3-117 .title-in-bg {\r\n\tbackground: rgba(255, 255, 255, 0.7); !important;\r\n\twhite-space: unset !important;\r\n\tmax-width: 90%;\r\n\tmin-width: 40%;\r\n\ttransform: initial !important;\r\n\t-webkit-transform: initial !important;\r\n\tfont-size: 14px !important;\r\n}\r\n\r\n#slider-pro-3-117 .desc-in {\r\n\tcolor: #FFFFFF !important;\r\n\ttext-align: center;\r\n}\r\n#slider-pro-3-117 .desc-in-bg {\r\n\tbackground: rgba(#00000, 0.7) !important;\r\n\twhite-space: unset !important;\r\n\twidth: 80% !important;\r\n\tmin-width: 30%;\r\n\ttransform: initial !important;\r\n\t-webkit-transform: initial !important;\r\n\tfont-size: 13px !important;\r\n}\r\n\r\n@media (max-width: 640px) {\r\n\t#slider-pro-3-117 .hide-small-screen {\r\n\t\tdisplay: none;\r\n\t}\r\n}\r\n\r\n@media (max-width: 860px) {\r\n\t#slider-pro-3-117 .sp-layer {\r\n\t\tfont-size: 18px;\r\n\t}\r\n\t\r\n\t#slider-pro-3-117 .hide-medium-screen {\r\n\t\tdisplay: none;\r\n\t}\r\n}\r\n.slides-not-found {\r\n\tbackground-color: #a92929;\r\n\tborder-radius: 5px;\r\n\tcolor: #fff;\r\n\tfont-family: initial;\r\n\ttext-align: center;\r\n\tpadding:12px;\r\n}\r\n\/* Custom CSS *\/\r\n<\/style>\r\n<h3 class=\"uris-slider-post-title\"><\/h3>\r\n\t\t<div id=\"slider-pro-3-117\" class=\"slider-pro\">\r\n\t\t\t<!---- slides div start ---->\r\n\t\t\t<div class=\"sp-slides\">\r\n\t\t\t\t\t\t\t<\/div>\r\n\t\t\t\r\n\t\t\t<!---- slides div end ---->\r\n\t\t\t\t\t\t<!-- slides thumbnails div start -->\r\n\t\t\t<div class=\"sp-thumbnails\">\r\n\t\t\t\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<!-- slides thumbnails div end -->\r\n\t\t<\/div>\r\n<\/div><div class='clear_column'><\/div><!--&nbsp;--><br \/><strong> <!--\r\n<p style=\"font-size: 20px; font-weight: bold;\">Publications<\/p>\r\n\r\n\r\n--><\/strong><h6 class=\"collapseomatic arrowright shorty\" id=\"id69f0b964ae9b6\"  tabindex=\"0\" title=\"Publications\"    >Publications<\/h6><div id=\"target-id69f0b964ae9b6\" class=\"collapseomatic_content \">\r\n<p style=\"font-size: 16px;\">Lopez D, Tyson DR, <strong>Hong T *<\/strong>. Intercellular signaling reinforces single-cell level phenotypic transitions and facilitates robust re-equilibrium of heterogeneous cancer cell populations<em>.  Cell Commun Signal <\/em>2025; 23(1):386 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/biosignaling.biomedcentral.com\/articles\/10.1186\/s12964-025-02405-7\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2025\/09\/s12964-025-02405-7.pdf\">[Article]<\/a><\/span><\/p>\r\n\r\n<p style=\"font-size: 16px;\"><strong>Hong T *<\/strong>. Mathematical Modeling for Oscillations Driven by Noncoding RNAs (book chapter) In: Lai X, Gupta S, Gonzalez JV (eds) <em>Computational Biology of Non-Coding RNA. Methods and Protocols. Springer Nature<\/em> 2025, pp 155-165 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/link.springer.com\/protocol\/10.1007\/978-1-0716-4290-0_7\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2024\/12\/ReviewChapter7_Tian_Hong.pdf\">[Draft]<\/a><\/span><\/p>\r\n\r\n<p style=\"font-size: 16px;\"> Paul S, Adetunji J, <a style=\"display: inline; font-weight: bold;\">Hong T *<\/a>. Widespread biochemical reaction networks enable Turing patterns without imposed feedback. <em>Nat Commun<\/em> 2024, 15: 8380 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/www.nature.com\/articles\/s41467-024-52591-0\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2024\/10\/s41467-024-52591-0.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a style=\"display: inline; font-weight: bold;\">Hong T *<\/a>, Xing J*. Data\u2010and theory\u2010driven approaches for understanding paths of epithelial\u2013mesenchymal transition. <em>genesis<\/em> 2024, 62(2), p.e23591 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/dvg.23591\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2024\/08\/Genesis-2024-Hong-Data\u2010-and-theory\u2010driven-approaches-for-understanding-paths-of-epithelial-mesenchymal-transition.