Tongli Zhang , PhD

Cell Biologist, construct mechanistic models to connect cellular behaviors and molecular control mechanisms.

Doctoral Degree: Virginia Polytechnic Institute & State University Blacksburg, VA, 2008 (Genetics)

Postdoctoral Research Associate: University of Oxford Oxford, England, 2015

Cells, working machines in our body, respond to environmental signals (e.g. food, hormone, and infection, etc.) and make critical decisions such as proliferation, differentiation, defense, or even death. 

The decision makings of cells are carried out by their molecular control networks. Although no single molecule is directing the cellular behaviors by itself, the dynamical properties emerging from the interaction between the control molecules serve as clear commands to the cells. 

As we know more about the molecular control networks, they are getting more complex. These networks often include feedbacks, crosstalk, context-dependent changes, and time-dependent changes. Mathematical modeling is a powerful tool to handle such complexities. 

In my research, I combine biological intuition with mathematical modeling to make clear the seemingly confusing networks. My biological intuition is on cell cycle, apoptosis, p53 pathway and NF-κB pathway. My modeling expertise is on positive feedbacks, negative feedbacks, switches, and oscillations. 

Interested students are encouraged to send me CVs and discuss opportunities in my group.

Grant: #1R21CA227379 Investigators:Hong, Christian; Zhang, Tongli 07-01-2018 -06-30-2020 National Cancer Institute (PQ6) Roles of circadian rhythms in tumor development Role:Collaborator $208,800.00 Awarded Level:Federal

Grant: #W911NF-20-1-0192 Investigators:Zhang, Tongli 06-04-2020 -06-03-2023 Department of the Army Testing a “shot gun” approach to develop genome level predictive models Role:PI $22,413.25 Awarded Level:Federal

Grant: #FA9550-20-1-0117 Investigators:Heikenfeld, Jason; Zhang, Tongli 08-15-2020 -08-14-2023 Air Force Office of Scientific Research In-Vivo Validation of Analyte Partitioning Mechanisms for Peripheral Biochemical Monitoring Role:Collaborator $289,771.00 Awarded Level:Federal

Investigators:Zhang, Tongli 02-01-2023 -01-31-2024 Department of Veterans Affairs VA IPA for Zhang (Herman's Merit Award) Role:PI 4106.16 Hold Level:Federal

Grant: #W911NF-26-1-A004 02-01-2026 -01-31-2029 U.S. Army Contracting Command Developing an effective protocol to build credential biomedical models Role:PI 43094.13 Awarded Level:Federal

Grant: #W911NF-26-1-A004 02-01-2026 -01-31-2029 U.S. Army Contracting Command Developing an effective protocol to build credential biomedical models Role:PI 43094.13 Awarded Level:Federal

Peer Reviewed Publications

Zhang T, Kalantzaki M, Kitamura E, Novak B, Tanaka T An improved dynamical model of chromosome bi-orientation.

Barr A, Zhang T, Novak B, Bakal C Systemic characterization of G1/S transition.

Zhang T, Novak B, Tyson JJ Integrative analysis of cell cycle control in mammalian cells.

Lossaint G, Bacevic K, Zhang T, Fraillery D, Charrier-Savournin F, Piette J, Fisher D, Dulic V. Output of a reciprocally regulated Chk1-p21 network controls cell fate after DNA damage-induced G2 arrest.

Sero J, Sailem H, Ardy R, Almuttaqi H, Zhang T, Bakal C (2015. ) Cell shape and the microenvironment regulate nuclear translocation of NF-kB in breast epithelial and tumor cells. Mol Syst Biol, , (online ) ,

Kalantzaki M, Kitamura E, Zhang T, Mino A, Novak B, Tanaka T (2015. ) Kinetochore microtubule error correction is driven by differentially regulated interaction modes .Nat Cell Biol, , (online ) ,

Zhang T, TYson JJ, Novak B (2013. ) Role for regulated phosphatase activity in generating mitotic oscillations in Xenopus cell-free extracts .Proc Natl Acad Sci USA, , 110 ,20539-44

Cundell MJ, Bastos RN, Zhang T, Holder J, Gruneberg U, Novak B, Barr FA (2013. ) The BEG (PP2A-B55/ENSA/Greatwall) pathway ensures cytokinesis follows chromosome separation. Mol Cell, , 52 ,393-405

Zhang T, Oliveira RA, Schmierer B, Novak B (2013. ) Dynamical scenarios for chromosome bi-orientation. Biophys J, , 104 ,2595-606

