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
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
Sheng, Jennifer; Zhang, Tongli 2025. Advancing drug development with "Fit-for-Purpose" modeling informed approaches. Journal of pharmacokinetics and pharmacodynamics, 52 5, 52
Zhang, Tongli 2025. Integrating QSP and ML to Facilitate Drug Development and Personalized Medicine. Handbook of experimental pharmacology, 289 , 165-185
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
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,
Tanaka, Tomoyuki U; Zhang, Tongli 2022. SWAP, SWITCH, and STABILIZE: Mechanisms of Kinetochore-Microtubule Error Correction. Cells, 11 9,
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
Zhang, Tongli; Cho, Carolyn R; Bonate, Peter L 2022. Perspectives on training quantitative systems pharmacologists. CPT: pharmacometrics & systems pharmacology, 11 6, 669-672
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
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
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
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
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
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,
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
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,
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
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
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
Ballweg, Richard; Paek, Andrew L; Zhang, Tongli 2017. A dynamical framework for complex fractional killing. Scientific reports, 7 1, 8002
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
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
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
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
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
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,
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,
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
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
Zhang T, Oliveira RA, Schmierer B, Novak B 2013. Dynamical scenarios for chromosome bi-orientation. Biophys J, 104 , 2595-606
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
Barr A, Zhang T, Novak B, Bakal C . Systemic characterization of G1/S transition. , ,
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. , ,
Zhang T, Kalantzaki M, Kitamura E, Novak B, Tanaka T . An improved dynamical model of chromosome bi-orientation. , ,
Zhang T, Novak B, Tyson JJ . Integrative analysis of cell cycle control in mammalian cells. , ,