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Uzair M, Urquidi Camacho RA, Liu Z, Overholt AM, DeGennaro D, Zhang L, Herron BS, <strong>Hong T<\/strong>, Shpak ED. An updated model of shoot apical meristem regulation by ERECTA family and CLAVATA3 signaling pathways in Arabidopsis. <em>Development<\/em> 2024, 151 (12) pp.dev-202870<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/journals.biologists.com\/dev\/article-abstract\/151\/12\/dev202870\/358098\/An-updated-model-of-shoot-apical-meristem\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"https:\/\/journals.biologists.com\/dev\/article-pdf\/doi\/10.1242\/dev.202870\/3467203\/dev202870.pdf?casa_token=KO7QhkhmgoIAAAAA:34ZoBDwSuEkUkihRiq9Dx3fH_q2Sl280Q-EQO-GeoImZ6VjpufHVRTPJPRdi_WjWIJyE0-o\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Harrell MA, Liu Z, Campbell BF, Chinsen O, <strong>Hong T<\/strong>, Das M. Arp2\/3-dependent endocytosis ensures Cdc42 oscillations by removing Pak1-mediated negative feedback. <em>J. Cell Biol.<\/em> 2024, 223(10) <br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/rupress.org\/jcb\/article\/223\/10\/e202311139\/276859\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"https:\/\/rupress.org\/jcb\/article-pdf\/223\/10\/e202311139\/1930741\/jcb_202311139.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Gross LJ, McCord RP, LoRe S, Ganusov VV, <strong>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. <em>PLoS ONE<\/em> 2023 18(4), p.e0284982<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0284982\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2023\/05\/journal.pone_.0284982.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Mykins M, Layo-Carris D, Dunn LR, Skinner DW, McBryar AH, Perez S, Shultz TR, Willems A, Lau BY, <strong>Hong T<\/strong>, Krishnan K. Wild-type MECP2 expression coincides with age-dependent sensory phenotypes in a female mouse model for Rett syndrome. <em>J Neurosci Res<\/em> 2023;00:1\u201323<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jnr.25190\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2023\/05\/J-of-Neuroscience-Research-2023-Mykins-Wild\u2010type-MeCp2-expression-coincides-with-age\u2010dependent-sensory-phenotypes-in.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Groves SM, Panchy N, Tyson DR, Harris LA, Quaranta V, <strong>Hong T *<\/strong>. Involvement of epithelial-mesenchymal transition genes in small cell lung cancer phenotypic plasticity. <em>Cancers<\/em> 2023, 15(5):1477 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.3390\/cancers15051477\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2023\/03\/cancers-15-01477.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Willems A, Panchy N, <strong>Hong T *<\/strong>. Using single-cell RNA sequencing and microRNA targeting data to improve colorectal cancer survival prediction. <em>Cells<\/em> 2023, 12(2):228 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.3390\/cells12020228\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2023\/01\/cells-12-00228-v2.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a>Nordick B<\/a>, Park MCY, Quaranta V, <strong>Hong T *<\/strong>. Cooperative RNA degradation stabilizes intermediate epithelial-mesenchymal states and supports a phenotypic continuum. <em>iScience<\/em> 2022, 25(10):105224 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.1016\/j.isci.2022.105224\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2022\/10\/Nordick-Chae-yeon_2022_iScience-ll-intermediate-epithelial-mesenchymal-states-and-supports-a-phenotypic-continuum.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a>Panchy N<\/a>, Watanabe K, Takahashi M, <a>Willems A<\/a>, <strong>Hong T *<\/strong>. Comparative single-cell transcriptomes of dose and time dependent epithelial\u2013mesenchymal spectrums. <em>NAR Genom Bioinform<\/em> 2022, 4(3):lqac072 (Editor&#8217;s choice) (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.1093\/nargab\/lqac072\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2022\/09\/lqac072.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a>Nordick B<\/a>, Yu PY, Liao G, <strong>Hong T *<\/strong>. Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression. <em>Nucleic Acids Res<\/em> 2022, 50(7):3693 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkac217\/6563721\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2022\/04\/gkac217_final.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a>Willems A<\/a>, <strong>Hong T *<\/strong>. Fate decisions of CD4+ T Cells (book chapter) In: Kraikivski P. (eds) <em>Case Studies in Systems Biology. Springer, Cham.