Education/CredentialsPostdoctoral Research Associate: University of OxfordDoctoral Degree: Virginia Polytechnic Institute & State University (Genetics) Contact Information Medical Sciences Building 4260 Email zhangtl@ucmail.uc.edu Research InterestsCells, 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. ... Peer Reviewed Publications 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, 29Fostvedt, 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, 14Sheng, Jennifer; Zhang, Tongli 2025. Advancing drug development with "Fit-for-Purpose" modeling informed approaches. Journal of pharmacokinetics and pharmacodynamics, 52 5, 52Zhang, Tongli 2025. Integrating QSP and ML to Facilitate Drug Development and Personalized Medicine. Handbook of experimental pharmacology, 289 , 165-185Parker, 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 , 1375468Parker, 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, 5-18Zhang, Tongli; Cho, Carolyn R; Bonate, Peter L 2022. Perspectives on training quantitative systems pharmacologists. CPT: pharmacometrics & systems pharmacology, 11 6, 669-672Zhang, 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, 117-131Zhang, Tongli 2021. A Modeling and Machine Learning Pipeline to Rationally Design Treatments to Restore Neuroendocrine Disorders in Heterogeneous Individuals. Frontiers in genetics, 12 , 656508Ballweg, 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 , 1012Engevik, 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, 2673-2690Liu, 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, 40Liu, 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, e1007158Aihara, 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, 2250-2258Hauke, 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, 3750-3759Liu, 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, 77Ballweg, Richard; Paek, Andrew L; Zhang, Tongli 2017. A dynamical framework for complex fractional killing. Scientific reports, 7 1, 8002Ballweg, 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, 111Wetzel, 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 , 81-86Liu, 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, 101-7Matsu-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, 900-912Chen, 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, 49-62Kalantzaki 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 , 393-405Tuck C, Zhang T, Potapova T, Malumbres M, Novak B 2013. Robust mitotic entry is ensured by a latching switch. Biol Open, 2 , 924-31Zhang T, Oliveira RA, Schmierer B, Novak B 2013. Dynamical scenarios for chromosome bi-orientation. Biophys J, 104 , 2595-606Zhang 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 , 20539-44Barr 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. , ,
Research InterestsCells, 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. ...
Peer Reviewed Publications 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, 29Fostvedt, 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, 14Sheng, Jennifer; Zhang, Tongli 2025. Advancing drug development with "Fit-for-Purpose" modeling informed approaches. Journal of pharmacokinetics and pharmacodynamics, 52 5, 52Zhang, Tongli 2025. Integrating QSP and ML to Facilitate Drug Development and Personalized Medicine. Handbook of experimental pharmacology, 289 , 165-185Parker, 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 , 1375468Parker, 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, 5-18Zhang, Tongli; Cho, Carolyn R; Bonate, Peter L 2022. Perspectives on training quantitative systems pharmacologists. CPT: pharmacometrics & systems pharmacology, 11 6, 669-672Zhang, 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, 117-131Zhang, Tongli 2021. A Modeling and Machine Learning Pipeline to Rationally Design Treatments to Restore Neuroendocrine Disorders in Heterogeneous Individuals. Frontiers in genetics, 12 , 656508Ballweg, 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 , 1012Engevik, 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, 2673-2690Liu, 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, 40Liu, 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, e1007158Aihara, 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, 2250-2258Hauke, 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, 3750-3759Liu, 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, 77Ballweg, Richard; Paek, Andrew L; Zhang, Tongli 2017. A dynamical framework for complex fractional killing. Scientific reports, 7 1, 8002Ballweg, 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, 111Wetzel, 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 , 81-86Liu, 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, 101-7Matsu-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, 900-912Chen, 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, 49-62Kalantzaki 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 , 393-405Tuck C, Zhang T, Potapova T, Malumbres M, Novak B 2013. Robust mitotic entry is ensured by a latching switch. Biol Open, 2 , 924-31Zhang T, Oliveira RA, Schmierer B, Novak B 2013. Dynamical scenarios for chromosome bi-orientation. Biophys J, 104 , 2595-606Zhang 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 , 20539-44Barr 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. , ,
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, 29Fostvedt, 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, 14Sheng, Jennifer; Zhang, Tongli 2025. Advancing drug development with "Fit-for-Purpose" modeling informed approaches. Journal of pharmacokinetics and pharmacodynamics, 52 5, 52Zhang, Tongli 2025. Integrating QSP and ML to Facilitate Drug Development and Personalized Medicine. Handbook of experimental pharmacology, 289 , 165-185Parker, 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 , 1375468Parker, 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, 5-18Zhang, Tongli; Cho, Carolyn R; Bonate, Peter L 2022. Perspectives on training quantitative systems pharmacologists. CPT: pharmacometrics & systems pharmacology, 11 6, 669-672Zhang, 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, 117-131Zhang, Tongli 2021. A Modeling and Machine Learning Pipeline to Rationally Design Treatments to Restore Neuroendocrine Disorders in Heterogeneous Individuals. Frontiers in genetics, 12 , 656508Ballweg, 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 , 1012Engevik, 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, 2673-2690Liu, 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, 40Liu, 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, e1007158Aihara, 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, 2250-2258Hauke, 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, 3750-3759Liu, 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, 77Ballweg, Richard; Paek, Andrew L; Zhang, Tongli 2017. A dynamical framework for complex fractional killing. Scientific reports, 7 1, 8002Ballweg, 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, 111Wetzel, 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 , 81-86Liu, 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, 101-7Matsu-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, 900-912Chen, 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, 49-62Kalantzaki 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 , 393-405Tuck C, Zhang T, Potapova T, Malumbres M, Novak B 2013. Robust mitotic entry is ensured by a latching switch. Biol Open, 2 , 924-31Zhang T, Oliveira RA, Schmierer B, Novak B 2013. Dynamical scenarios for chromosome bi-orientation. Biophys J, 104 , 2595-606Zhang 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 , 20539-44Barr 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. , ,