Tuck C, Zhang T, Potapova T, Malumbres M, Novak B (2013. ) Robust mitotic entry is ensured by a latching switch. Biol Open, , 2 ,924-31

Sheng, Jennifer; Zhang, Tongli (2025. ) Advancing drug development with "Fit-for-Purpose" modeling informed approaches.Journal of pharmacokinetics and pharmacodynamics, , 52 (5 ) ,52 More Information

Androulakis, Ioannis P; Cheng, Limei; Cho, Carolyn R; Zhang, Tongli (2025. ) Leveraging large language models to compare perspectives on integrating QSP and AI/ML.Journal of pharmacokinetics and pharmacodynamics, , 52 (3 ) ,29 More Information

Fostvedt, Luke; Zhou, Jiawei; Kondic, Anna G; Androulakis, Ioannis P; Zhang, Tongli; Pryor, Meghan; Zhuang, Luning; Elassaiss-Schaap, Jeroen; Chan, Phyllis; Moore, Helen; Avedissian, Sean N; Tigh, Jeremy; Goteti, Kosalaram; Thanneer, Neelima; Su, Jing; Ait-Oudhia, Sihem (2025. ) Stronger together: a cross-SIG perspective on improving drug development.Journal of pharmacokinetics and pharmacodynamics, , 52 (1 ) ,14 More Information

Zhang, Tongli (2025. ) Integrating QSP and ML to Facilitate Drug Development and Personalized Medicine.Handbook of experimental pharmacology, , 289 ,165-185 More Information

Parker, Christopher; Nelson, Erik; Zhang, Tongli (2024. ) Applying neural ordinary differential equations for analysis of hormone dynamics in Trier Social Stress Tests.Frontiers in genetics, , 15 ,1375468 More Information

Parker, Christopher; Nelson, Erik; Zhang, Tongli (2022. ) VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models.Entropy (Basel, Switzerland), , 24 (12 ) , More Information

Zhang, Tongli; Cho, Carolyn R; Bonate, Peter L (2022. ) Perspectives on training quantitative systems pharmacologists.CPT: pharmacometrics & systems pharmacology, , 11 (6 ) ,669-672 More Information

Tanaka, Tomoyuki U; Zhang, Tongli (2022. ) SWAP, SWITCH, and STABILIZE: Mechanisms of Kinetochore-Microtubule Error Correction.Cells, , 11 (9 ) , More Information

Zhang, Tongli; Androulakis, Ioannis P; Bonate, Peter; Cheng, Limei; Helikar, Tomáš; Parikh, Jaimit; Rackauckas, Christopher; Subramanian, Kalyanasundaram; Cho, Carolyn R (2022. ) Two heads are better than one: current landscape of integrating QSP and machine learning : An ISoP QSP SIG white paper by the working group on the integration of quantitative systems pharmacology and machine learning.Journal of pharmacokinetics and pharmacodynamics, , 49 (1 ) ,5-18 More Information

Zhang, Tongli; Tyson, John J (2022. ) Understanding virtual patients efficiently and rigorously by combining machine learning with dynamical modelling.Journal of pharmacokinetics and pharmacodynamics, , 49 (1 ) ,117-131 More Information

Zhang, Tongli (2021. ) A Modeling and Machine Learning Pipeline to Rationally Design Treatments to Restore Neuroendocrine Disorders in Heterogeneous Individuals.Frontiers in genetics, , 12 ,656508 More Information

Ballweg, Richard; Engevik, Kristen A; Montrose, Marshall H; Aihara, Eitaro; Zhang, Tongli (2020. ) Extracting Insights From Temporal Data by Integrating Dynamic Modeling and Machine Learning.Frontiers in physiology, , 11 ,1012 More Information

Zhang, Yin; Huynh, Julie M; Liu, Guan-Sheng; Ballweg, Richard; Aryeh, Kayenat S; Paek, Andrew L; Zhang, Tongli (2019. ) Designing combination therapies with modeling chaperoned machine learning.PLoS computational biology, , 15 (9 ) ,e1007158 More Information

Liu, Guan-Sheng; Ballweg, Richard; Ashbaugh, Alan; Zhang, Yin; Facciolo, Joseph; Cushion, Melanie T; Zhang, Tongli (2019. ) Correction to: A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice.BMC systems biology, , 13 (1 ) ,40 More Information