<\/em> 2021, pp 149-162 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-3-030-67742-8_11\">[Link]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a>Nordick B<\/a>, <strong>Hong T *<\/strong>. Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks. <em>BMC Bioinform<\/em> 2021, 22:481 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-021-04405-z\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2021\/10\/Nordick-Hong_2021_Identification-visualization-statistical-analysis-and-mathematical-modeling-of-high-\u2011-feedback-loops-in-gene-regu.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Panchy N, <a>Watanabe K<\/a>, <strong>Hong T *<\/strong>. Interpretable, scalable, and transferrable functional projection of large-scale transcriptome data using constrained matrix decomposition. <em>Front Genet<\/em> 2021, 12:719099<br \/>(* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.3389\/fgene.2021.719099\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2021\/08\/fgene-12-719099.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Li C-J, Liau ES, Lee Y-H, Huang Y-Z, <a>Liu Z<\/a>, <a>Willems A<\/a>, Garside V, McGlinn E, Chen J-A, <strong>Hong T<\/strong> *. MicroRNAs govern bistable cell differentiation and lineage segregation via noncanonical feedback. <em>Mol Syst Biol<\/em> 2021, 17:e9945 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.15252\/msb.20209945\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2021\/04\/msb.20209945.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Liu Z, <a>Shpak ED<\/a>, <strong>Hong T<\/strong> *. A mathematical model for understanding synergistic regulations and paradoxical feedbacks in the shoot apical meristem. <em>Comput Struct Biotechnol J<\/em> 2020, 18:1878 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.1016\/j.csbj.2020.11.017\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2020\/12\/Liu-Shpak-Hong_2020_A-mathematical-model-for-understanding-synergistic-regulations-and-paradoxical-feedbacks-in-the-shoot-apical-meris.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a>Panchy N<\/a>, <a>von Arnim A<\/a>, <strong>Hong T *<\/strong>. Early Detection of Daylengths with a Feedforward Circuit Coregulated by Circadian and Diurnal Cycles. <em>Biophys J<\/em> 2020, 119(9):1878 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.1016\/j.bpj.2020.09.025\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2020\/11\/Panchy-von-Arnim-Hong_2020_Early-detection-of-daylengths-with-a-feedforward-circuit-coregulated-by-circadian-and-diurnal-cycles.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Pattarawat P, <strong>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. <em>British Journal of Cancer<\/em> 2020, 1-14<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/www.nature.com\/articles\/s41416-020-0877-8\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2020\/06\/Pattarawat-et-al._2020_Compensatory-combination-of-romidepsin-with-gemcitabine-and-cisplatin-to-effectively-and-safely-control-urothelia.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><a>Panchy N<\/a>, Azeredo-Tseng C, Luo M, Randall N, <strong>Hong T **<\/strong>. Integrative transcriptomic analysis reveals a multiphasic epithelial\u2013mesenchymal spectrum in cancer and non-tumorigenic cells. <em>Front Oncol<\/em> 2020, 9:1479<br \/>(** corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/doi.org\/10.3389\/fonc.2019.01479\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2020\/01\/fonc-09-01479.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Watanabe K *, <a>Panchy N *<\/a>, Noguchi S, Suzuki H, <strong>Hong T **<\/strong>. Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition. <em>npj Syst Biol Appl<\/em> 2019, 5: 1 <br \/>(* Co-first author, ** corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/www.nature.com\/articles\/s41540-019-0097-0\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2019\/06\/Watanabe_et_al-2019-npj_Systems_Biology_and_Applications.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Mukherjee T, Elmas M, Vo L, Alexiades L, <strong>Hong T<\/strong>, Alexandre G. Multiple CheY homologs control swimming reversals and transient pauses in Azospirillum brasilense. <em>Biophys J<\/em> 2019, 116(8): 1257 <br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006349519301924?via%3Dihub\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2019\/04\/Mukherjee-et-al._2019_Multiple-CheY-Homologs-Control-Swimming-Reversals-and-Transient-Pauses-in-Azospirillum-brasilense.