Publications

2025

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

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

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

2024

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

2022

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,

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

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; 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

2021

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

2020

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

2019

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

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

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, 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,

2018

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

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,

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

2017

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

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

2016

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

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

2015

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,

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