Engevik, Kristen A; Hanyu, Hikaru; Matthis, Andrea L; Zhang, Tongli; Frey, Mark R; Oshima, Yusuke; Aihara, Eitaro; Montrose, Marshall H (2019. ) Trefoil factor 2 activation of CXCR4 requires calcium mobilization to drive epithelial repair in gastric organoids.The Journal of physiology, , 597 (10 ) ,2673-2690 More Information

Liu, Ruixue; Moriggl, Richard; Zhang, Dongsheng; Li, Haifeng; Karns, Rebekah; Ruan, Hai-Bin; Niu, Haitao; Mayhew, Christopher; Watson, Carey; Bangar, Hansraj; Cha, Sang-Wook; Haslam, David; Zhang, Tongli; Gilbert, Shila; Li, Na; Helmrath, Michael; Wells, James; Denson, Lee; Han, Xiaonan (2019. ) Constitutive STAT5 activation regulates Paneth and Paneth-like cells to control Clostridium difficile colitis.Life science alliance, , 2 (2 ) , More Information

Ballweg, Richard; Lee, Suengwon; Han, Xiaonan; Maini, Philip K; Byrne, Helen; Hong, Christian I; Zhang, Tongli (2018. ) Unraveling the Control of Cell Cycle Periods during Intestinal Stem Cell Differentiation.Biophysical journal, , 115 (11 ) ,2250-2258 More Information

Hauke, A; Simmers, P; Ojha, Y R; Cameron, B D; Ballweg, R; Zhang, T; Twine, N; Brothers, M; Gomez, E; Heikenfeld, J (2018. ) Complete validation of a continuous and blood-correlated sweat biosensing device with integrated sweat stimulation.Lab on a chip, , 18 (24 ) ,3750-3759 More Information

Aihara, Eitaro; Medina-Candelaria, Neisha M; Hanyu, Hikaru; Matthis, Andrea L; Engevik, Kristen A; Gurniak, Christine B; Witke, Walter; Turner, Jerrold R; Zhang, Tongli; Montrose, Marshall H (2018. ) Cell injury triggers actin polymerization to initiate epithelial restitution.Journal of cell science, , 131 (16 ) , More Information

Liu, Guan-Sheng; Ballweg, Richard; Ashbaugh, Alan; Zhang, Yin; Facciolo, Joseph; Cushion, Melanie T; Zhang, Tongli (2018. ) A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice.BMC systems biology, , 12 (1 ) ,77 More Information

Ballweg, Richard; Schozer, Frederick; Elliott, Kelsey; Kuhn, Alexander; Spotts, Logan; Aihara, Eitaro; Zhang, Tongli (2017. ) Multiscale positive feedbacks contribute to unidirectional gastric disease progression induced by helicobacter pylori infection.BMC systems biology, , 11 (1 ) ,111 More Information

Wetzel, Hanna N; Zhang, Tongli; Norman, Andrew B (2017. ) A mathematical model of a recombinant humanized anti-cocaine monoclonal antibody's effects on cocaine pharmacokinetics in mice.Life sciences, , 184 ,81-86 More Information

Ballweg, Richard; Paek, Andrew L; Zhang, Tongli (2017. ) A dynamical framework for complex fractional killing.Scientific reports, , 7 (1 ) ,8002 More Information

Matsu-Ura, Toru; Dovzhenok, Andrey; Aihara, Eitaro; Rood, Jill; Le, Hung; Ren, Yan; Rosselot, Andrew E; Zhang, Tongli; Lee, Choogon; Obrietan, Karl; Montrose, Marshall H; Lim, Sookkyung; Moore, Sean R; Hong, Christian I (2016. ) Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture.Molecular cell, , 64 (5 ) ,900-912 More Information

Liu, Junbo; Xiao, Yanyu; Zhang, Tongli; Ma, Jun (2016. ) Time to move on: Modeling transcription dynamics during an embryonic transition away from maternal control.Fly, , 10 (3 ) ,101-7 More Information

Chen, Shuang; Brunskill, Eric W; Potter, S Steven; Dexheimer, Phillip J; Salomonis, Nathan; Aronow, Bruce J; Hong, Christian I; Zhang, Tongli; Kopan, Raphael (2015. ) Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan.Developmental cell, , 35 (1 ) ,49-62 More Information

University of Cincinnati College of Medicine
231 Albert Sabin Way
Cincinnati  Ohio, 45267-0576
Phone: 513-558-6156
Fax: 513-558-5738
Tongli.Zhang@uc.edu