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Ye Y, Kang X, Bailey J, Li C, <strong>Hong T *<\/strong>. An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. <em>PLoS Comput Biol<\/em> 2019, 15(3): e1006855 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1006855\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2019\/03\/Ye-et-al._Unknown_An-enriched-network-motif-family-regulates-multistep-cell-fate-transitions-with-restricted-reversibility.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">MacLean A*, <strong>Hong T *, <\/strong>Nie Q. Exploring intermediate cell states through the lens of single cells. <em>Curr Opin Sys Biol <\/em>2018, 2: 009 (* equal contributions)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2452310017302238\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2018\/03\/MacLean-Hong-Nie_2018_Exploring-intermediate-cell-states-through-the-lens-of-single-cells.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Peterlin B, Liu P, Wang X, Cary D, Shao W, Leoz M, <strong>Hong T<\/strong>, Pan T, Fujinaga K. Hili inhibits HIV replication in activated T cells. <em>J Virol <\/em>2017 pii: JVI.00237-17<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/jvi.asm.org\/content\/early\/2017\/03\/16\/JVI.00237-17.abstract\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2017\/04\/J.-Virol.-2017-Peterlin-JVI.00237-17.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Li C *, <strong>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. <em>Nat Commun <\/em>2017, 8: 14685 (* equal contributions)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/www.nature.com\/articles\/ncomms14685\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2017\/03\/Li-et-al._2017_MicroRNA-filters-Hox-temporal-transcription-noise-to-confer-boundary-formation-in-the-spinal-cord.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Li C, <strong>Hong T<\/strong>, Webb C, Karner H, Sun S, Nie Q. A self-enhanced transport feedback mechanism for X chromosome inactivation. <em>Sci Rep<\/em> 2016, 6:31517<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/www.nature.com\/articles\/srep31517\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Li-et-al._2016_A-self-enhanced-transport-mechanism-through-long-noncoding-RNAs-for-X-chromosome-inactivation.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Ta CH, Nie Q, <strong>Hong T *<\/strong>. Controlling stochasticity in epithelial-mesenchymal transition through multiple intermediate cellular states. <em>Discrete Continuous Dyn Syst Ser B<\/em> 2016, 21(7): 2275-2291 (* corresponding author)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/aimsciences.org\/journals\/displayArticlesnew.jsp?paperID=12933\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Ta-Nie-Hong_2016_Controlling-stochasticity-in-epithelial-mesenchymal-transition-through-multiple-intermediate-cellular-states.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Li C, <strong>Hong T<\/strong>, Nie Q. Quantifying the landscape and kinetic paths for epithelial\u2013mesenchymal transition from a core circuit. <em>Phys Chem Chem Phys<\/em> 2016, 18: 17949-17956<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/pubs.rsc.org\/is\/content\/articlehtml\/2016\/cp\/c6cp03174a\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Li-Hong-Nie_2016_Quantifying-the-landscape-and-kinetic-paths-for-epithelial-mesenchymal-transition-from-a-core-circuit.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><strong>Hong T *<\/strong>, 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. <em>PLoS Comput Biol<\/em> 2015, 11(11): e1004569 (* equal contributions)<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1004569\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Hong-et-al._2015_An-Ovol2-Zeb1-Mutual-Inhibitory-Circuit-Governs-Bidirectional-and-Multi-step-Transition-between-Epithelial-and-Mesenchy.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><strong>Hong T<\/strong>, Fung ES, Zhang L, Huynh G, Monuki ES, Nie Q. Semi-adaptive response and noise attenuation in BMP signaling. <em>J R Soc Interface <\/em>2015, 12 (107): 20150258<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/rsif.royalsocietypublishing.org\/content\/12\/107\/20150258.full\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Hong-et-al._2015_Semi-adaptive-response-and-noise-attenuation-in-bone-morphogenetic-protein-signalling.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><strong>Hong T<\/strong>, Oguz C, Tyson JJ. A mathematical framework for understanding four-dimensional heterogeneous differentiation of CD4<sup>+<\/sup> T cells. <em>Bull Math Biol<\/em> 2015, 77 (6): 1046-1064<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/link.springer.com\/article\/10.1007\/s11538-015-0076-6\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Hong-Oguz-Tyson_2015_A-Mathematical-Framework-for-Understanding-Four-Dimensional-Heterogeneous-Differentiation-of-CD4-T-Cells.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">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, <strong>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. <em>Immunity<\/em> 2013, 39(2):272-85<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1074761313003348\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Chen-et-al._2013_The-ubiquitin-ligase-stub1-negatively-modulates-regulatory-T-cell-suppressive-activity-by-promoting-degradation-of-the.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Jensen RV, DePasquale, SM, Harbolick EA, <strong>Hong T<\/strong>, Kernell AL, Kruchko DH, Modise T, Smith CE, McCarter LL, Stevens AM. Complete Genome Sequence of Pre-pandemic <em>Vibrio parahaemolyticus <\/em>BB22OP. <em>Genome Announcements<\/em> 2013, 1<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/genomea.asm.org\/content\/1\/1\/e00002-12.short\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Jensen-et-al._2013_Complete-Genome-Sequence-of-Prepandemic-Vibrio-parahaemolyticus-BB22OP.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><strong>Hong T<\/strong>, Xing J, Li L, Tyson JJ. A simple theoretical framework for understanding heterogeneous differentiation of CD4<sup>+<\/sup> T cells. <em>BMC Syst Biol<\/em> 2012, 6: 66<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-6-66\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Hong-et-al._2012_A-simple-theoretical-framework-for-understanding-heterogeneous-differentiation-of-CD4-T-cells.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\">Lin X, <strong>Hong T<\/strong>, Mu Y, Torres J. Identification of residues involved in water versus glycerol selectivity in aquaporins by differential residue pair co-evolution. <em>Biochim Biophys Acta<\/em> 2012, 1818(3):907-14<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0005273611004548\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Lin-et-al._2012_Identification-of-residues-involved-in-water-versus-glycerol-selectivity-in-aquaporins-by-differential-residue-pair-co-e.pdf\">[Article]<\/a><\/span><\/p>\r\n<p style=\"font-size: 16px;\"><strong>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. <em>PLoS Comput Biol <\/em>2011, 7(7):e1002122<br \/><span style=\"color: #ff6600;\"><a style=\"color: #ff6600;\" href=\"http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1002122\">[Link]<\/a> <a style=\"color: #ff6600;\" href=\"http:\/\/www.tianhonglab.org\/WordPress\/wp-content\/uploads\/2016\/05\/Hong-et-al._2011_A-Mathematical-Model-for-the-Reciprocal-Differentiation-of-T-Helper-17-Cells-and-Induced-Regulatory-T-Cells.pdf\">[Article]<\/a><\/span><\/p>\r\n<\/div><\/div><\/div>\r\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":26,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"custom-templates\/full-wdith.php","meta":{"footnotes":""},"class_list":["post-32","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages\/32","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=32"}],"version-history":[{"count":170,"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages\/32\/revisions"}],"predecessor-version":[{"id":619,"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages\/32\/revisions\/619"}],"up":[{"embeddable":true,"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/pages\/26"}],"wp:attachment":[{"href":"https:\/\/www.tianhonglab.org\/WordPress\/wp-json\/wp\/v2\/media?parent=32"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}